From 49964e2ca091068009568e45db2edab5ef349de3 Mon Sep 17 00:00:00 2001 From: Michael Heppler Date: Fri, 22 Jul 2016 14:41:30 -0400 Subject: [PATCH 001/172] Wired the File pg back up to the Dataset pg, commented out broken file thumbnail render logic, added placeholder tabs for Provenance and Versions. [ref #2295] --- src/main/webapp/file.xhtml | 34 +++++++++++++++------ src/main/webapp/filesFragment.xhtml | 9 ++++-- src/main/webapp/resources/css/structure.css | 2 +- 3 files changed, 32 insertions(+), 13 deletions(-) diff --git a/src/main/webapp/file.xhtml b/src/main/webapp/file.xhtml index ee3d4f71af4..7f0b370cf3a 100644 --- a/src/main/webapp/file.xhtml +++ b/src/main/webapp/file.xhtml @@ -145,13 +145,22 @@
-
+
+ + + + + + +
@@ -166,10 +175,10 @@
-
-
-
-
+
+
+
@@ -177,9 +186,9 @@
-
-
-
+
+
 
+
@@ -322,7 +331,14 @@
- + + + Coming soon... + + + + Coming soon... +
diff --git a/src/main/webapp/filesFragment.xhtml b/src/main/webapp/filesFragment.xhtml index e6df7598d8e..3828e391caa 100644 --- a/src/main/webapp/filesFragment.xhtml +++ b/src/main/webapp/filesFragment.xhtml @@ -244,12 +244,15 @@ - + - + + + +
diff --git a/src/main/webapp/resources/css/structure.css b/src/main/webapp/resources/css/structure.css index be453524dc7..6af8ef7e02a 100644 --- a/src/main/webapp/resources/css/structure.css +++ b/src/main/webapp/resources/css/structure.css @@ -694,7 +694,7 @@ div.manageTable.ui-datatable div.ui-datatable-tablewrapper, div.manageTable.ui-d } @media screen and (min-width: 1000px) { - #file-preview-icon-block span[class^='icon-'] {font-size:28em;} + #file-preview-icon-block span[class^='icon-'] {font-size:22em;} } /* BLOCK UI */ From 2eb1f345a3cce4172d0af67fddc1bd56c209b334 Mon Sep 17 00:00:00 2001 From: Don Sizemore Date: Fri, 5 Aug 2016 14:58:47 -0400 Subject: [PATCH 002/172] create migrate_passwords.sql which, pending testing, may alleviate https://github.com/IQSS/dataverse/issues/3240 --- scripts/migration/migrate_passwords.sql | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 scripts/migration/migrate_passwords.sql diff --git a/scripts/migration/migrate_passwords.sql b/scripts/migration/migrate_passwords.sql new file mode 100644 index 00000000000..ec2176ea8a6 --- /dev/null +++ b/scripts/migration/migrate_passwords.sql @@ -0,0 +1,5 @@ +update builtinuser +set passwordencryptionversion = 0, +encryptedpassword= _dvn3_vdcuser.encryptedpassword +from _dvn3_vdcuser +where _dvn3_vdcuser.username=builtinuser.username; From 76a130e5d2be7e1fccac933ec0fb59cf6d4d70f1 Mon Sep 17 00:00:00 2001 From: "Calvin Winkowski (Telnoratti)" Date: Wed, 17 Aug 2016 16:27:19 -0400 Subject: [PATCH 003/172] Fix psql_exec commands to work with different passwords. --- scripts/installer/install | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scripts/installer/install b/scripts/installer/install index 0475c37171f..744f86f0997 100755 --- a/scripts/installer/install +++ b/scripts/installer/install @@ -807,7 +807,7 @@ else print TMPCMD $sql_command; close TMPCMD; - my $psql_commandline = $psql_exec . "/psql -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -U postgres -d postgres -f /tmp/pgcmd.$$.tmp >/dev/null 2>&1"; + my $psql_commandline = $psql_admin_exec . "/psql -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -U postgres -d postgres -f /tmp/pgcmd.$$.tmp >/dev/null 2>&1"; my $out = qx($psql_commandline 2>&1); my $exitcode = $?; @@ -829,8 +829,8 @@ else print "\nCreating Postgres database:\n"; my $psql_command = - $psql_admin_exec - . "/createdb -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -U postgres " + $psql_exec + . "/createdb -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -U dvnapp " . $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} . " --owner=" . $CONFIG_DEFAULTS{'POSTGRES_USER'}; From fd641a817be19435ff657b72bd9c3bc9e4afc9d3 Mon Sep 17 00:00:00 2001 From: Michael Heppler Date: Mon, 12 Sep 2016 15:57:28 -0400 Subject: [PATCH 004/172] Added static placeholders (e.g. download, request access, and explore buttons) on file pg. [ref #2465] --- src/main/webapp/file.xhtml | 90 +++++++++++++++++++++++++++++++------- 1 file changed, 75 insertions(+), 15 deletions(-) diff --git a/src/main/webapp/file.xhtml b/src/main/webapp/file.xhtml index 7f0b370cf3a..651ea66a43c 100644 --- a/src/main/webapp/file.xhtml +++ b/src/main/webapp/file.xhtml @@ -15,7 +15,7 @@ - + @@ -67,7 +67,26 @@ + + + + Download + + + + + + Request Access + + + + + + Explore + + +
-
+
- - + + + + + + + + - + +
@@ -178,17 +203,39 @@
-
- -
-
 
+ + +
+
+ + +
+
+ Learn about Data Citation Standards. +
+
@@ -198,6 +245,10 @@ + + + + @@ -214,8 +265,8 @@
-
- #{bundle['file.description.label']} #{FilePage.fileMetadata.description} +
+ #{FilePage.fileMetadata.description}
@@ -229,6 +280,15 @@ + + +
+ + Add + Edit Metadata + +
+ +
#{bundle['file.metadataTab.fileMetadata.header']}   From d813105d67a130fb7f60d7fd34fbda616d599497 Mon Sep 17 00:00:00 2001 From: Michael Bar-Sinai Date: Thu, 15 Sep 2016 09:42:25 +0300 Subject: [PATCH 005/172] #3358: Illegal command translates to , which is in line with HTTP/1.1 spec. Code cleanup --- .../iq/dataverse/api/AbstractApiBean.java | 6 +++++- .../edu/harvard/iq/dataverse/api/Datasets.java | 17 ----------------- .../harvard/iq/dataverse/api/Dataverses.java | 6 ++---- .../edu/harvard/iq/dataverse/api/Roles.java | 3 +-- 4 files changed, 8 insertions(+), 24 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java b/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java index 2b2cb6f03fd..6169bd7082c 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java @@ -424,7 +424,11 @@ protected Response badApiKey( String apiKey ) { } protected Response permissionError( PermissionException pe ) { - return errorResponse( Status.UNAUTHORIZED, pe.getMessage() ); + return permissionError( pe.getMessage() ); + } + + protected Response permissionError( String message ) { + return errorResponse( Status.UNAUTHORIZED, message ); } protected static Response errorResponse( Status sts ) { diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index f0af8490c3d..3594ba77b6e 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -1,12 +1,10 @@ package edu.harvard.iq.dataverse.api; import edu.harvard.iq.dataverse.DOIEZIdServiceBean; -import edu.harvard.iq.dataverse.DataFile; import edu.harvard.iq.dataverse.Dataset; import edu.harvard.iq.dataverse.DatasetField; import edu.harvard.iq.dataverse.DatasetFieldServiceBean; import edu.harvard.iq.dataverse.DatasetFieldType; -import edu.harvard.iq.dataverse.DatasetFieldValue; import edu.harvard.iq.dataverse.DatasetServiceBean; import edu.harvard.iq.dataverse.DatasetVersion; import edu.harvard.iq.dataverse.Dataverse; @@ -14,16 +12,12 @@ import edu.harvard.iq.dataverse.MetadataBlock; import edu.harvard.iq.dataverse.MetadataBlockServiceBean; import edu.harvard.iq.dataverse.RoleAssignment; -import edu.harvard.iq.dataverse.api.imports.ImportException; -import edu.harvard.iq.dataverse.api.imports.ImportUtil; import edu.harvard.iq.dataverse.authorization.DataverseRole; import edu.harvard.iq.dataverse.authorization.RoleAssignee; import edu.harvard.iq.dataverse.authorization.users.User; import edu.harvard.iq.dataverse.engine.command.Command; import edu.harvard.iq.dataverse.engine.command.DataverseRequest; -import edu.harvard.iq.dataverse.engine.command.exception.CommandException; import edu.harvard.iq.dataverse.engine.command.impl.AssignRoleCommand; -import edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetCommand; import edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetVersionCommand; import edu.harvard.iq.dataverse.engine.command.impl.CreatePrivateUrlCommand; import edu.harvard.iq.dataverse.engine.command.impl.DeleteDatasetCommand; @@ -49,15 +43,12 @@ import edu.harvard.iq.dataverse.settings.SettingsServiceBean; import edu.harvard.iq.dataverse.util.SystemConfig; import edu.harvard.iq.dataverse.util.json.JsonParseException; -import edu.harvard.iq.dataverse.util.json.JsonParser; import static edu.harvard.iq.dataverse.util.json.JsonPrinter.*; import java.io.ByteArrayOutputStream; -import java.io.InputStream; import java.io.OutputStream; import java.io.StringReader; import java.util.List; import java.util.Map; -import java.util.Set; import java.util.logging.Level; import java.util.logging.Logger; import javax.ejb.EJB; @@ -65,11 +56,6 @@ import javax.json.JsonArrayBuilder; import javax.json.JsonObject; import javax.json.JsonObjectBuilder; -import javax.json.JsonReader; -import javax.validation.ConstraintViolation; -import javax.validation.Validation; -import javax.validation.Validator; -import javax.validation.ValidatorFactory; import javax.ws.rs.DELETE; import javax.ws.rs.GET; import javax.ws.rs.POST; @@ -362,14 +348,11 @@ public Response getVersion( @PathParam("id") String datasetId, @PathParam("versi @GET @Path("{id}/versions/{versionId}/files") public Response getVersionFiles( @PathParam("id") String datasetId, @PathParam("versionId") String versionId) { - try { - return okResponse( jsonFileMetadatas( getDatasetVersionOrDie(createDataverseRequest(findUserOrDie()), versionId, findDatasetOrDie(datasetId)).getFileMetadatas())); - } catch (WrappedResponse ex) { return ex.getResponse(); } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java b/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java index 2c0322e719c..7051cfe341f 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java @@ -550,11 +550,9 @@ public Response getGroupByOwnerAndAliasInOwner( @PathParam("identifier") String @PathParam("aliasInOwner") String grpAliasInOwner ) { try { - ExplicitGroup eg = findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), + return okResponse( json(findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), createDataverseRequest(findUserOrDie()), - grpAliasInOwner); - - return (eg!=null) ? okResponse( json(eg) ) : notFound("Can't find " + grpAliasInOwner + " in dataverse " + dvIdtf); + grpAliasInOwner)) ); } catch (WrappedResponse wr) { return wr.getResponse(); diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Roles.java b/src/main/java/edu/harvard/iq/dataverse/api/Roles.java index d573274998b..4b439dc6262 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Roles.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Roles.java @@ -44,8 +44,7 @@ public Response viewRole( @PathParam("id") Long id) { return notFound("role with id " + id + " not found"); } else { return ( permissionSvc.userOn(findUserOrDie(), role.getOwner()).has(Permission.ManageDataversePermissions) ) - ? okResponse( json(role) ) - : errorResponse(Status.UNAUTHORIZED, ""); + ? okResponse( json(role) ) : permissionError("Permission required to view roles."); } } catch (WrappedResponse ex) { return ex.getResponse(); From d15b48965939195e18e7965484151e07952accdc Mon Sep 17 00:00:00 2001 From: Michael Bar-Sinai Date: Fri, 16 Sep 2016 00:04:42 +0300 Subject: [PATCH 006/172] Updated response for illegal commands --- src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java b/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java index 6169bd7082c..1dfcc8bbb52 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java @@ -334,7 +334,7 @@ protected T execCommand( Command cmd ) throws WrappedResponse { return engineSvc.submit(cmd); } catch (IllegalCommandException ex) { - throw new WrappedResponse( ex, errorResponse(Response.Status.BAD_REQUEST, ex.getMessage() ) ); + throw new WrappedResponse( ex, errorResponse(Response.Status.FORBIDDEN, ex.getMessage() ) ); } catch (PermissionException ex) { /** From 330d3590af0b35504431412843d1d3b82db300dd Mon Sep 17 00:00:00 2001 From: bmckinney Date: Fri, 16 Sep 2016 11:57:06 -0400 Subject: [PATCH 007/172] adds ability to get and set dataverseType via son --- .../harvard/iq/dataverse/util/json/JsonParser.java | 11 ++++++++++- .../harvard/iq/dataverse/util/json/JsonPrinter.java | 3 ++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java index 3e8a6152558..3a91fa74f23 100644 --- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java +++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java @@ -95,7 +95,16 @@ public Dataverse parseDataverse(JsonObject jobj) throws JsonParseException { dv.setDataverseTheme(theme); theme.setDataverse(dv); } - + + dv.setDataverseType(Dataverse.DataverseType.UNCATEGORIZED); // default + if (jobj.containsKey("dataverseType")) { + for (Dataverse.DataverseType dvtype : Dataverse.DataverseType.values()) { + if (dvtype.name().equalsIgnoreCase(jobj.getString("dataverseType"))) { + dv.setDataverseType(dvtype); + } + } + } + /* We decided that subject is not user set, but gotten from the subject of the dataverse's datasets - leavig this code in for now, in case we need to go back to it at some point diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java index f00bee0b140..9b11f1a9525 100644 --- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java +++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java @@ -173,7 +173,8 @@ public static JsonObjectBuilder json(Dataverse dv) { .add("affiliation", dv.getAffiliation()) .add("dataverseContacts", json(dv.getDataverseContacts())) .add("permissionRoot", dv.isPermissionRoot()) - .add("description", dv.getDescription()); + .add("description", dv.getDescription()) + .add("dataverseType", dv.getDataverseType().name()); if (dv.getOwner() != null) { bld.add("ownerId", dv.getOwner().getId()); } From b703e27ec2d785adff459d3ff806e10344a2ef06 Mon Sep 17 00:00:00 2001 From: Philip Durbin Date: Tue, 20 Sep 2016 13:45:21 -0400 Subject: [PATCH 008/172] Support SHA1 rather than MD5 as a checksum on a per file basis #3354 A dependency for rsync support (#3145) is the ability to persist SHA-1 checksums for files rather than MD5 checksums. A new installation-wide configuration setting called ":FileFixityChecksumAlgorithm" has been added which can be set to "SHA-1" to have Dataverse calculate and show SHA-1 checksums rather than MD5 checksums. In order to run this branch you must run the provided SQL upgrade script: scripts/database/upgrades/3354-alt-checksum.sql In addition, the Solr schema should be updated to the version in this branch. --- conf/solr/4.6.0/schema.xml | 2 + .../source/installation/config.rst | 7 ++ .../database/upgrades/3354-alt-checksum.sql | 7 ++ .../issues/3354/createDatasetWithSha1Files.sh | 5 ++ scripts/issues/3354/datasetWithSha1Files.json | 86 +++++++++++++++++++ scripts/issues/3354/mydata | 3 + scripts/search/search | 4 +- src/main/java/Bundle.properties | 7 +- .../edu/harvard/iq/dataverse/DataFile.java | 80 +++++++++++++++-- .../iq/dataverse/DataFileServiceBean.java | 32 +++++-- .../edu/harvard/iq/dataverse/DatasetPage.java | 4 +- .../dataverse/DatasetVersionDifference.java | 47 +++++++--- .../iq/dataverse/EditDatafilesPage.java | 4 +- .../harvard/iq/dataverse/api/Dataverses.java | 5 +- .../iq/dataverse/api/WorldMapRelatedData.java | 2 +- .../dataverse/ingest/IngestServiceBean.java | 23 +++-- .../iq/dataverse/mydata/DataRetrieverAPI.java | 12 +-- .../iq/dataverse/search/IndexServiceBean.java | 11 ++- .../iq/dataverse/search/SearchFields.java | 2 + .../search/SearchIncludeFragment.java | 8 +- .../dataverse/search/SearchServiceBean.java | 7 ++ .../iq/dataverse/search/SolrSearchResult.java | 37 +++++++- .../settings/SettingsServiceBean.java | 1 + .../harvard/iq/dataverse/util/FileUtil.java | 52 +++++++++++ .../iq/dataverse/util/MD5Checksum.java | 84 ------------------ .../iq/dataverse/util/SystemConfig.java | 13 +++ .../iq/dataverse/util/json/JsonParser.java | 41 +++++++-- .../iq/dataverse/util/json/JsonPrinter.java | 27 +++++- src/main/webapp/dataset.xhtml | 2 +- src/main/webapp/editFilesFragment.xhtml | 10 +-- src/main/webapp/file.xhtml | 13 +-- src/main/webapp/filesFragment.xhtml | 2 +- src/main/webapp/mydata_templates/cards.html | 1 + .../mydata_templates/cards_minimum.html | 2 +- src/main/webapp/search-include-fragment.xhtml | 2 +- .../harvard/iq/dataverse/api/DatasetsIT.java | 76 ++++++++++++++++ .../edu/harvard/iq/dataverse/api/UtilIT.java | 10 +++ 37 files changed, 567 insertions(+), 164 deletions(-) create mode 100644 scripts/database/upgrades/3354-alt-checksum.sql create mode 100755 scripts/issues/3354/createDatasetWithSha1Files.sh create mode 100644 scripts/issues/3354/datasetWithSha1Files.json create mode 100755 scripts/issues/3354/mydata delete mode 100644 src/main/java/edu/harvard/iq/dataverse/util/MD5Checksum.java diff --git a/conf/solr/4.6.0/schema.xml b/conf/solr/4.6.0/schema.xml index 10f9b07be5c..323429b62da 100644 --- a/conf/solr/4.6.0/schema.xml +++ b/conf/solr/4.6.0/schema.xml @@ -298,6 +298,8 @@ + + diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst index 142e69ff3e3..b1f13c0ec8e 100644 --- a/doc/sphinx-guides/source/installation/config.rst +++ b/doc/sphinx-guides/source/installation/config.rst @@ -454,3 +454,10 @@ This setting is experimental per :doc:`/installation/shibboleth`. ++++++++++++ Set to false to disallow local accounts to be created if you are using :doc:`shibboleth` but not for production use until https://github.com/IQSS/dataverse/issues/2838 has been fixed. + +:FileFixityChecksumAlgorithm +++++++++++++++++++++++++++++ + +Dataverse calculates checksums for uploaded files so that users can determine if their file was corrupted via upload or download. This is sometimes called "file fixity": https://en.wikipedia.org/wiki/File_Fixity + +The default checksum algorithm used is MD5 and should be sufficient for establishing file fixity. "SHA-1" is an experimental alternate value for this setting. diff --git a/scripts/database/upgrades/3354-alt-checksum.sql b/scripts/database/upgrades/3354-alt-checksum.sql new file mode 100644 index 00000000000..0c54d673aac --- /dev/null +++ b/scripts/database/upgrades/3354-alt-checksum.sql @@ -0,0 +1,7 @@ +ALTER TABLE datafile ADD COLUMN checksumtype character varying(255); +ALTER TABLE datafile ALTER COLUMN checksumtype SET NOT NULL; +UPDATE datafile SET checksumtype = 'MD5'; +-- alternate statement for sbgrid.org and others interested in SHA-1 support +-- note that in the database we use "SHA1" (no hyphen) but the GUI will show "SHA-1" +--UPDATE datafile SET checksumtype = 'SHA1'; +ALTER TABLE datafile RENAME md5 TO checksumvalue; diff --git a/scripts/issues/3354/createDatasetWithSha1Files.sh b/scripts/issues/3354/createDatasetWithSha1Files.sh new file mode 100755 index 00000000000..1792a9e33a3 --- /dev/null +++ b/scripts/issues/3354/createDatasetWithSha1Files.sh @@ -0,0 +1,5 @@ +#!/bin/sh +# existing, works, no files, commenting out +#curl -s -X POST -H "Content-type:application/json" -d @scripts/search/tests/data/dataset-finch1.json "http://localhost:8080/api/dataverses/root/datasets/?key=$API_TOKEN" +# new, has files +curl -s -X POST -H "Content-type:application/json" -d @scripts/issues/3354/datasetWithSha1Files.json "http://localhost:8080/api/dataverses/root/datasets/?key=$API_TOKEN" diff --git a/scripts/issues/3354/datasetWithSha1Files.json b/scripts/issues/3354/datasetWithSha1Files.json new file mode 100644 index 00000000000..95a4d3b88d0 --- /dev/null +++ b/scripts/issues/3354/datasetWithSha1Files.json @@ -0,0 +1,86 @@ +{ + "datasetVersion": { + "files": [ + { + "label": "foo.txt", + "dataFile": { + "filename": "foo.txt", + "contentType": "text/plain", + "storageIdentifier": "157484f9d6c-c36006fa39e5", + "originalFormatLabel": "UNKNOWN", + "checksum": { + "type": "SHA-1", + "value": "f1d2d2f924e986ac86fdf7b36c94bcdf32beec15" + } + } + } + ], + "metadataBlocks": { + "citation": { + "fields": [ + { + "value": "Dataset with SHA-1 files", + "typeClass": "primitive", + "multiple": false, + "typeName": "title" + }, + { + "value": [ + { + "authorName": { + "value": "Finch, Fiona", + "typeClass": "primitive", + "multiple": false, + "typeName": "authorName" + }, + "authorAffiliation": { + "value": "Birds Inc.", + "typeClass": "primitive", + "multiple": false, + "typeName": "authorAffiliation" + } + } + ], + "typeClass": "compound", + "multiple": true, + "typeName": "author" + }, + { + "value": [ + { "datasetContactEmail" : { + "typeClass": "primitive", + "multiple": false, + "typeName": "datasetContactEmail", + "value" : "finch@mailinator.com" + } + }], + "typeClass": "compound", + "multiple": true, + "typeName": "datasetContact" + }, + { + "value": [ { + "dsDescriptionValue":{ + "value": "Some people prefer SHA-1 to MD5 for file fixity.", + "multiple":false, + "typeClass": "primitive", + "typeName": "dsDescriptionValue" + }}], + "typeClass": "compound", + "multiple": true, + "typeName": "dsDescription" + }, + { + "value": [ + "Other" + ], + "typeClass": "controlledVocabulary", + "multiple": true, + "typeName": "subject" + } + ], + "displayName": "Citation Metadata" + } + } + } +} diff --git a/scripts/issues/3354/mydata b/scripts/issues/3354/mydata new file mode 100755 index 00000000000..eb76d06e3f9 --- /dev/null +++ b/scripts/issues/3354/mydata @@ -0,0 +1,3 @@ +#!/bin/sh +# FIXME: Make this into a REST Assured test. +curl -s "http://localhost:8080/api/mydata/retrieve?key=$API_TOKEN&role_ids=1&dvobject_types=DataFile&published_states=Published&published_states=Unpublished&published_states=Draft&published_states=In+Review&published_states=Deaccessioned" | jq .data.items diff --git a/scripts/search/search b/scripts/search/search index b058dbdacb9..ac14596ac2a 100755 --- a/scripts/search/search +++ b/scripts/search/search @@ -1,11 +1,11 @@ #!/bin/sh if [ -z "$1" ]; then - curl -s 'http://localhost:8080/api/search?q=*' + curl -H "X-Dataverse-key: $API_TOKEN" -s 'http://localhost:8080/api/search?q=*' #curl -s 'http://localhost:8080/api/search?q=*&key=pete' else # i.e. ./search 'q=*&fq=filetype_s:"image"&fq=dvtype:files' # i.e. ./search 'q=*&start=10' # i.e. ./search 'q=*&sort=name_sort&order=asc' # i.e. ./search 'q=*&sort=name_sort&order=asc' | jq '.itemsJson[] | {name_sort}' - curl -s "http://localhost:8080/api/search?$1" + curl -H "X-Dataverse-key: $API_TOKEN" -s "http://localhost:8080/api/search?$1" fi diff --git a/src/main/java/Bundle.properties b/src/main/java/Bundle.properties index bc39855adc6..2a1a04e37b0 100755 --- a/src/main/java/Bundle.properties +++ b/src/main/java/Bundle.properties @@ -1076,7 +1076,6 @@ dataset.metadata.persistentId.tip=The unique persistent identifier for a Dataset dataset.versionDifferences.termsOfUseAccess=Terms of Use and Access dataset.versionDifferences.termsOfUseAccessChanged=Terms of Use/Access Changed file.viewDiffDialog.restricted=Restricted -file.viewDiffDialog.md5=MD5 dataset.template.tip=Changing the template will clear any fields you may have entered data into. dataset.noTemplate.label=None @@ -1133,9 +1132,8 @@ file.download.header=Download file.preview=Preview: file.fileName=File Name file.type.tabularData=Tabular Data -file.MD5=MD5 -file.MD5.origal=Original File MD5 -file.MD5.exists.tip=A file with this MD5 already exists in the dataset. +file.originalChecksumType=Original File {0} +file.checksum.exists.tip=A file with this checksum already exists in the dataset. file.selectedThumbnail=Thumbnail file.selectedThumbnail.tip=The thumbnail for this file is used as the default thumbnail for the dataset. Click 'Advanced Options' button of another file to select that file. @@ -1371,7 +1369,6 @@ file.tags.label=Tags file.metadataTab.fileMetadata.header=File Metadata file.metadataTab.fileMetadata.persistentid.label=Data File Persistent ID -file.metadataTab.fileMetadata.md5.label=MD5 file.metadataTab.fileMetadata.unf.label=UNF file.metadataTab.fileMetadata.size.label=Size file.metadataTab.fileMetadata.type.label=Type diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFile.java b/src/main/java/edu/harvard/iq/dataverse/DataFile.java index 24c01e3b107..7cfca585054 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataFile.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataFile.java @@ -7,6 +7,7 @@ import edu.harvard.iq.dataverse.dataaccess.DataFileIO; import edu.harvard.iq.dataverse.ingest.IngestReport; import edu.harvard.iq.dataverse.ingest.IngestRequest; +import edu.harvard.iq.dataverse.util.BundleUtil; import edu.harvard.iq.dataverse.util.FileUtil; import edu.harvard.iq.dataverse.util.ShapefileHandler; import java.io.IOException; @@ -16,11 +17,14 @@ import java.nio.file.Path; import java.nio.file.Paths; import java.nio.file.Files; +import java.util.Arrays; import javax.persistence.Entity; import javax.persistence.OneToMany; import javax.persistence.OneToOne; import javax.persistence.CascadeType; import javax.persistence.Column; +import javax.persistence.EnumType; +import javax.persistence.Enumerated; import javax.persistence.Index; import javax.persistence.JoinColumn; import javax.persistence.JoinTable; @@ -61,9 +65,56 @@ public class DataFile extends DvObject { @Column( nullable = false ) private String fileSystemName; - - @Column( nullable = false ) - private String md5; + + /** + * End users will see "SHA-1" (with a hyphen) rather than "SHA1" in the GUI + * and API but in the "datafile" table we persist "SHA1" (no hyphen) for + * type safety (using keys of the enum). In the "setting" table, we persist + * "SHA-1" (with a hyphen) to match the GUI and the "Algorithm Name" list at + * https://docs.oracle.com/javase/8/docs/technotes/guides/security/StandardNames.html#MessageDigest + * + * The list of types should be limited to the list above in the technote + * because the string gets passed into MessageDigest.getInstance() and you + * can't just pass in any old string. + */ + public enum ChecksumType { + + MD5("MD5"), + SHA1("SHA-1"); + + private final String text; + + private ChecksumType(final String text) { + this.text = text; + } + + public static ChecksumType fromString(String text) { + if (text != null) { + for (ChecksumType checksumType : ChecksumType.values()) { + if (text.equals(checksumType.text)) { + return checksumType; + } + } + } + throw new IllegalArgumentException("ChecksumType must be one of these values: " + Arrays.asList(ChecksumType.values()) + "."); + } + + @Override + public String toString() { + return text; + } + } + + @Column(nullable = false) + @Enumerated(EnumType.STRING) + private ChecksumType checksumType; + + /** + * Examples include "f622da34d54bdc8ee541d6916ac1c16f" as an MD5 value or + * "3a484dfdb1b429c2e15eb2a735f1f5e4d5b04ec6" as a SHA-1 value" + */ + @Column(nullable = false) + private String checksumValue; @Column(nullable=true) private Long filesize; // Number of bytes in file. Allows 0 and null, negative numbers not permitted @@ -364,15 +415,26 @@ public void setRestricted(boolean restricted) { this.restricted = restricted; } + public ChecksumType getChecksumType() { + return checksumType; + } - public String getmd5() { - return this.md5; + public void setChecksumType(ChecksumType checksumType) { + this.checksumType = checksumType; } - - public void setmd5(String md5) { - this.md5 = md5; + + public String getChecksumValue() { + return this.checksumValue; } - + + public void setChecksumValue(String checksumValue) { + this.checksumValue = checksumValue; + } + + public String getOriginalChecksumType() { + return BundleUtil.getStringFromBundle("file.originalChecksumType", Arrays.asList(this.checksumType.toString()) ); + } + public DataFileIO getAccessObject() throws IOException { DataFileIO dataAccess = DataAccess.createDataAccessObject(this); diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java index c2ecce1543e..c41b2aa1caf 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java @@ -255,7 +255,7 @@ public DataFile findCheapAndEasy(Long id) { Object[] result = null; try { - result = (Object[]) em.createNativeQuery("SELECT t0.ID, t0.CREATEDATE, t0.INDEXTIME, t0.MODIFICATIONTIME, t0.PERMISSIONINDEXTIME, t0.PERMISSIONMODIFICATIONTIME, t0.PUBLICATIONDATE, t0.CREATOR_ID, t0.RELEASEUSER_ID, t0.PREVIEWIMAGEAVAILABLE, t1.CONTENTTYPE, t1.FILESYSTEMNAME, t1.FILESIZE, t1.INGESTSTATUS, t1.MD5, t1.RESTRICTED, t3.ID, t3.AUTHORITY, t3.IDENTIFIER FROM DVOBJECT t0, DATAFILE t1, DVOBJECT t2, DATASET t3 WHERE ((t0.ID = " + id + ") AND (t0.OWNER_ID = t2.ID) AND (t2.ID = t3.ID) AND (t1.ID = t0.ID))").getSingleResult(); + result = (Object[]) em.createNativeQuery("SELECT t0.ID, t0.CREATEDATE, t0.INDEXTIME, t0.MODIFICATIONTIME, t0.PERMISSIONINDEXTIME, t0.PERMISSIONMODIFICATIONTIME, t0.PUBLICATIONDATE, t0.CREATOR_ID, t0.RELEASEUSER_ID, t0.PREVIEWIMAGEAVAILABLE, t1.CONTENTTYPE, t1.FILESYSTEMNAME, t1.FILESIZE, t1.INGESTSTATUS, t1.CHECKSUMVALUE, t1.RESTRICTED, t3.ID, t3.AUTHORITY, t3.IDENTIFIER, t1.CHECKSUMTYPE FROM DVOBJECT t0, DATAFILE t1, DVOBJECT t2, DATASET t3 WHERE ((t0.ID = " + id + ") AND (t0.OWNER_ID = t2.ID) AND (t2.ID = t3.ID) AND (t1.ID = t0.ID))").getSingleResult(); } catch (Exception ex) { return null; } @@ -346,14 +346,14 @@ public DataFile findCheapAndEasy(Long id) { String md5 = (String) result[14]; if (md5 != null) { - dataFile.setmd5(md5); + dataFile.setChecksumValue(md5); } Boolean restricted = (Boolean) result[15]; if (restricted != null) { dataFile.setRestricted(restricted); } - + Dataset owner = new Dataset(); @@ -362,6 +362,17 @@ public DataFile findCheapAndEasy(Long id) { owner.setId((Long)result[16]); owner.setAuthority((String)result[17]); owner.setIdentifier((String)result[18]); + + String checksumType = (String) result[19]; + if (checksumType != null) { + try { + // In the database we store "SHA1" rather than "SHA-1". + DataFile.ChecksumType typeFromStringInDatabase = DataFile.ChecksumType.valueOf(checksumType); + dataFile.setChecksumType(typeFromStringInDatabase); + } catch (IllegalArgumentException ex) { + logger.info("Exception trying to convert " + checksumType + " to enum: " + ex); + } + } dataFile.setOwner(owner); @@ -465,7 +476,7 @@ public void findFileMetadataOptimizedExperimental(Dataset owner, DatasetVersion i = 0; - List fileResults = em.createNativeQuery("SELECT t0.ID, t0.CREATEDATE, t0.INDEXTIME, t0.MODIFICATIONTIME, t0.PERMISSIONINDEXTIME, t0.PERMISSIONMODIFICATIONTIME, t0.PUBLICATIONDATE, t0.CREATOR_ID, t0.RELEASEUSER_ID, t1.CONTENTTYPE, t1.FILESYSTEMNAME, t1.FILESIZE, t1.INGESTSTATUS, t1.MD5, t1.RESTRICTED FROM DVOBJECT t0, DATAFILE t1 WHERE ((t0.OWNER_ID = " + owner.getId() + ") AND ((t1.ID = t0.ID) AND (t0.DTYPE = 'DataFile')))").getResultList(); + List fileResults = em.createNativeQuery("SELECT t0.ID, t0.CREATEDATE, t0.INDEXTIME, t0.MODIFICATIONTIME, t0.PERMISSIONINDEXTIME, t0.PERMISSIONMODIFICATIONTIME, t0.PUBLICATIONDATE, t0.CREATOR_ID, t0.RELEASEUSER_ID, t1.CONTENTTYPE, t1.FILESYSTEMNAME, t1.FILESIZE, t1.INGESTSTATUS, t1.CHECKSUMVALUE, t1.RESTRICTED, t1.CHECKSUMTYPE FROM DVOBJECT t0, DATAFILE t1 WHERE ((t0.OWNER_ID = " + owner.getId() + ") AND ((t1.ID = t0.ID) AND (t0.DTYPE = 'DataFile')))").getResultList(); for (Object[] result : fileResults) { Integer file_id = (Integer) result[0]; @@ -544,13 +555,24 @@ public void findFileMetadataOptimizedExperimental(Dataset owner, DatasetVersion String md5 = (String) result[13]; if (md5 != null) { - dataFile.setmd5(md5); + dataFile.setChecksumValue(md5); } Boolean restricted = (Boolean) result[14]; if (restricted != null) { dataFile.setRestricted(restricted); } + + String checksumType = (String) result[15]; + if (checksumType != null) { + try { + // In the database we store "SHA1" rather than "SHA-1". + DataFile.ChecksumType typeFromStringInDatabase = DataFile.ChecksumType.valueOf(checksumType); + dataFile.setChecksumType(typeFromStringInDatabase); + } catch (IllegalArgumentException ex) { + logger.info("Exception trying to convert " + checksumType + " to enum: " + ex); + } + } // TODO: // - if ingest status is "bad", look up the ingest report; diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java index 882608dff45..e744263f0f6 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java @@ -2837,7 +2837,7 @@ public String cancel() { } public boolean isDuplicate(FileMetadata fileMetadata) { - String thisMd5 = fileMetadata.getDataFile().getmd5(); + String thisMd5 = fileMetadata.getDataFile().getChecksumValue(); if (thisMd5 == null) { return false; } @@ -2854,7 +2854,7 @@ public boolean isDuplicate(FileMetadata fileMetadata) { Iterator fmIt = workingVersion.getFileMetadatas().iterator(); while (fmIt.hasNext()) { FileMetadata fm = fmIt.next(); - String md5 = fm.getDataFile().getmd5(); + String md5 = fm.getDataFile().getChecksumValue(); if (md5 != null) { if (MD5Map.get(md5) != null) { MD5Map.put(md5, MD5Map.get(md5).intValue() + 1); diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionDifference.java b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionDifference.java index 5fe3c9cd61e..09cc4ad50b2 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionDifference.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionDifference.java @@ -711,7 +711,8 @@ public int compare(FileMetadata l1, FileMetadata l2) { if (fileMetadataIsDifferent(fm1, fm2)) { datasetFileDifferenceItem fdi = selectFileMetadataDiffs(fm1, fm2); fdi.setFileId(fm1.getDataFile().getId().toString()); - fdi.setFileMD5(fm1.getDataFile().getmd5()); + fdi.setFileChecksumType(fm1.getDataFile().getChecksumType()); + fdi.setFileChecksumValue(fm1.getDataFile().getChecksumValue()); datasetFilesDiffList.add(fdi); } i++; @@ -719,14 +720,16 @@ public int compare(FileMetadata l1, FileMetadata l2) { } else if (fm2.getDataFile().getId() != null && fm1.getDataFile().getId().compareTo(fm2.getDataFile().getId()) > 0) { datasetFileDifferenceItem fdi = selectFileMetadataDiffs(null, fm2); fdi.setFileId(fm2.getDataFile().getId().toString()); - fdi.setFileMD5(fm2.getDataFile().getmd5()); + fdi.setFileChecksumType(fm2.getDataFile().getChecksumType()); + fdi.setFileChecksumValue(fm2.getDataFile().getChecksumValue()); datasetFilesDiffList.add(fdi); j++; } else if (fm2.getDataFile().getId() == null || fm1.getDataFile().getId().compareTo(fm2.getDataFile().getId()) < 0) { datasetFileDifferenceItem fdi = selectFileMetadataDiffs(fm1, null); fdi.setFileId(fm1.getDataFile().getId().toString()); - fdi.setFileMD5(fm1.getDataFile().getmd5()); + fdi.setFileChecksumType(fm1.getDataFile().getChecksumType()); + fdi.setFileChecksumValue(fm1.getDataFile().getChecksumValue()); datasetFilesDiffList.add(fdi); i++; @@ -740,7 +743,8 @@ public int compare(FileMetadata l1, FileMetadata l2) { fm1 = originalVersion.getFileMetadatas().get(i); datasetFileDifferenceItem fdi = selectFileMetadataDiffs(fm1, null); fdi.setFileId(fm1.getDataFile().getId().toString()); - fdi.setFileMD5(fm1.getDataFile().getmd5()); + fdi.setFileChecksumType(fm1.getDataFile().getChecksumType()); + fdi.setFileChecksumValue(fm1.getDataFile().getChecksumValue()); datasetFilesDiffList.add(fdi); i++; @@ -754,10 +758,18 @@ public int compare(FileMetadata l1, FileMetadata l2) { } else { fdi.setFileId("[UNASSIGNED]"); } - if (fm2.getDataFile().getmd5() != null) { - fdi.setFileMD5(fm2.getDataFile().getmd5()); + if (fm2.getDataFile().getChecksumValue() != null) { + fdi.setFileChecksumType(fm2.getDataFile().getChecksumType()); + fdi.setFileChecksumValue(fm2.getDataFile().getChecksumValue()); } else { - fdi.setFileMD5("[UNASSIGNED]"); + /** + * @todo What should we do here? checksumValue is set to + * "nullable = false" so it should never be non-null. Let's set + * it to "null" and see if this code path is ever reached. If + * not, the null check above can probably be safely removed. + */ + fdi.setFileChecksumType(null); + fdi.setFileChecksumValue("[UNASSIGNED]"); } datasetFilesDiffList.add(fdi); @@ -993,7 +1005,8 @@ public datasetFileDifferenceItem() { } private String fileId; - private String fileMD5; + private DataFile.ChecksumType fileChecksumType; + private String fileChecksumValue; private String fileName1; private String fileType1; @@ -1131,13 +1144,21 @@ public void setFile1Empty(boolean state) { public void setFile2Empty(boolean state) { file2Empty = state; } - - public String getFileMD5() { - return fileMD5; + + public DataFile.ChecksumType getFileChecksumType() { + return fileChecksumType; + } + + public void setFileChecksumType(DataFile.ChecksumType fileChecksumType) { + this.fileChecksumType = fileChecksumType; + } + + public String getFileChecksumValue() { + return fileChecksumValue; } - public void setFileMD5(String fileMD5) { - this.fileMD5 = fileMD5; + public void setFileChecksumValue(String fileChecksumValue) { + this.fileChecksumValue = fileChecksumValue; } } diff --git a/src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java b/src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java index a86374185e8..edbaa9516b5 100644 --- a/src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java +++ b/src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java @@ -1030,7 +1030,7 @@ public String cancel() { } public boolean isDuplicate(FileMetadata fileMetadata) { - String thisMd5 = fileMetadata.getDataFile().getmd5(); + String thisMd5 = fileMetadata.getDataFile().getChecksumValue(); if (thisMd5 == null) { return false; } @@ -1052,7 +1052,7 @@ public boolean isDuplicate(FileMetadata fileMetadata) { while (fmIt.hasNext()) { FileMetadata fm = fmIt.next(); - String md5 = fm.getDataFile().getmd5(); + String md5 = fm.getDataFile().getChecksumValue(); if (md5 != null) { if (MD5Map.get(md5) != null) { MD5Map.put(md5, MD5Map.get(md5).intValue() + 1); diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java b/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java index 2c0322e719c..e73a3a53e13 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java @@ -180,7 +180,10 @@ public Response createDataset( String jsonBody, @PathParam("identifier") String } try { try { - DatasetVersion version = jsonParser().parseDatasetVersion(jsonVersion); + DatasetVersion version = new DatasetVersion(); + version.setDataset(ds); + // Use the two argument version so that the version knows which dataset it's associated with. + version = jsonParser().parseDatasetVersion(jsonVersion, version); // force "initial version" properties version.setMinorVersionNumber(null); diff --git a/src/main/java/edu/harvard/iq/dataverse/api/WorldMapRelatedData.java b/src/main/java/edu/harvard/iq/dataverse/api/WorldMapRelatedData.java index 616d5c6ccce..58787fa5423 100755 --- a/src/main/java/edu/harvard/iq/dataverse/api/WorldMapRelatedData.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/WorldMapRelatedData.java @@ -494,7 +494,7 @@ public Response getWorldMapDatafileInfo(String jsonTokenData, @Context HttpServl jsonData.add("datafile_id", dfile.getId()); jsonData.add("datafile_label", dfile_meta.getLabel()); //jsonData.add("filename", dfile_meta.getLabel()); - jsonData.add("datafile_expected_md5_checksum", dfile.getmd5()); + jsonData.add("datafile_expected_md5_checksum", dfile.getChecksumValue()); Long fsize = dfile.getFilesize(); if (fsize == null){ fsize= new Long(-1); diff --git a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java index 77dbeebdf22..8f5c0fc99c8 100644 --- a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java @@ -62,7 +62,6 @@ import edu.harvard.iq.dataverse.ingest.tabulardata.impl.plugins.por.PORFileReader; import edu.harvard.iq.dataverse.ingest.tabulardata.impl.plugins.por.PORFileReaderSpi; import edu.harvard.iq.dataverse.util.FileUtil; -import edu.harvard.iq.dataverse.util.MD5Checksum; import edu.harvard.iq.dataverse.util.ShapefileHandler; import edu.harvard.iq.dataverse.util.SumStatCalculator; import edu.harvard.iq.dataverse.util.SystemConfig; @@ -600,11 +599,12 @@ public List createDataFiles(DatasetVersion version, InputStream inputS if (!tempFile.toFile().renameTo(new File(getFilesTempDirectory() + "/" + datafile.getStorageIdentifier()))) { return null; } - - // MD5: - MD5Checksum md5Checksum = new MD5Checksum(); + try { - datafile.setmd5(md5Checksum.CalculateMD5(getFilesTempDirectory() + "/" + datafile.getStorageIdentifier())); + // We persist "SHA1" rather than "SHA-1". + datafile.setChecksumType(systemConfig.getFileFixityChecksumAlgorithm()); + FileUtil fileUtil = new FileUtil(); + datafile.setChecksumValue(fileUtil.CalculateCheckSum(getFilesTempDirectory() + "/" + datafile.getStorageIdentifier(), datafile.getChecksumType())); } catch (Exception md5ex) { logger.warning("Could not calculate MD5 signature for new file " + fileName); } @@ -853,12 +853,17 @@ private DataFile createSingleDataFile(DatasetVersion version, InputStream inputS outputStream.close(); } catch (IOException ioex) {} } - - // MD5: + + /** + * @todo Can this block and the similar block above be refactored + * into a common code path? + */ if (datafile != null) { - MD5Checksum md5Checksum = new MD5Checksum(); + FileUtil fileUtil = new FileUtil(); try { - datafile.setmd5(md5Checksum.CalculateMD5(getFilesTempDirectory() + "/" + datafile.getStorageIdentifier())); + // We persist "SHA1" rather than "SHA-1". + datafile.setChecksumType(systemConfig.getFileFixityChecksumAlgorithm()); + datafile.setChecksumValue(fileUtil.CalculateCheckSum(getFilesTempDirectory() + "/" + datafile.getStorageIdentifier(), datafile.getChecksumType())); } catch (Exception md5ex) { logger.warning("Could not calculate MD5 signature for new file " + fileName); } diff --git a/src/main/java/edu/harvard/iq/dataverse/mydata/DataRetrieverAPI.java b/src/main/java/edu/harvard/iq/dataverse/mydata/DataRetrieverAPI.java index 3744a90241a..e5ffce5ea88 100644 --- a/src/main/java/edu/harvard/iq/dataverse/mydata/DataRetrieverAPI.java +++ b/src/main/java/edu/harvard/iq/dataverse/mydata/DataRetrieverAPI.java @@ -1,7 +1,5 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. +/** + * @todo Shouldn't this be in the "edu.harvard.iq.dataverse.api" package? Is the only one that isn't. */ package edu.harvard.iq.dataverse.mydata; @@ -267,7 +265,11 @@ private String getJSONErrorString(String jsonMsg, String optionalLoggerMsg){ } - + + /** + * @todo This should support the "X-Dataverse-key" header like the other + * APIs. + */ @Path(retrieveDataPartialAPIPath) @GET @Produces({"application/json"}) diff --git a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java index 5da94dc34df..648bebaa4c7 100644 --- a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java @@ -950,7 +950,16 @@ private String addOrUpdateDataset(IndexableDataset indexableDataset) { datafileSolrInputDocument.addField(SearchFields.FILE_TYPE, FileUtil.getFacetFileType(fileMetadata.getDataFile())); datafileSolrInputDocument.addField(SearchFields.FILE_TYPE_SEARCHABLE, FileUtil.getFacetFileType(fileMetadata.getDataFile())); datafileSolrInputDocument.addField(SearchFields.FILE_SIZE_IN_BYTES, fileMetadata.getDataFile().getFilesize()); - datafileSolrInputDocument.addField(SearchFields.FILE_MD5, fileMetadata.getDataFile().getmd5()); + if (DataFile.ChecksumType.MD5.equals(fileMetadata.getDataFile().getChecksumType())) { + /** + * @todo Someday we should probably deprecate this + * FILE_MD5 in favor of a combination of + * FILE_CHECKSUM_TYPE and FILE_CHECKSUM_VALUE. + */ + datafileSolrInputDocument.addField(SearchFields.FILE_MD5, fileMetadata.getDataFile().getChecksumValue()); + } + datafileSolrInputDocument.addField(SearchFields.FILE_CHECKSUM_TYPE, fileMetadata.getDataFile().getChecksumType().toString()); + datafileSolrInputDocument.addField(SearchFields.FILE_CHECKSUM_VALUE, fileMetadata.getDataFile().getChecksumValue()); datafileSolrInputDocument.addField(SearchFields.DESCRIPTION, fileMetadata.getDescription()); datafileSolrInputDocument.addField(SearchFields.FILE_DESCRIPTION, fileMetadata.getDescription()); datafileSolrInputDocument.addField(SearchFields.UNF, fileMetadata.getDataFile().getUnf()); diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchFields.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchFields.java index 871b28e7858..0dddfd3b22e 100644 --- a/src/main/java/edu/harvard/iq/dataverse/search/SearchFields.java +++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchFields.java @@ -147,6 +147,8 @@ public class SearchFields { public static final String FILE_TYPE = "fileTypeGroupFacet"; public static final String FILE_SIZE_IN_BYTES = "fileSizeInBytes"; public static final String FILE_MD5 = "fileMd5"; + public static final String FILE_CHECKSUM_TYPE = "fileChecksumType"; + public static final String FILE_CHECKSUM_VALUE = "fileChecksumValue"; public static final String FILENAME_WITHOUT_EXTENSION = "fileNameWithoutExtension"; /** * Indexed as a string so we can facet on it. diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java index 8eab46a3556..28803e8d1bb 100644 --- a/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java +++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java @@ -1043,13 +1043,15 @@ public String dataFileSizeDisplay(DataFile datafile) { } - public String dataFileMD5Display(DataFile datafile) { + public String dataFileChecksumDisplay(DataFile datafile) { if (datafile == null) { return ""; } - if (datafile.getmd5() != null && datafile.getmd5() != "") { - return " MD5: " + datafile.getmd5() + " "; + if (datafile.getChecksumValue() != null && datafile.getChecksumValue() != "") { + if (datafile.getChecksumType() != null) { + return " " + datafile.getChecksumType() + ": " + datafile.getChecksumValue() + " "; + } } return ""; diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java index 54c06214383..bd2fbcc75a2 100644 --- a/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java @@ -1,5 +1,6 @@ package edu.harvard.iq.dataverse.search; +import edu.harvard.iq.dataverse.DataFile; import edu.harvard.iq.dataverse.DataFileServiceBean; import edu.harvard.iq.dataverse.DatasetFieldConstant; import edu.harvard.iq.dataverse.DatasetFieldServiceBean; @@ -527,6 +528,12 @@ public SolrQueryResponse search(User user, Dataverse dataverse, String query, Li } } solrSearchResult.setFileMd5((String) solrDocument.getFieldValue(SearchFields.FILE_MD5)); + try { + solrSearchResult.setFileChecksumType((DataFile.ChecksumType) DataFile.ChecksumType.fromString((String) solrDocument.getFieldValue(SearchFields.FILE_CHECKSUM_TYPE))); + } catch (IllegalArgumentException ex) { + logger.info("Exception setting setFileChecksumType: " + ex); + } + solrSearchResult.setFileChecksumValue((String) solrDocument.getFieldValue(SearchFields.FILE_CHECKSUM_VALUE)); solrSearchResult.setUnf((String) solrDocument.getFieldValue(SearchFields.UNF)); solrSearchResult.setDatasetVersionId(datasetVersionId); List fileCategories = (ArrayList) solrDocument.getFieldValues(SearchFields.FILE_TAG); diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java b/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java index fa738f0ea6d..bb084c3c69f 100644 --- a/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java +++ b/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java @@ -4,6 +4,7 @@ import edu.harvard.iq.dataverse.Dataset; import edu.harvard.iq.dataverse.DvObject; import edu.harvard.iq.dataverse.api.Util; +import edu.harvard.iq.dataverse.util.json.JsonPrinter; import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder; import java.util.ArrayList; import java.util.Date; @@ -15,6 +16,8 @@ import javax.json.JsonObject; import javax.json.JsonObjectBuilder; import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder; +import java.math.BigDecimal; +import javax.json.JsonValue; public class SolrSearchResult { @@ -67,7 +70,12 @@ public class SolrSearchResult { private String filetype; private String fileContentType; private Long fileSizeInBytes; + /** + * fileMD5 is here for legacy and backward-compatibility reasons. It might be deprecated some day in favor of "fileChecksumType" and "fileChecksumValue" + */ private String fileMd5; + private DataFile.ChecksumType fileChecksumType; + private String fileChecksumValue; private String dataverseAlias; private String dataverseParentAlias; // private boolean statePublished; @@ -494,7 +502,13 @@ public JsonObjectBuilder json(boolean showRelevance, boolean showEntityIds, bool .add("file_type", this.filetype) .add("file_content_type", this.fileContentType) .add("size_in_bytes", getFileSizeInBytes()) + /** + * "md5" was the only possible value so it's hard-coded here but + * we might want to deprecate it someday since we now put the + * MD5 or SHA-1 in "checksum". + */ .add("md5", getFileMd5()) + .add("checksum", JsonPrinter.getChecksumTypeAndValue(getFileChecksumType(), getFileChecksumValue())) .add("unf", getUnf()) .add("dataset_citation", datasetCitation) .add("deaccession_reason", this.deaccessionReason) @@ -807,13 +821,33 @@ public void setFileSizeInBytes(Long fileSizeInBytes) { } public String getFileMd5() { - return fileMd5; + if (DataFile.ChecksumType.MD5.equals(getFileChecksumType())) { + return fileMd5; + } else { + return null; + } } public void setFileMd5(String fileMd5) { this.fileMd5 = fileMd5; } + public DataFile.ChecksumType getFileChecksumType() { + return fileChecksumType; + } + + public void setFileChecksumType(DataFile.ChecksumType fileChecksumType) { + this.fileChecksumType = fileChecksumType; + } + + public String getFileChecksumValue() { + return fileChecksumValue; + } + + public void setFileChecksumValue(String fileChecksumValue) { + this.fileChecksumValue = fileChecksumValue; + } + public String getNameSort() { return nameSort; } @@ -1020,4 +1054,5 @@ public void setUserRole(List userRole) { this.userRole = userRole; } + } diff --git a/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java index 65c3278eb8b..e6b6c827760 100644 --- a/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java @@ -33,6 +33,7 @@ public class SettingsServiceBean { * So there. */ public enum Key { + FileFixityChecksumAlgorithm, /** * Override Solr highlighting "fragsize" * https://wiki.apache.org/solr/HighlightingParameters#hl.fragsize diff --git a/src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java index 3addc9513fa..5e6766a3dcf 100644 --- a/src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java +++ b/src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java @@ -21,10 +21,12 @@ package edu.harvard.iq.dataverse.util; import edu.harvard.iq.dataverse.DataFile; +import edu.harvard.iq.dataverse.DataFile.ChecksumType; import edu.harvard.iq.dataverse.ingest.IngestableDataChecker; import java.io.BufferedInputStream; import java.io.File; import java.io.FileInputStream; +import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.FileReader; import java.io.IOException; @@ -33,6 +35,8 @@ import java.util.MissingResourceException; import java.nio.channels.FileChannel; import java.nio.channels.WritableByteChannel; +import java.security.MessageDigest; +import java.security.NoSuchAlgorithmException; import java.util.HashMap; import java.util.Map; import java.util.logging.Logger; @@ -403,4 +407,52 @@ public static String getFriendlySize(Long filesize) { return displaySize; } + + // from MD5Checksum.java + public synchronized String CalculateCheckSum(String datafile, ChecksumType checksumType) { + + FileInputStream fis = null; + try { + fis = new FileInputStream(datafile); + } catch (FileNotFoundException ex) { + throw new RuntimeException(ex); + } + + return CalculateChecksum(fis, checksumType); + } + + // from MD5Checksum.java + public synchronized String CalculateChecksum(InputStream in, ChecksumType checksumType) { + MessageDigest md = null; + try { + // Use "SHA-1" (toString) rather than "SHA1", for example. + md = MessageDigest.getInstance(checksumType.toString()); + } catch (NoSuchAlgorithmException e) { + throw new RuntimeException(e); + } + + byte[] dataBytes = new byte[1024]; + + int nread; + try { + while ((nread = in.read(dataBytes)) != -1) { + md.update(dataBytes, 0, nread); + } + } catch (IOException ex) { + throw new RuntimeException(ex); + } finally { + try { + in.close(); + } catch (Exception e) { + } + } + + byte[] mdbytes = md.digest(); + StringBuilder sb = new StringBuilder(""); + for (int i = 0; i < mdbytes.length; i++) { + sb.append(Integer.toString((mdbytes[i] & 0xff) + 0x100, 16).substring(1)); + } + return sb.toString(); + } + } diff --git a/src/main/java/edu/harvard/iq/dataverse/util/MD5Checksum.java b/src/main/java/edu/harvard/iq/dataverse/util/MD5Checksum.java deleted file mode 100644 index 2b4d8755743..00000000000 --- a/src/main/java/edu/harvard/iq/dataverse/util/MD5Checksum.java +++ /dev/null @@ -1,84 +0,0 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ - -package edu.harvard.iq.dataverse.util; - -import java.io.InputStream; -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.security.MessageDigest; -import java.security.NoSuchAlgorithmException; - -/** - * (from v.3.6) - * @author xyang - */ -public class MD5Checksum implements java.io.Serializable { - - public MD5Checksum() { - } - - public synchronized String CalculateMD5 (String datafile) { - - FileInputStream fis = null; - try { - fis = new FileInputStream(datafile); - } catch (FileNotFoundException ex) { - throw new RuntimeException(ex); - } - - return CalculateMD5(fis); - /* - byte[] dataBytes = new byte[1024]; - - int nread; - try { - while ((nread = fis.read(dataBytes)) != -1) { - md.update(dataBytes, 0, nread); - } - } catch (IOException ex) { - throw new RuntimeException(ex); - } - - byte[] mdbytes = md.digest(); - StringBuilder sb = new StringBuilder(""); - for (int i = 0; i < mdbytes.length; i++) { - sb.append(Integer.toString((mdbytes[i] & 0xff) + 0x100, 16).substring(1)); - } - return sb.toString(); - */ - } - - public synchronized String CalculateMD5 (InputStream in) { - MessageDigest md = null; - try { - md = MessageDigest.getInstance("MD5"); - } catch (NoSuchAlgorithmException e) { - throw new RuntimeException(e); - } - - byte[] dataBytes = new byte[1024]; - - int nread; - try { - while ((nread = in.read(dataBytes)) != -1) { - md.update(dataBytes, 0, nread); - } - } catch (IOException ex) { - throw new RuntimeException(ex); - } finally { - try {in.close();} catch (Exception e) {} - } - - byte[] mdbytes = md.digest(); - StringBuilder sb = new StringBuilder(""); - for (int i = 0; i < mdbytes.length; i++) { - sb.append(Integer.toString((mdbytes[i] & 0xff) + 0x100, 16).substring(1)); - } - return sb.toString(); - } -} diff --git a/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java b/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java index f03ae885e61..30bd8c1250a 100644 --- a/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java +++ b/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java @@ -1,6 +1,7 @@ package edu.harvard.iq.dataverse.util; import com.ocpsoft.pretty.PrettyContext; +import edu.harvard.iq.dataverse.DataFile; import edu.harvard.iq.dataverse.settings.SettingsServiceBean; import java.io.FileInputStream; import java.io.IOException; @@ -509,4 +510,16 @@ public boolean isTimerServer() { } return false; } + + public DataFile.ChecksumType getFileFixityChecksumAlgorithm() { + DataFile.ChecksumType saneDefault = DataFile.ChecksumType.MD5; + String checksumStringFromDatabase = settingsService.getValueForKey(SettingsServiceBean.Key.FileFixityChecksumAlgorithm, saneDefault.toString()); + try { + DataFile.ChecksumType checksumTypeFromDatabase = DataFile.ChecksumType.fromString(checksumStringFromDatabase); + return checksumTypeFromDatabase; + } catch (IllegalArgumentException ex) { + logger.info("The setting " + SettingsServiceBean.Key.FileFixityChecksumAlgorithm + " is misconfigured. " + ex.getMessage() + " Returning sane default: " + saneDefault + "."); + return saneDefault; + } + } } diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java index 3e8a6152558..2fe6b7f36ff 100644 --- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java +++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java @@ -35,6 +35,7 @@ import java.util.LinkedList; import java.util.List; import java.util.Set; +import java.util.logging.Logger; import javax.json.Json; import javax.json.JsonArray; import javax.json.JsonObject; @@ -49,6 +50,8 @@ */ public class JsonParser { + private static final Logger logger = Logger.getLogger(JsonParser.class.getCanonicalName()); + DatasetFieldServiceBean datasetFieldSvc; MetadataBlockServiceBean blockService; SettingsServiceBean settingsService; @@ -373,18 +376,44 @@ public DataFile parseDataFile(JsonObject datafileJson) { contentType = "application/octet-stream"; } String storageIdentifier = datafileJson.getString("storageIdentifier"); - String md5 = datafileJson.getString("md5", null); - - if (md5 == null) { - md5 = "unknown"; + JsonObject checksum = datafileJson.getJsonObject("checksum"); + if (checksum != null) { + // newer style that allows for SHA-1 rather than MD5 + /** + * @todo Add more error checking. Do we really expect people to set + * file metadata without uploading files? Some day we'd like to work + * on a "native" API that allows for multipart upload of the JSON + * describing the files (this "parseDataFile" method) and the bits + * of the files themselves. See + * https://github.com/IQSS/dataverse/issues/1612 + */ + String type = checksum.getString("type"); + if (type != null) { + String value = checksum.getString("value"); + if (value != null) { + try { + dataFile.setChecksumType(DataFile.ChecksumType.fromString(type)); + dataFile.setChecksumValue(value); + } catch (IllegalArgumentException ex) { + logger.info("Invalid"); + } + } + } + } else { + // older, MD5 logic, still her for backward compatibility + String md5 = datafileJson.getString("md5", null); + if (md5 == null) { + md5 = "unknown"; + } + dataFile.setChecksumType(DataFile.ChecksumType.MD5); + dataFile.setChecksumValue(md5); } - + // TODO: // unf (if available)... etc.? dataFile.setContentType(contentType); dataFile.setStorageIdentifier(storageIdentifier); - dataFile.setmd5(md5); return dataFile; } diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java index f00bee0b140..cf6e04283d3 100644 --- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java +++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java @@ -29,6 +29,7 @@ import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser; import edu.harvard.iq.dataverse.authorization.users.User; import edu.harvard.iq.dataverse.privateurl.PrivateUrl; +import edu.harvard.iq.dataverse.search.SolrSearchResult; import edu.harvard.iq.dataverse.util.DatasetFieldWalker; import edu.harvard.iq.dataverse.util.StringUtil; import java.util.Set; @@ -468,7 +469,12 @@ public static JsonObjectBuilder json(DataFile df, FileMetadata fileMetadata) { .add("originalFileFormat", df.getOriginalFileFormat()) .add("originalFormatLabel", df.getOriginalFormatLabel()) .add("UNF", df.getUnf()) - .add("md5", df.getmd5()) + /** + * @todo Should we deprecate "md5" now that it's under + * "checksum" (which may also be a SHA-1 rather than an MD5)? + */ + .add("md5", getMd5IfItExists(df.getChecksumType(), df.getChecksumValue())) + .add("checksum", getChecksumTypeAndValue(df.getChecksumType(), df.getChecksumValue())) .add("description", df.getDescription()); } @@ -589,4 +595,23 @@ public static JsonArrayBuilder json(Collection jc) { } return bld; } + + public static String getMd5IfItExists(DataFile.ChecksumType checksumType, String checksumValue) { + if (DataFile.ChecksumType.MD5.equals(checksumType)) { + return checksumValue; + } else { + return null; + } + } + + public static JsonObjectBuilder getChecksumTypeAndValue(DataFile.ChecksumType checksumType, String checksumValue) { + if (checksumType != null) { + return Json.createObjectBuilder() + .add("type", checksumType.toString()) + .add("value", checksumValue); + } else { + return null; + } + } + } diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 22079d4576c..4abaeedb8a1 100755 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -825,7 +825,7 @@

- + diff --git a/src/main/webapp/editFilesFragment.xhtml b/src/main/webapp/editFilesFragment.xhtml index 8650b50c5e4..872900a7cd6 100644 --- a/src/main/webapp/editFilesFragment.xhtml +++ b/src/main/webapp/editFilesFragment.xhtml @@ -149,16 +149,16 @@ - +
-
- - +
+ + -
#{bundle['file.MD5.exists.tip']}
+
#{bundle['file.checksum.exists.tip']}
diff --git a/src/main/webapp/file.xhtml b/src/main/webapp/file.xhtml index ee3d4f71af4..da8fbc3f48b 100644 --- a/src/main/webapp/file.xhtml +++ b/src/main/webapp/file.xhtml @@ -194,8 +194,9 @@
- + +
@@ -236,12 +237,13 @@
-
+
- +
@@ -304,8 +306,9 @@ FITS stuff....
  • + #{bundle['file.metadataTab.fileMetadata.md5.label']} - +
    • diff --git a/src/main/webapp/filesFragment.xhtml b/src/main/webapp/filesFragment.xhtml index 0a87c89198f..1af77330d03 100644 --- a/src/main/webapp/filesFragment.xhtml +++ b/src/main/webapp/filesFragment.xhtml @@ -264,7 +264,7 @@
    - +
    diff --git a/src/main/webapp/mydata_templates/cards.html b/src/main/webapp/mydata_templates/cards.html index 1d12409e7cd..39e9cba22a3 100644 --- a/src/main/webapp/mydata_templates/cards.html +++ b/src/main/webapp/mydata_templates/cards.html @@ -75,6 +75,7 @@
    {{ sdoc.date_to_display_on_card }} - {{ sdoc.parentName }} {#
    {{ sdoc.dataset_citation|safe }}#} +
    {{ sdoc.file_type }} - {{ sdoc.size_in_bytes }} KB - MD5: {{ sdoc.md5 }} {% endif %}
    diff --git a/src/main/webapp/mydata_templates/cards_minimum.html b/src/main/webapp/mydata_templates/cards_minimum.html index 6fa4066d48b..c0dd50db7f1 100644 --- a/src/main/webapp/mydata_templates/cards_minimum.html +++ b/src/main/webapp/mydata_templates/cards_minimum.html @@ -83,7 +83,7 @@
    {{ card_info.file_type }} - {{ card_info.size_in_bytes }} KB - - MD5: {{ card_info.md5 }} + {{ card_info.checksum.type }}: {{ card_info.checksum.value }} {% endif %}
    diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml index 22336165006..40e689c9869 100644 --- a/src/main/webapp/search-include-fragment.xhtml +++ b/src/main/webapp/search-include-fragment.xhtml @@ -608,7 +608,7 @@ - + Date: Wed, 21 Sep 2016 14:00:05 -0400 Subject: [PATCH 009/172] add more tests for setting dv category via API #3371 Also, be more strict. Require ALL CAPS. We can always loosen this later. --- .../iq/dataverse/util/json/JsonParser.java | 2 +- .../iq/dataverse/api/DataversesIT.java | 83 ++++++++++++------- .../harvard/iq/dataverse/api/SearchIT.java | 41 --------- .../edu/harvard/iq/dataverse/api/UtilIT.java | 11 ++- .../dataverse/util/json/JsonParserTest.java | 3 + .../resources/json/complete-dataverse.json | 1 + 6 files changed, 64 insertions(+), 77 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java index 3a91fa74f23..0130bf81979 100644 --- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java +++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java @@ -99,7 +99,7 @@ public Dataverse parseDataverse(JsonObject jobj) throws JsonParseException { dv.setDataverseType(Dataverse.DataverseType.UNCATEGORIZED); // default if (jobj.containsKey("dataverseType")) { for (Dataverse.DataverseType dvtype : Dataverse.DataverseType.values()) { - if (dvtype.name().equalsIgnoreCase(jobj.getString("dataverseType"))) { + if (dvtype.name().equals(jobj.getString("dataverseType"))) { dv.setDataverseType(dvtype); } } diff --git a/src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java b/src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java index 2d243e9bb50..e7227321146 100644 --- a/src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java +++ b/src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java @@ -2,39 +2,32 @@ import com.jayway.restassured.RestAssured; import com.jayway.restassured.response.Response; +import edu.harvard.iq.dataverse.Dataverse; import java.util.logging.Logger; -import org.junit.AfterClass; +import javax.ws.rs.core.Response.Status; import org.junit.BeforeClass; import org.junit.Test; import static junit.framework.Assert.assertEquals; +import static org.hamcrest.CoreMatchers.equalTo; public class DataversesIT { private static final Logger logger = Logger.getLogger(DataversesIT.class.getCanonicalName()); - private static String username1; - private static String apiToken1; - private static String dataverseAlias1; - private static String dataverseAlias2; - @BeforeClass public static void setUpClass() { - RestAssured.baseURI = UtilIT.getRestAssuredBaseUri(); - - Response createUserResponse = UtilIT.createRandomUser(); -// createUserResponse.prettyPrint(); - assertEquals(200, createUserResponse.getStatusCode()); - - apiToken1 = UtilIT.getApiTokenFromResponse(createUserResponse); - username1 = UtilIT.getUsernameFromResponse(createUserResponse); - } @Test public void testAttemptToCreateDuplicateAlias() throws Exception { - Response createDataverse1Response = UtilIT.createRandomDataverse(apiToken1); + Response createUser = UtilIT.createRandomUser(); +// createUser.prettyPrint(); + String username = UtilIT.getUsernameFromResponse(createUser); + String apiToken = UtilIT.getApiTokenFromResponse(createUser); + + Response createDataverse1Response = UtilIT.createRandomDataverse(apiToken); if (createDataverse1Response.getStatusCode() != 201) { // purposefully using println here to the error shows under "Test Results" in Netbeans System.out.println("A workspace for testing (a dataverse) couldn't be created in the root dataverse. The output was:\n\n" + createDataverse1Response.body().asString()); @@ -44,36 +37,62 @@ public void testAttemptToCreateDuplicateAlias() throws Exception { } assertEquals(201, createDataverse1Response.getStatusCode()); - dataverseAlias1 = UtilIT.getAliasFromResponse(createDataverse1Response); - dataverseAlias2 = dataverseAlias1.toUpperCase(); + String dataverseAlias1 = UtilIT.getAliasFromResponse(createDataverse1Response); + String dataverseAlias2 = dataverseAlias1.toUpperCase(); logger.info("Attempting to creating dataverse with alias '" + dataverseAlias2 + "' (uppercase version of existing '" + dataverseAlias1 + "' dataverse, should fail)..."); - Response attemptToCreateDataverseWithDuplicateAlias = UtilIT.createDataverse(dataverseAlias2, apiToken1); + String category = null; + Response attemptToCreateDataverseWithDuplicateAlias = UtilIT.createDataverse(dataverseAlias2, category, apiToken); attemptToCreateDataverseWithDuplicateAlias.prettyPrint(); assertEquals(400, attemptToCreateDataverseWithDuplicateAlias.getStatusCode()); logger.info("Deleting dataverse " + dataverseAlias1); - Response deleteDataverse1Response = UtilIT.deleteDataverse(dataverseAlias1, apiToken1); + Response deleteDataverse1Response = UtilIT.deleteDataverse(dataverseAlias1, apiToken); deleteDataverse1Response.prettyPrint(); assertEquals(200, deleteDataverse1Response.getStatusCode()); logger.info("Checking response code for attempting to delete a non-existent dataverse."); - Response attemptToDeleteDataverseThatShouldNotHaveBeenCreated = UtilIT.deleteDataverse(dataverseAlias2, apiToken1); + Response attemptToDeleteDataverseThatShouldNotHaveBeenCreated = UtilIT.deleteDataverse(dataverseAlias2, apiToken); attemptToDeleteDataverseThatShouldNotHaveBeenCreated.prettyPrint(); assertEquals(404, attemptToDeleteDataverseThatShouldNotHaveBeenCreated.getStatusCode()); } - @AfterClass - public static void tearDownClass() { - boolean disabled = false; - - if (disabled) { - return; - } - - Response deleteUser1Response = UtilIT.deleteUser(username1); - deleteUser1Response.prettyPrint(); - assertEquals(200, deleteUser1Response.getStatusCode()); + @Test + public void dataverseCategory() { + Response createUser = UtilIT.createRandomUser(); + createUser.prettyPrint(); + String username = UtilIT.getUsernameFromResponse(createUser); + String apiToken = UtilIT.getApiTokenFromResponse(createUser); + + Response createDataverseWithoutCategory = UtilIT.createRandomDataverse(apiToken); + createDataverseWithoutCategory.prettyPrint(); + createDataverseWithoutCategory.then().assertThat() + .body("data.dataverseType", equalTo("UNCATEGORIZED")) + .statusCode(Status.CREATED.getStatusCode()); + + String alias1 = UtilIT.getRandomIdentifier(); + String category1 = Dataverse.DataverseType.LABORATORY.toString(); + Response createDataverseWithCategory = UtilIT.createDataverse(alias1, category1, apiToken); + createDataverseWithCategory.prettyPrint(); + createDataverseWithCategory.then().assertThat() + .body("data.dataverseType", equalTo("LABORATORY")) + .statusCode(Status.CREATED.getStatusCode()); + + String alias2 = UtilIT.getRandomIdentifier(); + String madeUpCategory = "madeUpCategory"; + Response createDataverseWithInvalidCategory = UtilIT.createDataverse(alias2, madeUpCategory, apiToken); + createDataverseWithInvalidCategory.prettyPrint(); + createDataverseWithInvalidCategory.then().assertThat() + .body("data.dataverseType", equalTo("UNCATEGORIZED")) + .statusCode(Status.CREATED.getStatusCode()); + + String alias3 = UtilIT.getRandomIdentifier(); + String category3 = Dataverse.DataverseType.LABORATORY.toString().toLowerCase(); + Response createDataverseWithLowerCaseCategory = UtilIT.createDataverse(alias3, category3, apiToken); + createDataverseWithLowerCaseCategory.prettyPrint(); + createDataverseWithLowerCaseCategory.then().assertThat() + .body("data.dataverseType", equalTo("UNCATEGORIZED")) + .statusCode(Status.CREATED.getStatusCode()); } diff --git a/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java b/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java index 5cc8bb17ddb..ae5f8ec7182 100644 --- a/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java +++ b/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java @@ -73,7 +73,6 @@ public class SearchIT { private static TestUser homer; private static TestUser ned; private static TestUser clancy; - private static final String categoryTestDataverse = "categoryTestDataverse"; private static final String dvForPermsTesting = "dvForPermsTesting"; private static String dataset1; private static String dataset2; @@ -89,7 +88,6 @@ public class SearchIT { private static final boolean disableTestPermsonRootDv = false; private static final boolean disableTestPermsOnNewDv = false; private static final boolean homerPublishesVersion2AfterDeletingFile = false; - private static final boolean disableTestCategory = false; private Stopwatch timer; private boolean haveToUseCurlForUpload = false; @@ -731,40 +729,6 @@ public void homerPublishesVersion2AfterDeletingFile() throws InterruptedExceptio } - @Ignore - @Test - public void dataverseCategory() { - - if (disableTestCategory) { - return; - } - - Response enableNonPublicSearch = enableSetting(SettingsServiceBean.Key.SearchApiNonPublicAllowed); - assertEquals(200, enableNonPublicSearch.getStatusCode()); - - /** - * Unfortunately, it appears that the ability to specify the category of - * a dataverse when creating it is a GUI-only feature. It can't - * currently be done via the API, to our knowledge. You also can't tell - * from the API which category was persisted but it always seems to be - * "UNCATEGORIZED" - */ - TestDataverse dataverseToCreate = new TestDataverse(categoryTestDataverse, categoryTestDataverse, Dataverse.DataverseType.ORGANIZATIONS_INSTITUTIONS); - Response createDvResponse = createDataverse(dataverseToCreate, homer); - assertEquals(201, createDvResponse.getStatusCode()); - - TestSearchQuery query = new TestSearchQuery(categoryTestDataverse); - Response searchResponse = search(query, homer); -// searchResponse.prettyPrint(); - JsonPath jsonPath = JsonPath.from(searchResponse.body().asString()); - String category = jsonPath.get("data.facets." + SearchFields.DATAVERSE_CATEGORY).toString(); - String msg = "category: " + category; - assertEquals("category: [null]", msg); - - Response disableNonPublicSearch = deleteSetting(SettingsServiceBean.Key.SearchApiNonPublicAllowed); - assertEquals(200, disableNonPublicSearch.getStatusCode()); - } - @AfterClass public static void cleanup() { @@ -805,11 +769,6 @@ public static void cleanup() { assertEquals(200, destroyDataset.getStatusCode()); } - if (!disableTestCategory) { - Response deleteCategoryDataverseResponse = deleteDataverse(categoryTestDataverse, homer); - assertEquals(200, deleteCategoryDataverseResponse.getStatusCode()); - } - if (!disableTestPermsOnNewDv) { Response deleteDvResponse = deleteDataverse(dvForPermsTesting, homer); assertEquals(200, deleteDvResponse.getStatusCode()); diff --git a/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java b/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java index 6fefbdcd8a7..ef24d5da3bf 100644 --- a/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java +++ b/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java @@ -20,7 +20,9 @@ import edu.harvard.iq.dataverse.settings.SettingsServiceBean; import static com.jayway.restassured.RestAssured.given; import static com.jayway.restassured.path.xml.XmlPath.from; +import java.math.BigDecimal; import java.util.List; +import javax.json.JsonValue; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertNull; @@ -85,7 +87,7 @@ private static String getRandomUsername() { return "user" + getRandomIdentifier().substring(0, 8); } - private static String getRandomIdentifier() { + public static String getRandomIdentifier() { return UUID.randomUUID().toString().substring(0, 8); } @@ -133,7 +135,7 @@ public static Response getServiceDocument(String apiToken) { return response; } - static Response createDataverse(String alias, String apiToken) { + static Response createDataverse(String alias, String category, String apiToken) { JsonArrayBuilder contactArrayBuilder = Json.createArrayBuilder(); contactArrayBuilder.add(Json.createObjectBuilder().add("contactEmail", getEmailFromUserName(getRandomIdentifier()))); JsonArrayBuilder subjectArrayBuilder = Json.createArrayBuilder(); @@ -143,6 +145,8 @@ static Response createDataverse(String alias, String apiToken) { .add("name", alias) .add("dataverseContacts", contactArrayBuilder) .add("dataverseSubjects", subjectArrayBuilder) + // don't send "dataverseType" if category is null, must be a better way + .add(category != null ? "dataverseType" : "notTheKeyDataverseType", category != null ? category : "whatever") .build(); Response createDataverseResponse = given() .body(dvData.toString()).contentType(ContentType.JSON) @@ -152,7 +156,8 @@ static Response createDataverse(String alias, String apiToken) { static Response createRandomDataverse(String apiToken) { String alias = getRandomIdentifier(); - return createDataverse(alias, apiToken); + String category = null; + return createDataverse(alias, category, apiToken); } static Response showDataverseContents(String alias, String apiToken) { diff --git a/src/test/java/edu/harvard/iq/dataverse/util/json/JsonParserTest.java b/src/test/java/edu/harvard/iq/dataverse/util/json/JsonParserTest.java index 8a6b945a710..c80ef237ba6 100644 --- a/src/test/java/edu/harvard/iq/dataverse/util/json/JsonParserTest.java +++ b/src/test/java/edu/harvard/iq/dataverse/util/json/JsonParserTest.java @@ -239,6 +239,7 @@ public void testParseCompleteDataverse() throws JsonParseException { assertEquals("testAlias", actual.getAlias()); assertEquals("Test-Driven University", actual.getAffiliation()); assertEquals("test Description.", actual.getDescription()); + assertEquals("LABORATORY", actual.getDataverseType().toString()); assertEquals(2, actual.getDataverseContacts().size()); assertEquals("test@example.com,test@example.org", actual.getContactEmails()); assertEquals(0, actual.getDataverseContacts().get(0).getDisplayOrder()); @@ -261,6 +262,7 @@ public void testParseThemeDataverse() throws JsonParseException { assertEquals("testAlias", actual.getAlias()); assertEquals("Test-Driven University", actual.getAffiliation()); assertEquals("test Description.", actual.getDescription()); + assertEquals("UNCATEGORIZED", actual.getDataverseType().toString()); assertEquals("gray", actual.getDataverseTheme().getBackgroundColor()); assertEquals("red", actual.getDataverseTheme().getLinkColor()); assertEquals("http://www.cnn.com", actual.getDataverseTheme().getLinkUrl()); @@ -292,6 +294,7 @@ public void testParseMinimalDataverse() throws JsonParseException { Dataverse actual = sut.parseDataverse(dvJson); assertEquals("testDv", actual.getName()); assertEquals("testAlias", actual.getAlias()); + assertEquals("UNCATEGORIZED", actual.getDataverseType().toString()); assertTrue(actual.getDataverseContacts().isEmpty()); assertEquals("", actual.getContactEmails()); assertFalse(actual.isPermissionRoot()); diff --git a/src/test/resources/json/complete-dataverse.json b/src/test/resources/json/complete-dataverse.json index 98679af44ff..3e3056f2e74 100644 --- a/src/test/resources/json/complete-dataverse.json +++ b/src/test/resources/json/complete-dataverse.json @@ -11,5 +11,6 @@ } ], "permissionRoot": true, + "dataverseType": "LABORATORY", "description": "test Description." } From 6f4165a932a497e65f1094cd8025aab18cb00b76 Mon Sep 17 00:00:00 2001 From: Philip Durbin Date: Fri, 23 Sep 2016 14:20:31 -0400 Subject: [PATCH 010/172] set values before applying null constraint, cleanup #3354 --- scripts/database/upgrades/3354-alt-checksum.sql | 2 +- src/main/java/edu/harvard/iq/dataverse/DataFile.java | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/scripts/database/upgrades/3354-alt-checksum.sql b/scripts/database/upgrades/3354-alt-checksum.sql index 0c54d673aac..42956fcc65d 100644 --- a/scripts/database/upgrades/3354-alt-checksum.sql +++ b/scripts/database/upgrades/3354-alt-checksum.sql @@ -1,6 +1,6 @@ ALTER TABLE datafile ADD COLUMN checksumtype character varying(255); -ALTER TABLE datafile ALTER COLUMN checksumtype SET NOT NULL; UPDATE datafile SET checksumtype = 'MD5'; +ALTER TABLE datafile ALTER COLUMN checksumtype SET NOT NULL; -- alternate statement for sbgrid.org and others interested in SHA-1 support -- note that in the database we use "SHA1" (no hyphen) but the GUI will show "SHA-1" --UPDATE datafile SET checksumtype = 'SHA1'; diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFile.java b/src/main/java/edu/harvard/iq/dataverse/DataFile.java index 1a66914b2ae..fe3de11e3a3 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataFile.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataFile.java @@ -17,7 +17,6 @@ import java.nio.file.Path; import java.nio.file.Paths; import java.nio.file.Files; -import java.util.Comparator; import java.util.Arrays; import javax.persistence.Entity; import javax.persistence.OneToMany; From 2b2a3c79a022af3fe590694f067af30ec0d36c90 Mon Sep 17 00:00:00 2001 From: Philip Durbin Date: Fri, 23 Sep 2016 15:52:57 -0400 Subject: [PATCH 011/172] removed unused cruft #3354 --- src/main/webapp/mydata_templates/cards.html | 83 --------------------- 1 file changed, 83 deletions(-) delete mode 100644 src/main/webapp/mydata_templates/cards.html diff --git a/src/main/webapp/mydata_templates/cards.html b/src/main/webapp/mydata_templates/cards.html deleted file mode 100644 index 39e9cba22a3..00000000000 --- a/src/main/webapp/mydata_templates/cards.html +++ /dev/null @@ -1,83 +0,0 @@ -{% if data.selected_filters %} - {% for pub_stat in data.selected_filters.publication_statuses %} - Status: {{ pub_stat }} - {% endfor %} - {% for role_name in data.selected_filters.role_names %} - Role: {{ role_name }} - {% endfor %} -{% endif %} - -{# #} - -{% set card_bg_color = cycler("", "background-color:#f7f7f7;") %} -{% for sdoc in data.items -%} - {# #} - {% if sdoc.type == "dataverse" %} - {% set card_border_color = "#c55b28" %} - {% elif sdoc.type == "dataset" %} - {% set card_border_color = "#428bca" %} - {% elif sdoc.type == "file" %} - {% set card_border_color = "#ccc" %} - {% endif %} - -
    - - {#({{ loop.index }})#} {% if sdoc.is_draft_state %}Draft {% endif %} - {% if sdoc.is_unpublished_state %}Unpublished {% endif %} - {% if sdoc.is_published %} Published {% endif %} - - {% for role_name in sdoc.user_roles %} - {{ role_name }} - {% endfor %} - - {% if sdoc.type == "dataverse" %} -
    - - {{ sdoc.name }} - (affiliation?) -
    -
    - - {# icon image #} -
    - {{ sdoc.date_to_display_on_card }} - {% if sdoc.parentId %} - {% if sdoc.parentId != sdoc.identifier %} - - {{ sdoc.parentName }} - {% endif %} - {% endif %} - - {% if parent_alias %} - {{ parent_alias }} - {% endif %} -
    {{ sdoc.description }} - - {% elif sdoc.type == "dataset" %} - -
    - {{ sdoc.name }} -
    -
    - -
    {{ sdoc.date_to_display_on_card }} - - {{ sdoc.parentName }} -
    {{ sdoc.citation|safe }} -
    {{ sdoc.description|safe }} - - {% elif sdoc.type == "file" %} -
    - - {{ sdoc.name }} -
    -
    - - -
    {{ sdoc.date_to_display_on_card }} - - {{ sdoc.parentName }} - {#
    {{ sdoc.dataset_citation|safe }}#} - -
    {{ sdoc.file_type }} - {{ sdoc.size_in_bytes }} KB - MD5: {{ sdoc.md5 }} -{% endif %} -
    - -{%- endfor %} From f04edc2cd6c98b86409bc33c5d07f5b4112150a2 Mon Sep 17 00:00:00 2001 From: Michael Bar-Sinai Date: Mon, 26 Sep 2016 00:44:36 +0300 Subject: [PATCH 012/172] Added infrastructure for better DSL-like API creation. Also, used it for Dataverses resource class. --- .../iq/dataverse/api/AbstractApiBean.java | 217 +++++++----- .../edu/harvard/iq/dataverse/api/Admin.java | 116 +++---- .../harvard/iq/dataverse/api/BatchImport.java | 10 +- .../iq/dataverse/api/BuiltinUsers.java | 14 +- .../harvard/iq/dataverse/api/DataTagsAPI.java | 2 +- .../dataverse/api/DatasetFieldServiceApi.java | 20 +- .../harvard/iq/dataverse/api/Datasets.java | 209 +++--------- .../harvard/iq/dataverse/api/Dataverses.java | 313 ++++++------------ .../edu/harvard/iq/dataverse/api/Groups.java | 34 +- .../iq/dataverse/api/HarvestingClients.java | 38 +-- .../iq/dataverse/api/HarvestingServer.java | 30 +- .../edu/harvard/iq/dataverse/api/Index.java | 74 ++--- .../edu/harvard/iq/dataverse/api/Info.java | 2 +- .../edu/harvard/iq/dataverse/api/Mail.java | 2 +- .../iq/dataverse/api/MetadataBlocks.java | 4 +- .../edu/harvard/iq/dataverse/api/Roles.java | 73 ++-- .../iq/dataverse/api/SavedSearches.java | 56 ++-- .../edu/harvard/iq/dataverse/api/Search.java | 10 +- .../edu/harvard/iq/dataverse/api/TestApi.java | 14 +- .../iq/dataverse/api/WorldMapRelatedData.java | 88 ++--- .../iq/dataverse/util/json/JsonPrinter.java | 118 +++---- 21 files changed, 647 insertions(+), 797 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java b/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java index 7e779c4cc65..6c0a4eb9c6d 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java @@ -38,6 +38,7 @@ import java.io.StringReader; import java.net.URI; import java.util.concurrent.Callable; +import java.util.function.Function; import java.util.logging.Level; import java.util.logging.Logger; import javax.ejb.EJB; @@ -99,7 +100,7 @@ public Response refineResponse( String message ) { final Throwable cause = getCause(); baseMessage = (cause!=null ? cause.getMessage() : ""); } - return errorResponse(statusCode, message+" "+baseMessage); + return error(statusCode, message+" "+baseMessage); } /** @@ -203,7 +204,59 @@ public JsonParser call() throws Exception { return new JsonParser(datasetFieldSvc, metadataBlockSvc,settingsSvc); } }); - + + /** + * Functional interface for handling HTTP requests in the APIs. + * + * @see #response(edu.harvard.iq.dataverse.api.AbstractApiBean.DataverseRequestHandler) + */ + protected static interface DataverseRequestHandler { + Response handle( DataverseRequest u ) throws WrappedResponse; + } + + + /* ===================== *\ + * Utility Methods * + * Get that DSL feelin' * + \* ===================== */ + + protected JsonParser jsonParser() { + return jsonParserRef.get(); + } + + protected boolean isNumeric( String str ) { + return Util.isNumeric(str); + } + + protected boolean parseBooleanOrDie( String input ) throws WrappedResponse { + if (input == null ) throw new WrappedResponse( badRequest("Boolean value missing")); + input = input.trim(); + if ( Util.isBoolean(input) ) { + return Util.isTrue(input); + } else { + throw new WrappedResponse( badRequest("Illegal boolean value '" + input + "'")); + } + } + + /** + * Returns the {@code key} query parameter from the current request, or {@code null} if + * the request has no such parameter. + * @param key Name of the requested parameter. + * @return Value of the requested parameter in the current request. + */ + protected String getRequestParameter( String key ) { + return httpRequest.getParameter(key); + } + + protected String getRequestApiKey() { + String headerParamApiKey = httpRequest.getHeader(DATAVERSE_KEY_HEADER_NAME); + String queryParamApiKey = httpRequest.getParameter("key"); + return headerParamApiKey!=null ? headerParamApiKey : queryParamApiKey; + } + + /* ========= *\ + * Finders * + \* ========= */ protected RoleAssignee findAssignee(String identifier) { try { RoleAssignee roleAssignee = roleAssigneeSvc.getRoleAssignee(identifier); @@ -228,22 +281,6 @@ protected AuthenticatedUser findUserByApiToken( String apiKey ) { return authSvc.lookupUser(apiKey); } - /** - * Returns the {@code key} query parameter from the current request, or {@code null} if - * the request has no such parameter. - * @param key Name of the requested parameter. - * @return Value of the requested parameter in the current request. - */ - protected String getRequestParameter( String key ) { - return httpRequest.getParameter(key); - } - - protected String getRequestApiKey() { - String headerParamApiKey = httpRequest.getHeader(DATAVERSE_KEY_HEADER_NAME); - String queryParamApiKey = httpRequest.getParameter("key"); - return headerParamApiKey!=null ? headerParamApiKey : queryParamApiKey; - } - /** * Returns the user of pointed by the API key, or the guest user * @return a user, may be a guest user. @@ -285,7 +322,13 @@ private AuthenticatedUser findAuthenticatedUserOrDie( String key ) throws Wrappe throw new WrappedResponse( badApiKey(key) ); } - + protected Dataverse findDataverseOrDie( String dvIdtf ) throws WrappedResponse { + Dataverse dv = findDataverse(dvIdtf); + if ( dv == null ) { + throw new WrappedResponse(error( Response.Status.NOT_FOUND, "Can't find dataverse with identifier='" + dvIdtf + "'")); + } + return dv; + } protected DataverseRequest createDataverseRequest( User u ) { return new DataverseRequest(u, httpRequest); @@ -322,7 +365,7 @@ protected DvObject findDvo( String id ) { protected T failIfNull( T t, String errorMessage ) throws WrappedResponse { if ( t != null ) return t; - throw new WrappedResponse( errorResponse( Response.Status.BAD_REQUEST,errorMessage) ); + throw new WrappedResponse( error( Response.Status.BAD_REQUEST,errorMessage) ); } protected MetadataBlock findMetadataBlock(Long id) { @@ -337,12 +380,24 @@ protected DatasetFieldType findDatasetFieldType(String idtf) throws NumberFormat : datasetFieldSvc.findByNameOpt(idtf); } + /* =================== *\ + * Command Execution * + \* =================== */ + + /** + * Executes a command, and returns the appropriate result/HTTP response. + * @param Return type for the command + * @param cmd The command to execute. + * @return Value from the command + * @throws edu.harvard.iq.dataverse.api.AbstractApiBean.WrappedResponse Unwrap and return. + * @see #response(java.util.concurrent.Callable) + */ protected T execCommand( Command cmd ) throws WrappedResponse { try { return engineSvc.submit(cmd); } catch (IllegalCommandException ex) { - throw new WrappedResponse( ex, errorResponse(Response.Status.FORBIDDEN, ex.getMessage() ) ); + throw new WrappedResponse( ex, error(Response.Status.FORBIDDEN, ex.getMessage() ) ); } catch (PermissionException ex) { /** @@ -350,31 +405,66 @@ protected T execCommand( Command cmd ) throws WrappedResponse { * There's valuable information in there that can help people reason * about permissions! */ - throw new WrappedResponse(errorResponse(Response.Status.UNAUTHORIZED, + throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "User " + cmd.getRequest().getUser().getIdentifier() + " is not permitted to perform requested action.") ); } catch (CommandException ex) { Logger.getLogger(AbstractApiBean.class.getName()).log(Level.SEVERE, "Error while executing command " + cmd, ex); - throw new WrappedResponse(ex, errorResponse(Status.INTERNAL_SERVER_ERROR, ex.getMessage())); + throw new WrappedResponse(ex, error(Status.INTERNAL_SERVER_ERROR, ex.getMessage())); + } + } + + /** + * A syntactically nicer way of using {@link #execCommand(edu.harvard.iq.dataverse.engine.command.Command)}. + * @param hdl The block to run. + * @return HTTP Response appropriate for the way {@code hdl} executed. + */ + protected Response response( Callable hdl ) { + try { + return hdl.call(); + } catch ( WrappedResponse rr ) { + return rr.getResponse(); + } catch ( Exception ex ) { + logger.log( Level.WARNING, "Error executing callable: " + ex.getMessage(), ex ); + return error(Status.INTERNAL_SERVER_ERROR, ex.getMessage()); + } + } + + /** + * The preferred way of handling a request that requires a user. The system + * looks for the user and, if found, handles it to the handler for doing the + * actual work. + * + * This is a relatively secure way to handle things, since if the user is not + * found, the response is about the bad API key, rather than something else + * (say, 404 NOT FOUND which leaks information about the existence of the + * sought object). + * + * @param hdl handling code block. + * @return HTTP Response appropriate for the way {@code hdl} executed. + */ + protected Response response( DataverseRequestHandler hdl ) { + try { + return hdl.handle(createDataverseRequest(findUserOrDie())); + } catch ( WrappedResponse rr ) { + return rr.getResponse(); + } catch ( Exception ex ) { + logger.log( Level.WARNING, "Error executing callable: " + ex.getMessage(), ex ); + return error(Status.INTERNAL_SERVER_ERROR, ex.getMessage()); } } - protected Response okResponse( JsonArrayBuilder bld ) { + /* ====================== *\ + * HTTP Response methods * + \* ====================== */ + + protected Response ok( JsonArrayBuilder bld ) { return Response.ok(Json.createObjectBuilder() .add("status", "OK") .add("data", bld).build()).build(); } - protected Response createdResponse( String uri, JsonObjectBuilder bld ) { - return Response.created( URI.create(uri) ) - .entity( Json.createObjectBuilder() - .add("status", "OK") - .add("data", bld).build()) - .type(MediaType.APPLICATION_JSON) - .build(); - } - - protected Response okResponse( JsonObjectBuilder bld ) { + protected Response ok( JsonObjectBuilder bld ) { return Response.ok( Json.createObjectBuilder() .add("status", "OK") .add("data", bld).build() ) @@ -382,7 +472,7 @@ protected Response okResponse( JsonObjectBuilder bld ) { .build(); } - protected Response okResponse( String msg ) { + protected Response ok( String msg ) { return Response.ok().entity(Json.createObjectBuilder() .add("status", "OK") .add("data", Json.createObjectBuilder().add("message",msg)).build() ) @@ -390,24 +480,21 @@ protected Response okResponse( String msg ) { .build(); } - /** - * Returns an OK response (HTTP 200, status:OK) with the passed value - * in the data field. - * @param value the value for the data field - * @return a HTTP OK response with the passed value as data. - */ - protected Response okResponseWithValue( String value ) { - return Response.ok(Json.createObjectBuilder() - .add("status", "OK") - .add("data", value).build(), MediaType.APPLICATION_JSON_TYPE ).build(); - } - - protected Response okResponseWithValue( boolean value ) { + protected Response ok( boolean value ) { return Response.ok().entity(Json.createObjectBuilder() .add("status", "OK") .add("data", value).build() ).build(); } + protected Response created( String uri, JsonObjectBuilder bld ) { + return Response.created( URI.create(uri) ) + .entity( Json.createObjectBuilder() + .add("status", "OK") + .add("data", bld).build()) + .type(MediaType.APPLICATION_JSON) + .build(); + } + protected Response accepted() { return Response.accepted() .entity(Json.createObjectBuilder() @@ -415,20 +502,16 @@ protected Response accepted() { ).build(); } - protected JsonParser jsonParser() { - return jsonParserRef.get(); - } - protected Response notFound( String msg ) { - return errorResponse(Status.NOT_FOUND, msg); + return error(Status.NOT_FOUND, msg); } protected Response badRequest( String msg ) { - return errorResponse( Status.BAD_REQUEST, msg ); + return error( Status.BAD_REQUEST, msg ); } protected Response badApiKey( String apiKey ) { - return errorResponse(Status.UNAUTHORIZED, (apiKey != null ) ? "Bad api key '" + apiKey +"'" : "Please provide a key query parameter (?key=XXX) or via the HTTP header " + DATAVERSE_KEY_HEADER_NAME ); + return error(Status.UNAUTHORIZED, (apiKey != null ) ? "Bad api key '" + apiKey +"'" : "Please provide a key query parameter (?key=XXX) or via the HTTP header " + DATAVERSE_KEY_HEADER_NAME ); } protected Response permissionError( PermissionException pe ) { @@ -436,35 +519,17 @@ protected Response permissionError( PermissionException pe ) { } protected Response permissionError( String message ) { - return errorResponse( Status.UNAUTHORIZED, message ); - } - - protected static Response errorResponse( Status sts ) { - return errorResponse(sts, null); + return error( Status.UNAUTHORIZED, message ); } - protected static Response errorResponse( Status sts, String msg ) { + protected static Response error( Status sts, String msg ) { return Response.status(sts) .entity( NullSafeJsonBuilder.jsonObjectBuilder() .add("status", "ERROR") .add( "message", msg ).build() ).type(MediaType.APPLICATION_JSON_TYPE).build(); } - - protected Response execute( Command c ) { - try { - engineSvc.submit( c ); - return accepted(); - - } catch ( PermissionException pex ) { - return permissionError( pex ); - - } catch ( CommandException ce ) { - return errorResponse(Status.INTERNAL_SERVER_ERROR, ce.getLocalizedMessage()); - } - } - - protected boolean isNumeric( String str ) { return Util.isNumeric(str); }; + } class LazyRef { diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Admin.java b/src/main/java/edu/harvard/iq/dataverse/api/Admin.java index ac1128d3aeb..b1ecae4635a 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Admin.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Admin.java @@ -48,7 +48,7 @@ import javax.validation.ConstraintViolationException; import javax.ws.rs.Produces; import javax.ws.rs.core.Response.Status; -import static edu.harvard.iq.dataverse.api.AbstractApiBean.errorResponse; +import static edu.harvard.iq.dataverse.api.AbstractApiBean.error; /** * Where the secure, setup API calls live. * @author michael @@ -70,14 +70,14 @@ public Response listAllSettings() { JsonObjectBuilder bld = jsonObjectBuilder(); settingsSvc.listAll().forEach( s -> bld.add(s.getName(), s.getContent())); - return okResponse(bld); + return ok(bld); } @Path("settings/{name}") @PUT public Response putSetting( @PathParam("name") String name, String content ) { Setting s = settingsSvc.set(name, content); - return okResponse( jsonObjectBuilder().add(s.getName(), s.getContent()) ); + return ok( jsonObjectBuilder().add(s.getName(), s.getContent()) ); } @Path("settings/{name}") @@ -86,7 +86,7 @@ public Response getSetting( @PathParam("name") String name ) { String s = settingsSvc.get(name); return ( s != null ) - ? okResponse( s ) + ? ok( s ) : notFound("Setting " + name + " not found"); } @@ -95,7 +95,7 @@ public Response getSetting( @PathParam("name") String name ) { public Response deleteSetting( @PathParam("name") String name ) { settingsSvc.delete(name); - return okResponse("Setting " + name + " deleted."); + return ok("Setting " + name + " deleted."); } @Path("authenticationProviderFactories") @@ -108,7 +108,7 @@ public Response listAuthProviderFactories() { .add("info", f.getInfo() )); } - return okResponse(arb); + return ok(arb); } @@ -121,7 +121,7 @@ public Response listAuthProviders() { arb.add( json(r) ); } - return okResponse(arb); + return ok(arb); } @Path("authenticationProviders") @@ -140,9 +140,9 @@ public Response addProvider( AuthenticationProviderRow row ) { authSvc.deregisterProvider(provider.getId()); authSvc.registerProvider(provider); } - return createdResponse("/s/authenticationProviders/"+managed.getId(), json(managed)); + return created("/s/authenticationProviders/"+managed.getId(), json(managed)); } catch ( AuthorizationSetupException e ) { - return errorResponse(Response.Status.INTERNAL_SERVER_ERROR, e.getMessage() ); + return error(Response.Status.INTERNAL_SERVER_ERROR, e.getMessage() ); } } @@ -150,8 +150,8 @@ public Response addProvider( AuthenticationProviderRow row ) { @GET public Response showProvider( @PathParam("id") String id ) { AuthenticationProviderRow row = em.find(AuthenticationProviderRow.class, id); - return (row != null ) ? okResponse( json(row) ) - : errorResponse(Status.NOT_FOUND,"Can't find authetication provider with id '" + id + "'"); + return (row != null ) ? ok( json(row) ) + : error(Status.NOT_FOUND,"Can't find authetication provider with id '" + id + "'"); } @POST @@ -160,13 +160,13 @@ public Response showProvider( @PathParam("id") String id ) { public Response enableAuthenticationProvider( @PathParam("id")String id, String body ) { if ( ! Util.isBoolean(body) ) { - return errorResponse(Response.Status.BAD_REQUEST, "Illegal value '" + body + "'. Try 'true' or 'false'"); + return error(Response.Status.BAD_REQUEST, "Illegal value '" + body + "'. Try 'true' or 'false'"); } boolean enable = Util.isTrue(body); AuthenticationProviderRow row = em.find(AuthenticationProviderRow.class, id); if ( row == null ) { - return errorResponse( Status.NOT_FOUND, "Can't find authentication provider with id '" + id + "'"); + return error( Status.NOT_FOUND, "Can't find authentication provider with id '" + id + "'"); } row.setEnabled(enable); @@ -175,25 +175,25 @@ public Response enableAuthenticationProvider( @PathParam("id")String id, String if ( enable ) { // enable a provider if ( authSvc.getAuthenticationProvider(id) != null ) { - return okResponse( String.format("Authentication provider '%s' already enabled", id)); + return ok( String.format("Authentication provider '%s' already enabled", id)); } try { authSvc.registerProvider( authSvc.loadProvider(row) ); - return okResponse(String.format("Authentication Provider %s enabled", row.getId())); + return ok(String.format("Authentication Provider %s enabled", row.getId())); } catch (AuthenticationProviderFactoryNotFoundException ex) { - return errorResponse(Response.Status.BAD_REQUEST, + return error(Response.Status.BAD_REQUEST, String.format("Can't instantiate provider, as there's no factory with alias %s", row.getFactoryAlias())); } catch (AuthorizationSetupException ex) { logger.log(Level.WARNING, "Error instantiating authentication provider: " + ex.getMessage(), ex); - return errorResponse(Response.Status.BAD_REQUEST, + return error(Response.Status.BAD_REQUEST, String.format("Can't instantiate provider: %s", ex.getMessage())); } } else { // disable a provider authSvc.deregisterProvider(id); - return okResponse("Authentication Provider '" + id + "' disabled. " + return ok("Authentication Provider '" + id + "' disabled. " + ( authSvc.getAuthenticationProviderIds().isEmpty() ? "WARNING: no enabled authentication providers left." : "") ); } @@ -208,7 +208,7 @@ public Response deleteAuthenticationProvider( @PathParam("id") String id ) { em.remove( row ); } - return okResponse("AuthenticationProvider " + id + " deleted. " + return ok("AuthenticationProvider " + id + " deleted. " + ( authSvc.getAuthenticationProviderIds().isEmpty() ? "WARNING: no enabled authentication providers left." : "")); } @@ -218,9 +218,9 @@ public Response deleteAuthenticationProvider( @PathParam("id") String id ) { public Response getAuthenticatedUser(@PathParam("identifier") String identifier) { AuthenticatedUser authenticatedUser = authSvc.getAuthenticatedUser(identifier); if (authenticatedUser != null) { - return okResponse(jsonForAuthUser(authenticatedUser)); + return ok(jsonForAuthUser(authenticatedUser)); } - return errorResponse(Response.Status.BAD_REQUEST, "User " + identifier + " not found."); + return error(Response.Status.BAD_REQUEST, "User " + identifier + " not found."); } @DELETE @@ -229,9 +229,9 @@ public Response deleteAuthenticatedUser(@PathParam("identifier") String identifi AuthenticatedUser user = authSvc.getAuthenticatedUser(identifier); if (user!=null) { authSvc.deleteAuthenticatedUser(user.getId()); - return okResponse("AuthenticatedUser " +identifier + " deleted. "); + return ok("AuthenticatedUser " +identifier + " deleted. "); } - return errorResponse(Response.Status.BAD_REQUEST, "User "+ identifier+" not found."); + return error(Response.Status.BAD_REQUEST, "User "+ identifier+" not found."); } @POST @@ -241,9 +241,9 @@ public Response publishDataverseAsCreator(@PathParam("id") long id) { Dataverse dataverse = dataverseSvc.find(id); if (dataverse != null) { AuthenticatedUser authenticatedUser = dataverse.getCreator(); - return okResponse(json(execCommand(new PublishDataverseCommand(createDataverseRequest(authenticatedUser), dataverse)))); + return ok(json(execCommand(new PublishDataverseCommand(createDataverseRequest(authenticatedUser), dataverse)))); } else { - return errorResponse(Status.BAD_REQUEST, "Could not find dataverse with id " + id); + return error(Status.BAD_REQUEST, "Could not find dataverse with id " + id); } } catch (WrappedResponse wr) { return wr.getResponse(); @@ -256,16 +256,16 @@ public Response listAuthenticatedUsers() { try { AuthenticatedUser user = findAuthenticatedUserOrDie(); if (!user.isSuperuser()) { - return errorResponse(Response.Status.FORBIDDEN, "Superusers only."); + return error(Response.Status.FORBIDDEN, "Superusers only."); } } catch (WrappedResponse ex) { - return errorResponse(Response.Status.FORBIDDEN, "Superusers only."); + return error(Response.Status.FORBIDDEN, "Superusers only."); } JsonArrayBuilder userArray = Json.createArrayBuilder(); authSvc.findAllAuthenticatedUsers().stream().forEach((user) -> { userArray.add(jsonForAuthUser(user)); }); - return okResponse(userArray); + return ok(userArray); } /** @@ -278,20 +278,20 @@ public Response convertShibUserToBuiltin(@PathParam("id") Long id, String newEma try { AuthenticatedUser user = findAuthenticatedUserOrDie(); if (!user.isSuperuser()) { - return errorResponse(Response.Status.FORBIDDEN, "Superusers only."); + return error(Response.Status.FORBIDDEN, "Superusers only."); } } catch (WrappedResponse ex) { - return errorResponse(Response.Status.FORBIDDEN, "Superusers only."); + return error(Response.Status.FORBIDDEN, "Superusers only."); } try { BuiltinUser builtinUser = authSvc.convertShibToBuiltIn(id, newEmailAddress); if (builtinUser == null) { - return errorResponse(Response.Status.BAD_REQUEST, "User id " + id + " could not be converted from Shibboleth to BuiltIn. An Exception was not thrown."); + return error(Response.Status.BAD_REQUEST, "User id " + id + " could not be converted from Shibboleth to BuiltIn. An Exception was not thrown."); } JsonObjectBuilder output = Json.createObjectBuilder(); output.add("email", builtinUser.getEmail()); output.add("username", builtinUser.getUserName()); - return okResponse(output); + return ok(output); } catch (Throwable ex) { StringBuilder sb = new StringBuilder(); sb.append(ex + " "); @@ -301,7 +301,7 @@ public Response convertShibUserToBuiltin(@PathParam("id") Long id, String newEma } String msg = "User id " + id + " could not be converted from Shibboleth to BuiltIn. Details from Exception: " + sb; logger.info(msg); - return errorResponse(Response.Status.BAD_REQUEST, msg); + return error(Response.Status.BAD_REQUEST, msg); } } @@ -316,14 +316,14 @@ public Response builtin2shib(String content) { try { AuthenticatedUser userToRunThisMethod = findAuthenticatedUserOrDie(); if (!userToRunThisMethod.isSuperuser()) { - return errorResponse(Response.Status.FORBIDDEN, "Superusers only."); + return error(Response.Status.FORBIDDEN, "Superusers only."); } } catch (WrappedResponse ex) { - return errorResponse(Response.Status.FORBIDDEN, "Superusers only."); + return error(Response.Status.FORBIDDEN, "Superusers only."); } boolean disabled = false; if (disabled) { - return errorResponse(Response.Status.BAD_REQUEST, "API endpoint disabled."); + return error(Response.Status.BAD_REQUEST, "API endpoint disabled."); } AuthenticatedUser builtInUserToConvert = null; String emailToFind; @@ -337,7 +337,7 @@ public Response builtin2shib(String content) { newEmailAddressToUse = args[2]; // authuserId = args[666]; } catch (ArrayIndexOutOfBoundsException ex) { - return errorResponse(Response.Status.BAD_REQUEST, "Problem with content <<<" + content + ">>>: " + ex.toString()); + return error(Response.Status.BAD_REQUEST, "Problem with content <<<" + content + ">>>: " + ex.toString()); } AuthenticatedUser existingAuthUserFoundByEmail = shibService.findAuthUserByEmail(emailToFind); String existing = "NOT FOUND"; @@ -350,7 +350,7 @@ public Response builtin2shib(String content) { if (specifiedUserToConvert != null) { builtInUserToConvert = specifiedUserToConvert; } else { - return errorResponse(Response.Status.BAD_REQUEST, "No user to convert. We couldn't find a *single* existing user account based on " + emailToFind + " and no user was found using specified id " + longToLookup); + return error(Response.Status.BAD_REQUEST, "No user to convert. We couldn't find a *single* existing user account based on " + emailToFind + " and no user was found using specified id " + longToLookup); } } String shibProviderId = ShibAuthenticationProvider.PROVIDER_ID; @@ -369,7 +369,7 @@ public Response builtin2shib(String content) { boolean validEmail = EMailValidator.isEmailValid(overwriteEmail, null); if (!validEmail) { // See https://github.com/IQSS/dataverse/issues/2998 - return errorResponse(Response.Status.BAD_REQUEST, "invalid email: " + overwriteEmail); + return error(Response.Status.BAD_REQUEST, "invalid email: " + overwriteEmail); } /** * @todo If affiliation is not null, put it in RoleAssigneeDisplayInfo @@ -426,7 +426,7 @@ public Response builtin2shib(String content) { * @todo Someday we should make a errorResponse method that * takes JSON arrays and objects. */ - return errorResponse(Status.BAD_REQUEST, problems.build().toString()); + return error(Status.BAD_REQUEST, problems.build().toString()); } // response.add("knows existing password", knowsExistingPassword); } @@ -441,7 +441,7 @@ public Response builtin2shib(String content) { response.add("affiliation", overwriteAffiliation); } response.add("problems", problems); - return okResponse(response); + return ok(response); } @DELETE @@ -450,9 +450,9 @@ public Response deleteAuthenticatedUserById(@PathParam("id") Long id) { AuthenticatedUser user = authSvc.findByID(id); if (user != null) { authSvc.deleteAuthenticatedUser(user.getId()); - return okResponse("AuthenticatedUser " + id + " deleted. "); + return ok("AuthenticatedUser " + id + " deleted. "); } - return errorResponse(Response.Status.BAD_REQUEST, "User " + id + " not found."); + return error(Response.Status.BAD_REQUEST, "User " + id + " not found."); } @Path("roles") @@ -461,11 +461,11 @@ public Response createNewBuiltinRole(RoleDTO roleDto) { ActionLogRecord alr = new ActionLogRecord(ActionLogRecord.ActionType.Admin, "createBuiltInRole") .setInfo(roleDto.getAlias() + ":" + roleDto.getDescription() ); try { - return okResponse(json(rolesSvc.save(roleDto.asRole()))); + return ok(json(rolesSvc.save(roleDto.asRole()))); } catch (Exception e) { alr.setActionResult(ActionLogRecord.Result.InternalError); alr.setInfo( alr.getInfo() + "// " + e.getMessage() ); - return errorResponse(Response.Status.INTERNAL_SERVER_ERROR, e.getMessage()); + return error(Response.Status.INTERNAL_SERVER_ERROR, e.getMessage()); } finally { actionLogSvc.log(alr); } @@ -475,9 +475,9 @@ public Response createNewBuiltinRole(RoleDTO roleDto) { @GET public Response listBuiltinRoles() { try { - return okResponse( rolesToJson(rolesSvc.findBuiltinRoles()) ); + return ok( rolesToJson(rolesSvc.findBuiltinRoles()) ); } catch (Exception e) { - return errorResponse(Response.Status.INTERNAL_SERVER_ERROR, e.getMessage()); + return error(Response.Status.INTERNAL_SERVER_ERROR, e.getMessage()); } } @@ -492,11 +492,11 @@ public Response toggleSuperuser(@PathParam("identifier") String identifier) { user.setSuperuser(!user.isSuperuser()); - return okResponse("User " + user.getIdentifier() + " " + (user.isSuperuser() ? "set": "removed") + " as a superuser."); + return ok("User " + user.getIdentifier() + " " + (user.isSuperuser() ? "set": "removed") + " as a superuser."); } catch (Exception e) { alr.setActionResult(ActionLogRecord.Result.InternalError); alr.setInfo( alr.getInfo() + "// " + e.getMessage() ); - return errorResponse(Response.Status.INTERNAL_SERVER_ERROR, e.getMessage()); + return error(Response.Status.INTERNAL_SERVER_ERROR, e.getMessage()); } finally { actionLogSvc.log(alr); } @@ -522,13 +522,13 @@ public Response validate() { violation.add("entityClassDatabaseTableRowId", databaseRow); violation.add("field", field); violation.add("invalidValue", invalidValue); - return okResponse(violation); + return ok(violation); } } cause = cause.getCause(); } } - return okResponse(msg); + return ok(msg); } /** @@ -544,10 +544,10 @@ public Response getConfirmEmailToken(@PathParam("userId") long userId) { if (user != null) { ConfirmEmailData confirmEmailData = confirmEmailSvc.findSingleConfirmEmailDataByUser(user); if (confirmEmailData != null) { - return okResponse(Json.createObjectBuilder().add("token", confirmEmailData.getToken())); + return ok(Json.createObjectBuilder().add("token", confirmEmailData.getToken())); } } - return errorResponse(Status.BAD_REQUEST, "Could not find confirm email token for user " + userId); + return error(Status.BAD_REQUEST, "Could not find confirm email token for user " + userId); } /** @@ -563,16 +563,16 @@ public Response startConfirmEmailProcess(@PathParam("userId") long userId) { try { ConfirmEmailInitResponse confirmEmailInitResponse = confirmEmailSvc.beginConfirm(user); ConfirmEmailData confirmEmailData = confirmEmailInitResponse.getConfirmEmailData(); - return okResponse( + return ok( Json.createObjectBuilder() .add("tokenCreated", confirmEmailData.getCreated().toString()) .add("identifier", user.getUserIdentifier() )); } catch (ConfirmEmailException ex) { - return errorResponse(Status.BAD_REQUEST, "Could not start confirm email process for user " + userId + ": " + ex.getLocalizedMessage()); + return error(Status.BAD_REQUEST, "Could not start confirm email process for user " + userId + ": " + ex.getLocalizedMessage()); } } - return errorResponse(Status.BAD_REQUEST, "Could not find user based on " + userId); + return error(Status.BAD_REQUEST, "Could not find user based on " + userId); } /** @@ -588,7 +588,7 @@ public Response convertUserFromBcryptToSha1(String json) { BuiltinUser builtinUser = builtinUserService.find(new Long(object.getInt("builtinUserId"))); builtinUser.updateEncryptedPassword("4G7xxL9z11/JKN4jHPn4g9iIQck=", 0); // password is "sha-1Pass", 0 means SHA-1 BuiltinUser savedUser = builtinUserService.save(builtinUser); - return okResponse("foo: " + savedUser); + return ok("foo: " + savedUser); } @@ -601,6 +601,6 @@ public Response getAssignmentsFor( @PathParam("raIdtf") String raIdtf ) { JsonArrayBuilder arr = Json.createArrayBuilder(); roleAssigneeSvc.getAssignmentsFor(raIdtf).forEach( a -> arr.add(json(a))); - return okResponse(arr); + return ok(arr); } } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/BatchImport.java b/src/main/java/edu/harvard/iq/dataverse/api/BatchImport.java index a94d36ddd3b..7d29e9e2334 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/BatchImport.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/BatchImport.java @@ -92,15 +92,15 @@ public Response postImport(String body, @QueryParam("dv") String parentIdtf, @Qu } Dataverse owner = findDataverse(parentIdtf); if (owner == null) { - return errorResponse(Response.Status.NOT_FOUND, "Can't find dataverse with identifier='" + parentIdtf + "'"); + return error(Response.Status.NOT_FOUND, "Can't find dataverse with identifier='" + parentIdtf + "'"); } try { PrintWriter cleanupLog = null; // Cleanup log isn't needed for ImportType == NEW. We don't do any data cleanup in this mode. String filename = null; // Since this is a single input from a POST, there is no file that we are reading from. JsonObjectBuilder status = importService.doImport(dataverseRequest, owner, body, filename, ImportType.NEW, cleanupLog); - return this.okResponse(status); + return this.ok(status); } catch (ImportException | IOException e) { - return this.errorResponse(Response.Status.BAD_REQUEST, e.getMessage()); + return this.error(Response.Status.BAD_REQUEST, e.getMessage()); } } @@ -140,13 +140,13 @@ private Response startBatchJob(String fileDir, String parentIdtf, String apiKey, if (createDV) { owner = importService.createDataverse(parentIdtf, dataverseRequest); } else { - return errorResponse(Response.Status.NOT_FOUND, "Can't find dataverse with identifier='" + parentIdtf + "'"); + return error(Response.Status.NOT_FOUND, "Can't find dataverse with identifier='" + parentIdtf + "'"); } } batchService.processFilePath(fileDir, parentIdtf, dataverseRequest, owner, importType, createDV); } catch (ImportException e) { - return this.errorResponse(Response.Status.BAD_REQUEST, "Import Exception, " + e.getMessage()); + return this.error(Response.Status.BAD_REQUEST, "Import Exception, " + e.getMessage()); } return this.accepted(); } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/BuiltinUsers.java b/src/main/java/edu/harvard/iq/dataverse/api/BuiltinUsers.java index 2709e17387e..d1f0e7e1297 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/BuiltinUsers.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/BuiltinUsers.java @@ -69,7 +69,7 @@ public Response getApiToken( @PathParam("username") String username, @QueryParam ApiToken t = authSvc.findApiTokenByUser(authUser); - return (t != null ) ? okResponse(t.getTokenString()) : notFound("User " + username + " does not have an API token"); + return (t != null ) ? ok(t.getTokenString()) : notFound("User " + username + " does not have an API token"); } /** @@ -98,7 +98,7 @@ private Response internalSave(BuiltinUser user, String password, String key) { String expectedKey = settingsSvc.get(API_KEY_IN_SETTINGS); if (expectedKey == null) { - return errorResponse(Status.SERVICE_UNAVAILABLE, "Dataverse config issue: No API key defined for built in user management"); + return error(Status.SERVICE_UNAVAILABLE, "Dataverse config issue: No API key defined for built in user management"); } if (!expectedKey.equals(key)) { return badApiKey(key); @@ -115,7 +115,7 @@ private Response internalSave(BuiltinUser user, String password, String key) { // Make sure the identifier is unique if ( (builtinUserSvc.findByUserName(user.getUserName()) != null) || ( authSvc.identifierExists(user.getUserName())) ) { - return errorResponse(Status.BAD_REQUEST, "username '" + user.getUserName() + "' already exists"); + return error(Status.BAD_REQUEST, "username '" + user.getUserName() + "' already exists"); } user = builtinUserSvc.save(user); @@ -150,23 +150,23 @@ private Response internalSave(BuiltinUser user, String password, String key) { resp.add("apiToken", token.getTokenString()); alr.setInfo("builtinUser:" + user.getUserName() + " authenticatedUser:" + au.getIdentifier() ); - return okResponse(resp); + return ok(resp); } catch ( EJBException ejbx ) { alr.setActionResult(ActionLogRecord.Result.InternalError); alr.setInfo( alr.getInfo() + "// " + ejbx.getMessage()); if ( ejbx.getCausedByException() instanceof IllegalArgumentException ) { - return errorResponse(Status.BAD_REQUEST, "Bad request: can't save user. " + ejbx.getCausedByException().getMessage()); + return error(Status.BAD_REQUEST, "Bad request: can't save user. " + ejbx.getCausedByException().getMessage()); } else { logger.log(Level.WARNING, "Error saving user: ", ejbx); - return errorResponse(Status.INTERNAL_SERVER_ERROR, "Can't save user: " + ejbx.getMessage()); + return error(Status.INTERNAL_SERVER_ERROR, "Can't save user: " + ejbx.getMessage()); } } catch (Exception e) { logger.log(Level.WARNING, "Error saving user", e); alr.setActionResult(ActionLogRecord.Result.InternalError); alr.setInfo( alr.getInfo() + "// " + e.getMessage()); - return errorResponse(Status.INTERNAL_SERVER_ERROR, "Can't save user: " + e.getMessage()); + return error(Status.INTERNAL_SERVER_ERROR, "Can't save user: " + e.getMessage()); } finally { actionLogSvc.log(alr); } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/DataTagsAPI.java b/src/main/java/edu/harvard/iq/dataverse/api/DataTagsAPI.java index f81778f0408..063033d4747 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/DataTagsAPI.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/DataTagsAPI.java @@ -83,7 +83,7 @@ public Response receiveTags(JsonObject tags, @PathParam("uniqueCacheId") String CACHE.put(uniqueCacheId, container); // return an OK message with the redirect URL for the user to return to Dataverse through postBackTo or unacceptableDataset in DataTags - return okResponse( USER_REDIRECT_URL ); + return ok( USER_REDIRECT_URL ); } } \ No newline at end of file diff --git a/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java b/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java index 438c076efd9..2095161fc52 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java @@ -76,7 +76,7 @@ public Response getAll() { for ( DatasetFieldType dt : requiredFields ) { requiredFieldNames.add( dt.getName() ); } - return okResponse( Json.createObjectBuilder().add("haveParents", asJsonArray(listOfIsHasParentsTrue)) + return ok( Json.createObjectBuilder().add("haveParents", asJsonArray(listOfIsHasParentsTrue)) .add("noParents", asJsonArray(listOfIsHasParentsFalse)) .add("allowsMultiples", asJsonArray(listOfIsAllowsMultiplesTrue)) .add("allowsMultiples", asJsonArray(listOfIsAllowsMultiplesTrue)) @@ -107,7 +107,7 @@ public Response getAll() { } } } - return errorResponse(Status.INTERNAL_SERVER_ERROR, sb.toString()); + return error(Status.INTERNAL_SERVER_ERROR, sb.toString()); } } @@ -132,7 +132,7 @@ public Response getByName(@PathParam("name") String name) { parentAllowsMultiplesBoolean = parent.isAllowMultiples(); parentAllowsMultiplesDisplay = Boolean.toString(parentAllowsMultiplesBoolean); } - return okResponse(NullSafeJsonBuilder.jsonObjectBuilder() + return ok(NullSafeJsonBuilder.jsonObjectBuilder() .add("name", dsf.getName()) .add("id", id ) .add("title", title) @@ -163,7 +163,7 @@ public Response getByName(@PathParam("name") String name) { } } } - return errorResponse( Status.INTERNAL_SERVER_ERROR, sb.toString() ); + return error( Status.INTERNAL_SERVER_ERROR, sb.toString() ); } } @@ -185,7 +185,7 @@ public Response showControlledVocabularyForSubject() { possibleSubjects.add(subject); } } - return okResponse(possibleSubjects); + return ok(possibleSubjects); } @@ -202,10 +202,10 @@ public Response loadNAControlledVocabularyValue() { ControlledVocabularyValue naValue = new ControlledVocabularyValue(); naValue.setStrValue(DatasetField.NA_VALUE); datasetFieldService.save(naValue); - return okResponse("NA value created."); + return ok("NA value created."); } else { - return okResponse("NA value exists."); + return ok("NA value exists."); } } @@ -274,13 +274,13 @@ public Response loadDatasetFields(File file) { } catch (FileNotFoundException e) { alr.setActionResult(ActionLogRecord.Result.BadRequest); alr.setInfo( alr.getInfo() + "// file not found"); - return errorResponse(Status.EXPECTATION_FAILED, "File not found"); + return error(Status.EXPECTATION_FAILED, "File not found"); } catch (Exception e) { Logger.getLogger(DatasetFieldServiceApi.class.getName()).log(Level.WARNING, "Error parsing dataset fields:" + e.getMessage(), e); alr.setActionResult(ActionLogRecord.Result.InternalError); alr.setInfo( alr.getInfo() + "// " + e.getMessage()); - return errorResponse(Status.INTERNAL_SERVER_ERROR, e.getMessage()); + return error(Status.INTERNAL_SERVER_ERROR, e.getMessage()); } finally { if (br != null) { @@ -294,7 +294,7 @@ public Response loadDatasetFields(File file) { actionLogSvc.log(alr); } - return okResponse( Json.createObjectBuilder().add("added", responseArr) ); + return ok( Json.createObjectBuilder().add("added", responseArr) ); } private String parseMetadataBlock(String[] values) { diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index 3594ba77b6e..dfe9a32056b 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -8,10 +8,8 @@ import edu.harvard.iq.dataverse.DatasetServiceBean; import edu.harvard.iq.dataverse.DatasetVersion; import edu.harvard.iq.dataverse.Dataverse; -import edu.harvard.iq.dataverse.DataverseServiceBean; import edu.harvard.iq.dataverse.MetadataBlock; import edu.harvard.iq.dataverse.MetadataBlockServiceBean; -import edu.harvard.iq.dataverse.RoleAssignment; import edu.harvard.iq.dataverse.authorization.DataverseRole; import edu.harvard.iq.dataverse.authorization.RoleAssignee; import edu.harvard.iq.dataverse.authorization.users.User; @@ -77,9 +75,6 @@ public class Datasets extends AbstractApiBean { @EJB DatasetServiceBean datasetService; - @EJB - DataverseServiceBean dataverseService; - @EJB DOIEZIdServiceBean doiEZIdServiceBean; @@ -116,97 +111,18 @@ public Response getDataset(@PathParam("id") String id) { try { final DataverseRequest r = createDataverseRequest(findUserOrDie()); - + Dataset retrieved = execCommand(new GetDatasetCommand(r, findDatasetOrDie(id))); DatasetVersion latest = execCommand(new GetLatestAccessibleDatasetVersionCommand(r, retrieved)); final JsonObjectBuilder jsonbuilder = json(retrieved); - return okResponse(jsonbuilder.add("latestVersion", (latest != null) ? json(latest) : null)); + return ok(jsonbuilder.add("latestVersion", (latest != null) ? json(latest) : null)); } catch (WrappedResponse ex) { return ex.refineResponse("GETting dataset " + id + " failed."); } } - /* An experimental method for creating a new dataset, from scratch, all from json metadata file - @POST - @Path("") - public Response createDataset(String jsonBody) { - Dataset importedDataset = null; - try { - final DataverseRequest r = createDataverseRequest(findUserOrDie()); - - StringReader rdr = new StringReader(jsonBody); - JsonObject json = Json.createReader(rdr).readObject(); - JsonParser parser = new JsonParser(datasetfieldService, metadataBlockService, settingsService); - parser.setLenient(true); - Dataset ds = parser.parseDataset(json); - - - Dataverse owner = dataverseService.find(1L); - ds.setOwner(owner); - ds.getLatestVersion().setDatasetFields(ds.getLatestVersion().initDatasetFields()); - - // Check data against required contraints - List violations = ds.getVersions().get(0).validateRequired(); - if (!violations.isEmpty()) { - // For migration and harvest, add NA for missing required values - for (ConstraintViolation v : violations) { - DatasetField f = ((DatasetField) v.getRootBean()); - f.setSingleValue(DatasetField.NA_VALUE); - } - } - - - Set invalidViolations = ds.getVersions().get(0).validate(); - ValidatorFactory factory = Validation.buildDefaultValidatorFactory(); - Validator validator = factory.getValidator(); - if (!invalidViolations.isEmpty()) { - for (ConstraintViolation v : invalidViolations) { - DatasetFieldValue f = ((DatasetFieldValue) v.getRootBean()); - boolean fixed = false; - boolean converted = false; - // TODO: Is this scrubbing something we want to continue doing? - // - //if (settingsService.isTrueForKey(SettingsServiceBean.Key.ScrubMigrationData, false)) { - // fixed = processMigrationValidationError(f, cleanupLog, metadataFile.getName()); - // converted = true; - // if (fixed) { - // Set> scrubbedViolations = validator.validate(f); - // if (!scrubbedViolations.isEmpty()) { - // fixed = false; - // } - // } - //} - if (!fixed) { - String msg = "Field: " + f.getDatasetField().getDatasetFieldType().getDisplayName() + "; " - + "Invalid value: '" + f.getValue() + "'" + " Converted Value:'" + DatasetField.NA_VALUE + "'"; - Logger.getLogger(Datasets.class.getName()).log(Level.INFO, null, msg); - f.setValue(DatasetField.NA_VALUE); - } - } - } - - //ds.setHarvestedFrom(harvestingClient); - //ds.setHarvestIdentifier(harvestIdentifier); - - importedDataset = engineSvc.submit(new CreateDatasetCommand(ds, r, false, ImportUtil.ImportType.HARVEST)); - - } catch (JsonParseException ex) { - Logger.getLogger(Datasets.class.getName()).log(Level.INFO, null, "Error parsing datasetVersion: " + ex.getMessage()); - return errorResponse(Response.Status.NOT_FOUND, "error parsing dataset"); - } catch (CommandException ex) { - Logger.getLogger(Datasets.class.getName()).log(Level.INFO, null, "Error excuting Create dataset command: " + ex.getMessage()); - return errorResponse(Response.Status.NOT_FOUND, "error executing create dataset command"); - } catch (WrappedResponse ex) { - return ex.refineResponse("Error: "+ex.getWrappedMessageWhenJson()); - } - - final JsonObjectBuilder jsonbuilder = json(importedDataset); - - return okResponse(jsonbuilder.add("latestVersion", json(importedDataset.getLatestVersion()))); - } */ - // TODO: // This API call should, ideally, call findUserOrDie() and the GetDatasetCommand // to obtain the dataset that we are trying to export - which would handle @@ -221,7 +137,7 @@ public Response exportDataset(@QueryParam("persistentId") String persistentId, @ try { Dataset dataset = datasetService.findByGlobalId(persistentId); if (dataset == null) { - return errorResponse(Response.Status.NOT_FOUND, "A dataset with the persistentId " + persistentId + " could not be found."); + return error(Response.Status.NOT_FOUND, "A dataset with the persistentId " + persistentId + " could not be found."); } ExportService instance = ExportService.getInstance(); @@ -248,7 +164,7 @@ public Response exportDataset(@QueryParam("persistentId") String persistentId, @ .type(mediaType). build(); } catch (Exception wr) { - return errorResponse(Response.Status.FORBIDDEN, "Export Failed"); + return error(Response.Status.FORBIDDEN, "Export Failed"); } } @@ -258,7 +174,7 @@ public Response deleteDataset( @PathParam("id") String id) { try { execCommand( new DeleteDatasetCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id))); - return okResponse("Dataset " + id + " deleted"); + return ok("Dataset " + id + " deleted"); } catch (WrappedResponse ex) { return ex.refineResponse( "Failed to delete dataset " + id ); @@ -271,7 +187,7 @@ public Response deleteDataset( @PathParam("id") String id) { public Response destroyDataset( @PathParam("id") String id) { try { execCommand( new DestroyDatasetCommand(findDatasetOrDie(id), createDataverseRequest(findUserOrDie()) )); - return okResponse("Dataset " + id + " destroyed"); + return ok("Dataset " + id + " destroyed"); } catch (WrappedResponse ex) { return ex.refineResponse( "Failed to detroy dataset " + id ); @@ -295,7 +211,7 @@ public Response setCitationDate( @PathParam("id") String id, String dsfTypeName) execCommand(new SetDatasetCitationDateCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id), dsfType)); - return okResponse("Citation Date for dataset " + id + " set to: " + (dsfType != null ? dsfType.getDisplayName() : "default")); + return ok("Citation Date for dataset " + id + " set to: " + (dsfType != null ? dsfType.getDisplayName() : "default")); } catch (WrappedResponse ex) { return ex.refineResponse("Unable to set citation date for dataset " + id + "."); @@ -305,29 +221,23 @@ public Response setCitationDate( @PathParam("id") String id, String dsfTypeName) @DELETE @Path("{id}/citationdate") public Response useDefaultCitationDate( @PathParam("id") String id) { - try { - execCommand(new SetDatasetCitationDateCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id), null)); - return okResponse("Citation Date for dataset " + id + " set to default"); - } catch (WrappedResponse ex) { - return ex.refineResponse("Unable to restore default citation date for dataset " + id + "."); - } + return response( ()->{ + execCommand(new SetDatasetCitationDateCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id), null)); + return ok("Citation Date for dataset " + id + " set to default"); + }); } @GET @Path("{id}/versions") public Response listVersions( @PathParam("id") String id ) { - try { - JsonArrayBuilder bld = Json.createArrayBuilder(); - for ( DatasetVersion dsv : execCommand( - new ListVersionsCommand( - createDataverseRequest(findUserOrDie()), findDatasetOrDie(id)) ) ) { - bld.add( json(dsv) ); - } - return okResponse( bld ); - - } catch (WrappedResponse ex) { - return ex.getResponse(); - } + return response( ()->{ + return ok( + execCommand( + new ListVersionsCommand(createDataverseRequest(findUserOrDie()), + findDatasetOrDie(id)) ) + .stream() + .map( d -> json(d) ) + .collect(toJsonArray()));}); } @GET @@ -338,7 +248,7 @@ public Response getVersion( @PathParam("id") String datasetId, @PathParam("versi DatasetVersion dsv = getDatasetVersionOrDie(createDataverseRequest(findUserOrDie()), versionId, findDatasetOrDie(datasetId)); return (dsv == null || dsv.getId() == null) ? notFound("Dataset version not found") - : okResponse(json(dsv)); + : ok(json(dsv)); } catch (WrappedResponse ex) { return ex.getResponse(); @@ -349,7 +259,7 @@ public Response getVersion( @PathParam("id") String datasetId, @PathParam("versi @Path("{id}/versions/{versionId}/files") public Response getVersionFiles( @PathParam("id") String datasetId, @PathParam("versionId") String versionId) { try { - return okResponse( jsonFileMetadatas( + return ok( jsonFileMetadatas( getDatasetVersionOrDie(createDataverseRequest(findUserOrDie()), versionId, findDatasetOrDie(datasetId)).getFileMetadatas())); @@ -363,7 +273,7 @@ public Response getVersionFiles( @PathParam("id") String datasetId, @PathParam(" public Response getVersionMetadata( @PathParam("id") String datasetId, @PathParam("versionId") String versionId) { try { - return okResponse( + return ok( jsonByBlocks( getDatasetVersionOrDie( createDataverseRequest(findUserOrDie()), versionId, findDatasetOrDie(datasetId) ) .getDatasetFields())); @@ -385,7 +295,7 @@ public Response getVersionMetadataBlock( @PathParam("id") String datasetId, Map> fieldsByBlock = DatasetField.groupByBlock(dsv.getDatasetFields()); for ( Map.Entry> p : fieldsByBlock.entrySet() ) { if ( p.getKey().getName().equals(blockName) ) { - return okResponse( json(p.getKey(), p.getValue()) ); + return ok( json(p.getKey(), p.getValue()) ); } } return notFound("metadata block named " + blockName + " not found"); @@ -405,7 +315,7 @@ public Response deleteDraftVersion( @PathParam("id") String id, @PathParam("ver try { execCommand( new DeleteDatasetVersionCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id)) ); - return okResponse("Draft version of dataset " + id + " deleted"); + return ok("Draft version of dataset " + id + " deleted"); } catch (WrappedResponse ex) { return ex.getResponse(); } @@ -418,7 +328,7 @@ public Response updateDatasetTargetURL(@PathParam("id") String id ) { try { execCommand(new UpdateDatasetTargetURLCommand(findDatasetOrDie(id), createDataverseRequest(findUserOrDie()))); - return okResponse("Dataset " + id + " target url updated"); + return ok("Dataset " + id + " target url updated"); } catch (WrappedResponse ex) { return ex.getResponse(); @@ -440,7 +350,7 @@ public Response updateDatasetTargetURLAll() { } } - return okResponse("Update All Dataset target url completed"); + return ok("Update All Dataset target url completed"); } @PUT @@ -448,7 +358,7 @@ public Response updateDatasetTargetURLAll() { public Response updateDraftVersion( String jsonBody, @PathParam("id") String id, @PathParam("versionId") String versionId ){ if ( ! ":draft".equals(versionId) ) { - return errorResponse( Response.Status.BAD_REQUEST, "Only the :draft version can be updated"); + return error( Response.Status.BAD_REQUEST, "Only the :draft version can be updated"); } try ( StringReader rdr = new StringReader(jsonBody) ) { @@ -470,11 +380,11 @@ public Response updateDraftVersion( String jsonBody, @PathParam("id") String id, DatasetVersion managedVersion = execCommand( updateDraft ? new UpdateDatasetVersionCommand(req, incomingVersion) : new CreateDatasetVersionCommand(req, ds, incomingVersion)); - return okResponse( json(managedVersion) ); + return ok( json(managedVersion) ); } catch (JsonParseException ex) { LOGGER.log(Level.SEVERE, "Semantic error parsing dataset version Json: " + ex.getMessage(), ex); - return errorResponse( Response.Status.BAD_REQUEST, "Error parsing dataset version: " + ex.getMessage() ); + return error( Response.Status.BAD_REQUEST, "Error parsing dataset version: " + ex.getMessage() ); } catch (WrappedResponse ex) { return ex.getResponse(); @@ -487,7 +397,7 @@ public Response updateDraftVersion( String jsonBody, @PathParam("id") String id, public Response publishDataset( @PathParam("id") String id, @QueryParam("type") String type ) { try { if ( type == null ) { - return errorResponse( Response.Status.BAD_REQUEST, "Missing 'type' parameter (either 'major' or 'minor')."); + return error( Response.Status.BAD_REQUEST, "Missing 'type' parameter (either 'major' or 'minor')."); } type = type.toLowerCase(); @@ -495,19 +405,19 @@ public Response publishDataset( @PathParam("id") String id, @QueryParam("type") switch ( type ) { case "minor": isMinor = true; break; case "major": isMinor = false; break; - default: return errorResponse( Response.Status.BAD_REQUEST, "Illegal 'type' parameter value '" + type + "'. It needs to be either 'major' or 'minor'."); + default: return error( Response.Status.BAD_REQUEST, "Illegal 'type' parameter value '" + type + "'. It needs to be either 'major' or 'minor'."); } long dsId; try { dsId = Long.parseLong(id); } catch ( NumberFormatException nfe ) { - return errorResponse( Response.Status.BAD_REQUEST, "Bad dataset id. Please provide a number."); + return error( Response.Status.BAD_REQUEST, "Bad dataset id. Please provide a number."); } Dataset ds = datasetService.find(dsId); return ( ds == null ) ? notFound("Can't find dataset with id '" + id + "'") - : okResponse( json(execCommand(new PublishDatasetCommand(ds, + : ok( json(execCommand(new PublishDatasetCommand(ds, createDataverseRequest(findAuthenticatedUserOrDie()), isMinor))) ); @@ -522,7 +432,7 @@ public Response getLinks(@PathParam("id") String idSupplied ) { try { User u = findUserOrDie(); if (!u.isSuperuser()) { - return errorResponse(Response.Status.FORBIDDEN, "Not a superuser"); + return error(Response.Status.FORBIDDEN, "Not a superuser"); } Dataset dataset = findDatasetOrDie(idSupplied); @@ -534,7 +444,7 @@ public Response getLinks(@PathParam("id") String idSupplied ) { } JsonObjectBuilder response = Json.createObjectBuilder(); response.add("dataverses that link to dataset id " + datasetId, dataversesThatLinkToThisDatasetIdBuilder); - return okResponse(response); + return ok(response); } catch (WrappedResponse wr) { return wr.getResponse(); } @@ -556,10 +466,10 @@ private T handleVersion( String versionId, DsVersionHandler hdl ) case 2: return hdl.handleSpecific( Long.parseLong(versions[0]), Long.parseLong(versions[1]) ); default: - throw new WrappedResponse(errorResponse( Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'")); + throw new WrappedResponse(error( Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'")); } } catch ( NumberFormatException nfe ) { - throw new WrappedResponse( errorResponse( Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'") ); + throw new WrappedResponse( error( Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'") ); } } } @@ -595,10 +505,8 @@ public Command handleLatestPublished() { Dataset findDatasetOrDie( String id ) throws WrappedResponse { Dataset dataset; - LOGGER.info("Looking for dataset " + id); if ( id.equals(PERSISTENT_ID_KEY) ) { String persistentId = getRequestParameter(PERSISTENT_ID_KEY.substring(1)); - LOGGER.info("Looking for dataset " + persistentId); if ( persistentId == null ) { throw new WrappedResponse( badRequest("When accessing a dataset based on persistent id, " @@ -638,18 +546,18 @@ Dataset findDatasetOrDie( String id ) throws WrappedResponse { public Response getDdi(@QueryParam("id") long id, @QueryParam("persistentId") String persistentId, @QueryParam("dto") boolean dto) { boolean ddiExportEnabled = systemConfig.isDdiExportEnabled(); if (!ddiExportEnabled) { - return errorResponse(Response.Status.FORBIDDEN, "Disabled"); + return error(Response.Status.FORBIDDEN, "Disabled"); } try { User u = findUserOrDie(); if (!u.isSuperuser()) { - return errorResponse(Response.Status.FORBIDDEN, "Not a superuser"); + return error(Response.Status.FORBIDDEN, "Not a superuser"); } LOGGER.fine("looking up " + persistentId); Dataset dataset = datasetService.findByGlobalId(persistentId); if (dataset == null) { - return errorResponse(Response.Status.NOT_FOUND, "A dataset with the persistentId " + persistentId + " could not be found."); + return error(Response.Status.NOT_FOUND, "A dataset with the persistentId " + persistentId + " could not be found."); } String xml = "XML_BEING_COOKED"; @@ -686,17 +594,17 @@ public Response getDdi(@QueryParam("id") long id, @QueryParam("persistentId") St public Response createAssignment(String userOrGroup, @PathParam("identifier") String id, @QueryParam("key") String apiKey) { boolean apiTestingOnly = true; if (apiTestingOnly) { - return errorResponse(Response.Status.FORBIDDEN, "This is only for API tests."); + return error(Response.Status.FORBIDDEN, "This is only for API tests."); } try { Dataset dataset = findDatasetOrDie(id); RoleAssignee assignee = findAssignee(userOrGroup); if (assignee == null) { - return errorResponse(Response.Status.BAD_REQUEST, "Assignee not found"); + return error(Response.Status.BAD_REQUEST, "Assignee not found"); } DataverseRole theRole = rolesSvc.findBuiltinRoleByAlias("admin"); String privateUrlToken = null; - return okResponse( + return ok( json(execCommand(new AssignRoleCommand(assignee, theRole, dataset, createDataverseRequest(findUserOrDie()), privateUrlToken)))); } catch (WrappedResponse ex) { LOGGER.log(Level.WARNING, "Can''t create assignment: {0}", ex.getMessage()); @@ -707,16 +615,10 @@ public Response createAssignment(String userOrGroup, @PathParam("identifier") St @GET @Path("{identifier}/assignments") public Response getAssignments(@PathParam("identifier") String id) { - try { - JsonArrayBuilder jab = Json.createArrayBuilder(); - for (RoleAssignment ra : execCommand(new ListRoleAssignments(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id)))) { - jab.add(json(ra)); - } - return okResponse(jab); - } catch (WrappedResponse ex) { - LOGGER.log(Level.WARNING, "Can't list assignments: {0}", ex.getMessage()); - return ex.getResponse(); - } + return response( ()-> + ok( execCommand( + new ListRoleAssignments(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id))) + .stream().map(ra->json(ra)).collect(toJsonArray())) ); } @GET @@ -725,9 +627,9 @@ public Response getPrivateUrlData(@PathParam("id") String idSupplied) { try { PrivateUrl privateUrl = execCommand(new GetPrivateUrlCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied))); if (privateUrl != null) { - return okResponse(json(privateUrl)); + return ok(json(privateUrl)); } else { - return errorResponse(Response.Status.NOT_FOUND, "Private URL not found."); + return error(Response.Status.NOT_FOUND, "Private URL not found."); } } catch (WrappedResponse wr) { return wr.getResponse(); @@ -737,11 +639,10 @@ public Response getPrivateUrlData(@PathParam("id") String idSupplied) { @POST @Path("{id}/privateUrl") public Response createPrivateUrl(@PathParam("id") String idSupplied) { - try { - return okResponse(json(execCommand(new CreatePrivateUrlCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied))))); - } catch (WrappedResponse wr) { - return wr.getResponse(); - } + return response( ()-> + ok(json(execCommand( + new CreatePrivateUrlCommand(createDataverseRequest(findUserOrDie()), + findDatasetOrDie(idSupplied)))))); } @DELETE @@ -753,9 +654,9 @@ public Response deletePrivateUrl(@PathParam("id") String idSupplied) { PrivateUrl privateUrl = execCommand(new GetPrivateUrlCommand(createDataverseRequest(user), dataset)); if (privateUrl != null) { execCommand(new DeletePrivateUrlCommand(createDataverseRequest(user), dataset)); - return okResponse("Private URL deleted."); + return ok("Private URL deleted."); } else { - return errorResponse(Response.Status.NOT_FOUND, "No Private URL to delete."); + return error(Response.Status.NOT_FOUND, "No Private URL to delete."); } } catch (WrappedResponse wr) { return wr.getResponse(); diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java b/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java index 8725e495daf..9964d8a8d16 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java @@ -90,7 +90,10 @@ public class Dataverses extends AbstractApiBean { private static final Logger LOGGER = Logger.getLogger(Dataverses.class.getName()); - + + @EJB + ExplicitGroupServiceBean explicitGroupSvc; + @POST public Response addRoot( String body ) { LOGGER.info("Creating root dataverse"); @@ -108,10 +111,10 @@ public Response addDataverse( String body, @PathParam("identifier") String paren d = jsonParser().parseDataverse(dvJson); } catch ( JsonParsingException jpe ) { LOGGER.log(Level.SEVERE, "Json: {0}", body); - return errorResponse( Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage() ); + return error( Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage() ); } catch (JsonParseException ex) { Logger.getLogger(Dataverses.class.getName()).log(Level.SEVERE, "Error parsing dataverse from json: " + ex.getMessage(), ex); - return errorResponse( Response.Status.BAD_REQUEST, + return error( Response.Status.BAD_REQUEST, "Error parsing the POSTed json into a dataverse: " + ex.getMessage() ); } @@ -128,7 +131,7 @@ public Response addDataverse( String body, @PathParam("identifier") String paren AuthenticatedUser u = findAuthenticatedUserOrDie(); d = execCommand( new CreateDataverseCommand(d, createDataverseRequest(u), null, null) ); - return createdResponse( "/dataverses/"+d.getAlias(), json(d) ); + return created( "/dataverses/"+d.getAlias(), json(d) ); } catch ( WrappedResponse ww ) { return ww.getResponse(); @@ -149,10 +152,10 @@ public Response addDataverse( String body, @PathParam("identifier") String paren } } LOGGER.log(Level.SEVERE, sb.toString()); - return errorResponse( Response.Status.INTERNAL_SERVER_ERROR, "Error creating dataverse: " + sb.toString() ); + return error( Response.Status.INTERNAL_SERVER_ERROR, "Error creating dataverse: " + sb.toString() ); } catch ( Exception ex ) { LOGGER.log(Level.SEVERE, "Error creating dataverse", ex); - return errorResponse( Response.Status.INTERNAL_SERVER_ERROR, "Error creating dataverse: " + ex.getMessage() ); + return error( Response.Status.INTERNAL_SERVER_ERROR, "Error creating dataverse: " + ex.getMessage() ); } } @@ -169,7 +172,7 @@ public Response createDataset( String jsonBody, @PathParam("identifier") String json = Json.createReader(rdr).readObject(); } catch ( JsonParsingException jpe ) { LOGGER.log(Level.SEVERE, "Json: {0}", jsonBody); - return errorResponse( Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage() ); + return error( Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage() ); } Dataset ds = new Dataset(); @@ -177,7 +180,7 @@ public Response createDataset( String jsonBody, @PathParam("identifier") String JsonObject jsonVersion = json.getJsonObject("datasetVersion"); if ( jsonVersion == null) { - return errorResponse(Status.BAD_REQUEST, "Json POST data are missing datasetVersion object."); + return error(Status.BAD_REQUEST, "Json POST data are missing datasetVersion object."); } try { try { @@ -197,14 +200,14 @@ public Response createDataset( String jsonBody, @PathParam("identifier") String } } catch (JsonParseException ex) { LOGGER.log( Level.INFO, "Error parsing dataset version from Json", ex); - return errorResponse(Status.BAD_REQUEST, "Error parsing datasetVersion: " + ex.getMessage() ); + return error(Status.BAD_REQUEST, "Error parsing datasetVersion: " + ex.getMessage() ); } catch ( Exception e ) { LOGGER.log( Level.WARNING, "Error parsing dataset version from Json", e); - return errorResponse(Status.INTERNAL_SERVER_ERROR, "Error parsing datasetVersion: " + e.getMessage() ); + return error(Status.INTERNAL_SERVER_ERROR, "Error parsing datasetVersion: " + e.getMessage() ); } Dataset managedDs = execCommand(new CreateDatasetCommand(ds, createDataverseRequest(u))); - return createdResponse( "/datasets/" + managedDs.getId(), + return created( "/datasets/" + managedDs.getId(), Json.createObjectBuilder().add("id", managedDs.getId()) ); } catch ( WrappedResponse ex ) { @@ -215,39 +218,26 @@ public Response createDataset( String jsonBody, @PathParam("identifier") String @GET @Path("{identifier}") public Response viewDataverse( @PathParam("identifier") String idtf ) { - try { - Dataverse retrieved = execCommand( new GetDataverseCommand( createDataverseRequest(findUserOrDie()), findDataverseOrDie(idtf)) ); - return okResponse( json(retrieved) ); - } catch ( WrappedResponse ex ) { - return ex.getResponse(); - } + return response( req -> ok(json(execCommand( + new GetDataverseCommand(req, findDataverseOrDie(idtf)))))); } @DELETE @Path("{identifier}") public Response deleteDataverse( @PathParam("identifier") String idtf ) { - try { - execCommand( new DeleteDataverseCommand(createDataverseRequest(findUserOrDie()), findDataverseOrDie(idtf)) ); - return okResponse( "Dataverse " + idtf +" deleted"); - } catch ( WrappedResponse ex ) { - return ex.getResponse(); - } + return response( req -> { + execCommand( new DeleteDataverseCommand(req, findDataverseOrDie(idtf))); + return ok( "Dataverse " + idtf +" deleted"); + }); } @GET @Path("{identifier}/metadatablocks") public Response listMetadataBlocks( @PathParam("identifier") String dvIdtf ) { - try { - JsonArrayBuilder jab = Json.createArrayBuilder(); - for ( MetadataBlock blk : execCommand( new ListMetadataBlocksCommand(createDataverseRequest(findUserOrDie()), findDataverseOrDie(dvIdtf)) )){ - jab.add( brief.json(blk) ); - } - - return okResponse(jab); - - } catch (WrappedResponse ex) { - return ex.refineResponse( "Error listing metadata blocks for dataverse " + dvIdtf + ":"); - } + return response( req ->ok( + execCommand( new ListMetadataBlocksCommand(req, findDataverseOrDie(dvIdtf))) + .stream().map(brief::json).collect( toJsonArray() ) + )); } @POST @@ -262,17 +252,17 @@ public Response setMetadataBlocks( @PathParam("identifier")String dvIdtf, String ? findMetadataBlock( ((JsonNumber)blockId).longValue() ) : findMetadataBlock( ((JsonString)blockId).getString() ); if ( blk == null ) { - return errorResponse(Response.Status.BAD_REQUEST, "Can't find metadata block '"+ blockId + "'"); + return error(Response.Status.BAD_REQUEST, "Can't find metadata block '"+ blockId + "'"); } blocks.add( blk ); } } catch( Exception e ) { - return errorResponse(Response.Status.BAD_REQUEST, e.getMessage()); + return error(Response.Status.BAD_REQUEST, e.getMessage()); } try { execCommand( new UpdateDataverseMetadataBlocksCommand.SetBlocks(createDataverseRequest(findUserOrDie()), findDataverseOrDie(dvIdtf), blocks)); - return okResponse("Metadata blocks of dataverse " + dvIdtf + " updated."); + return ok("Metadata blocks of dataverse " + dvIdtf + " updated."); } catch (WrappedResponse ex) { return ex.getResponse(); @@ -283,19 +273,16 @@ public Response setMetadataBlocks( @PathParam("identifier")String dvIdtf, String @Path("{identifier}/metadatablocks/:isRoot") @Produces(MediaType.APPLICATION_JSON) public Response getMetadataRoot( @PathParam("identifier")String dvIdtf ) { - - try { - Dataverse dataverse = findDataverseOrDie(dvIdtf); - if ( permissionSvc.request( createDataverseRequest(findUserOrDie()) ) + return response( req -> { + final Dataverse dataverse = findDataverseOrDie(dvIdtf); + if ( permissionSvc.request(req) .on(dataverse) .has(Permission.EditDataverse) ) { - return okResponseWithValue( dataverse.isMetadataBlockRoot() ); + return ok( dataverse.isMetadataBlockRoot() ); } else { - return errorResponse( Status.FORBIDDEN, "Not authorized" ); + return error( Status.FORBIDDEN, "Not authorized" ); } - } catch (WrappedResponse wr) { - return wr.getResponse(); - } + }); } @POST @@ -303,32 +290,20 @@ public Response getMetadataRoot( @PathParam("identifier")String dvIdtf ) { @Produces(MediaType.APPLICATION_JSON) @Consumes(MediaType.WILDCARD) public Response setMetadataRoot( @PathParam("identifier")String dvIdtf, String body ) { - - if ( ! Util.isBoolean(body) ) { - return errorResponse(Response.Status.BAD_REQUEST, "Illegal value '" + body + "'. Try 'true' or 'false'"); - } - boolean root = Util.isTrue(body); - - try { - Dataverse dataverse = findDataverseOrDie(dvIdtf); - execute(new UpdateDataverseMetadataBlocksCommand.SetRoot(createDataverseRequest(findUserOrDie()), dataverse, root)); - return okResponseWithValue("Dataverse " + dataverse.getName() + " is now a metadata " + (root? "" : "non-") + "root"); - } catch (WrappedResponse wr) { - return wr.getResponse(); - } - + return response( req -> { + final boolean root = parseBooleanOrDie(body); + final Dataverse dataverse = findDataverseOrDie(dvIdtf); + execCommand(new UpdateDataverseMetadataBlocksCommand.SetRoot(req, dataverse, root)); + return ok("Dataverse " + dataverse.getName() + " is now a metadata " + (root? "" : "non-") + "root"); + }); } @GET @Path("{identifier}/facets/") public Response listFacets( @PathParam("identifier") String dvIdtf ) { - try { - return okResponse( - execCommand(new ListFacetsCommand(createDataverseRequest(findUserOrDie()), findDataverseOrDie(dvIdtf)) ) - .stream().map(f->json(f).build()).collect(toJsonArray())); - } catch (WrappedResponse wr) { - return wr.getResponse(); - } + return response( req -> ok( + execCommand(new ListFacetsCommand(req, findDataverseOrDie(dvIdtf)) ) + .stream().map(f->json(f)).collect(toJsonArray()))); } @POST @@ -340,9 +315,9 @@ public Response setFacets( @PathParam("identifier")String dvIdtf, String facetId for ( JsonString facetId : Util.asJsonArray(facetIds).getValuesAs(JsonString.class) ) { DatasetFieldType dsfType = findDatasetFieldType(facetId.getString()); if ( dsfType == null ) { - return errorResponse(Response.Status.BAD_REQUEST, "Can't find dataset field type '"+ facetId + "'"); + return error(Response.Status.BAD_REQUEST, "Can't find dataset field type '"+ facetId + "'"); } else if (!dsfType.isFacetable()) { - return errorResponse(Response.Status.BAD_REQUEST, "Dataset field type '"+ facetId + "' is not facetable"); + return error(Response.Status.BAD_REQUEST, "Dataset field type '"+ facetId + "' is not facetable"); } facets.add( dsfType ); } @@ -351,7 +326,7 @@ public Response setFacets( @PathParam("identifier")String dvIdtf, String facetId Dataverse dataverse = findDataverseOrDie(dvIdtf); // by passing null for Featured Dataverses and DataverseFieldTypeInputLevel, those are not changed execCommand( new UpdateDataverseCommand(dataverse, facets, null, createDataverseRequest(findUserOrDie()), null) ); - return okResponse("Facets of dataverse " + dvIdtf + " updated."); + return ok("Facets of dataverse " + dvIdtf + " updated."); } catch (WrappedResponse ex) { return ex.getResponse(); @@ -361,81 +336,57 @@ public Response setFacets( @PathParam("identifier")String dvIdtf, String facetId @GET @Path("{identifier}/contents") public Response listContent( @PathParam("identifier") String dvIdtf ) { - - final JsonArrayBuilder jab = Json.createArrayBuilder(); - DvObject.Visitor ser = new DvObject.Visitor() { + DvObject.Visitor ser = new DvObject.Visitor() { @Override - public Void visit(Dataverse dv) { - jab.add( Json.createObjectBuilder().add("type", "dataverse") + public JsonObjectBuilder visit(Dataverse dv) { + return Json.createObjectBuilder().add("type", "dataverse") .add("id", dv.getId()) - .add("title",dv.getName() )); - return null; + .add("title",dv.getName() ); } @Override - public Void visit(Dataset ds) { - // TODO: check for permission to view drafts - jab.add( json(ds).add("type", "dataset") ); - return null; + public JsonObjectBuilder visit(Dataset ds) { + return json(ds).add("type", "dataset"); } @Override - public Void visit(DataFile df) { throw new UnsupportedOperationException("Files don't live directly in Dataverses"); } + public JsonObjectBuilder visit(DataFile df) { throw new UnsupportedOperationException("Files don't live directly in Dataverses"); } }; - try { - Dataverse dataverse = findDataverseOrDie(dvIdtf); - - for ( DvObject o : execCommand(new ListDataverseContentCommand(createDataverseRequest(findUserOrDie()), dataverse)) ) { - o.accept(ser); - } - return okResponse(jab); - } catch (WrappedResponse ex) { - return ex.getResponse(); - } + return response( req -> ok( + execCommand(new ListDataverseContentCommand(req, findDataverseOrDie(dvIdtf))) + .stream() + .map( dvo->(JsonObjectBuilder)dvo.accept(ser)) + .collect(toJsonArray()) + )); } @GET @Path("{identifier}/roles") public Response listRoles( @PathParam("identifier") String dvIdtf ) { - - try { - Dataverse d = findDataverseOrDie(dvIdtf); - JsonArrayBuilder jab = Json.createArrayBuilder(); - for ( DataverseRole r : execCommand( new ListRolesCommand(createDataverseRequest(findUserOrDie()), d)) ){ - jab.add( json(r) ); - } - return okResponse(jab); - } catch (WrappedResponse ex) { - return ex.getResponse(); - } + return response( req -> ok( + execCommand( new ListRolesCommand(req, findDataverseOrDie(dvIdtf)) ) + .stream().map(r->json(r)) + .collect( toJsonArray() ) + )); } @POST @Path("{identifier}/roles") public Response createRole( RoleDTO roleDto, @PathParam("identifier") String dvIdtf ) { - try { - Dataverse dataverse = findDataverseOrDie(dvIdtf); - return okResponse( json(execCommand(new CreateRoleCommand(roleDto.asRole(), createDataverseRequest(findUserOrDie()), dataverse)))); - } catch ( WrappedResponse ce ) { - return ce.getResponse(); - } + return response( req -> ok( json(execCommand(new CreateRoleCommand(roleDto.asRole(), req, findDataverseOrDie(dvIdtf)))))); } @GET @Path("{identifier}/assignments") public Response listAssignments( @PathParam("identifier") String dvIdtf) { - try { - JsonArrayBuilder jab = Json.createArrayBuilder(); - for ( RoleAssignment ra : execCommand(new ListRoleAssignments(createDataverseRequest(findUserOrDie()), findDataverseOrDie(dvIdtf))) ){ - jab.add( json(ra) ); - } - return okResponse(jab); - - } catch (WrappedResponse ex) { - return ex.getResponse(); - } + return response( req -> ok( + execCommand(new ListRoleAssignments(req, findDataverseOrDie(dvIdtf))) + .stream() + .map( a -> json(a) ) + .collect(toJsonArray()) + )); } @POST @@ -443,11 +394,12 @@ public Response listAssignments( @PathParam("identifier") String dvIdtf) { public Response createAssignment( RoleAssignmentDTO ra, @PathParam("identifier") String dvIdtf, @QueryParam("key") String apiKey ) { try { - Dataverse dataverse = findDataverseOrDie(dvIdtf); + final DataverseRequest req = createDataverseRequest(findUserOrDie()); + final Dataverse dataverse = findDataverseOrDie(dvIdtf); RoleAssignee assignee = findAssignee(ra.getAssignee()); if ( assignee==null ) { - return errorResponse( Status.BAD_REQUEST, "Assignee not found" ); + return error( Status.BAD_REQUEST, "Assignee not found" ); } DataverseRole theRole; @@ -463,13 +415,11 @@ public Response createAssignment( RoleAssignmentDTO ra, @PathParam("identifier") dv = dv.getOwner(); } if ( theRole == null ) { - return errorResponse( Status.BAD_REQUEST, "Can't find role named '" + ra.getRole() + "' in dataverse " + dataverse); + return error( Status.BAD_REQUEST, "Can't find role named '" + ra.getRole() + "' in dataverse " + dataverse); } String privateUrlToken = null; - return okResponse( - json( - execCommand(new AssignRoleCommand(assignee, theRole, dataverse, createDataverseRequest(findUserOrDie()), privateUrlToken)))); + return ok(json(execCommand(new AssignRoleCommand(assignee, theRole, dataverse, req, privateUrlToken)))); } catch (WrappedResponse ex) { LOGGER.log(Level.WARNING, "Can''t create assignment: {0}", ex.getMessage()); @@ -485,14 +435,14 @@ public Response deleteAssignment( @PathParam("id") long assignmentId, @PathParam try { findDataverseOrDie(dvIdtf); execCommand( new RevokeRoleCommand(ra, createDataverseRequest(findUserOrDie()))); - return okResponse("Role " + ra.getRole().getName() + return ok("Role " + ra.getRole().getName() + " revoked for assignee " + ra.getAssigneeIdentifier() + " in " + ra.getDefinitionPoint().accept(DvObject.NamePrinter) ); } catch (WrappedResponse ex) { return ex.getResponse(); } } else { - return errorResponse( Status.NOT_FOUND, "Role assignment " + assignmentId + " not found" ); + return error( Status.NOT_FOUND, "Role assignment " + assignmentId + " not found" ); } } @@ -501,70 +451,44 @@ public Response deleteAssignment( @PathParam("id") long assignmentId, @PathParam public Response publishDataverse( @PathParam("identifier") String dvIdtf ) { try { Dataverse dv = findDataverseOrDie(dvIdtf); - return okResponse( json(execCommand( new PublishDataverseCommand(createDataverseRequest(findAuthenticatedUserOrDie()), dv))) ); + return ok( json(execCommand( new PublishDataverseCommand(createDataverseRequest(findAuthenticatedUserOrDie()), dv))) ); } catch (WrappedResponse wr) { return wr.getResponse(); } } - - private Dataverse findDataverseOrDie( String dvIdtf ) throws WrappedResponse { - Dataverse dv = findDataverse(dvIdtf); - if ( dv == null ) { - throw new WrappedResponse(errorResponse( Response.Status.NOT_FOUND, "Can't find dataverse with identifier='" + dvIdtf + "'")); - } - return dv; - } - - @EJB - ExplicitGroupServiceBean explicitGroupSvc; - + @POST @Path("{identifier}/groups/") public Response createExplicitGroup( ExplicitGroupDTO dto, @PathParam("identifier") String dvIdtf) { - try { - + return response( req ->{ ExplicitGroupProvider prv = explicitGroupSvc.getProvider(); ExplicitGroup newGroup = dto.apply(prv.makeGroup()); - newGroup = execCommand( new CreateExplicitGroupCommand(createDataverseRequest(findUserOrDie()), findDataverseOrDie(dvIdtf), newGroup)); + newGroup = execCommand( new CreateExplicitGroupCommand(req, findDataverseOrDie(dvIdtf), newGroup)); String groupUri = String.format("%s/groups/%s", dvIdtf, newGroup.getGroupAliasInOwner()); - return createdResponse( groupUri, json(newGroup) ); - - } catch (WrappedResponse wr) { - return wr.getResponse(); - } + return created( groupUri, json(newGroup) ); + }); } @GET @Path("{identifier}/groups/") public Response listGroups( @PathParam("identifier") String dvIdtf, @QueryParam("key") String apiKey ) { - try { - JsonArrayBuilder arr = Json.createArrayBuilder(); - execCommand(new ListExplicitGroupsCommand(createDataverseRequest(findUserOrDie()), findDataverseOrDie(dvIdtf))) + return response( req -> ok( + execCommand(new ListExplicitGroupsCommand(req, findDataverseOrDie(dvIdtf))) .stream().map( eg->json(eg)) - .forEach( arr::add ); - return okResponse( arr ); - - } catch (WrappedResponse wr) { - return wr.getResponse(); - } + .collect( toJsonArray() ) + )); } @GET @Path("{identifier}/groups/{aliasInOwner}") public Response getGroupByOwnerAndAliasInOwner( @PathParam("identifier") String dvIdtf, - @PathParam("aliasInOwner") String grpAliasInOwner ) - { - try { - return okResponse( json(findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), - createDataverseRequest(findUserOrDie()), - grpAliasInOwner)) ); - - } catch (WrappedResponse wr) { - return wr.getResponse(); - } + @PathParam("aliasInOwner") String grpAliasInOwner ){ + return response( req -> ok(json(findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), + req, + grpAliasInOwner)))); } @PUT @@ -573,17 +497,9 @@ public Response updateGroup(ExplicitGroupDTO groupDto, @PathParam("identifier") String dvIdtf, @PathParam("aliasInOwner") String grpAliasInOwner ) { - try { - final DataverseRequest request = createDataverseRequest(findUserOrDie()); - return okResponse( - json( - execCommand( - new UpdateExplicitGroupCommand(request, - groupDto.apply( findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), request, grpAliasInOwner)))))); - - } catch (WrappedResponse wr) { - return wr.getResponse(); - } + return response( req-> ok(json(execCommand( + new UpdateExplicitGroupCommand(req, + groupDto.apply( findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), req, grpAliasInOwner))))))); } @DELETE @@ -591,16 +507,11 @@ public Response updateGroup(ExplicitGroupDTO groupDto, public Response deleteGroup(@PathParam("identifier") String dvIdtf, @PathParam("aliasInOwner") String grpAliasInOwner ) { - try { - final DataverseRequest req = createDataverseRequest(findUserOrDie()); + return response( req -> { execCommand( new DeleteExplicitGroupCommand(req, - findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), req, grpAliasInOwner)) ); - - return okResponse( "Group " + dvIdtf + "/" + grpAliasInOwner + " deleted" ); - - } catch (WrappedResponse wr) { - return wr.refineResponse("Error deleting group " + dvIdtf + "/" + grpAliasInOwner); - } + findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), req, grpAliasInOwner)) ); + return ok( "Group " + dvIdtf + "/" + grpAliasInOwner + " deleted" ); + }); } @POST @@ -610,17 +521,12 @@ public Response addRoleAssingees(List roleAssingeeIdentifiers, @PathParam("identifier") String dvIdtf, @PathParam("aliasInOwner") String grpAliasInOwner) { - try { - final DataverseRequest req = createDataverseRequest(findUserOrDie()); - return okResponse( + return response( req -> ok( json( execCommand( new AddRoleAssigneesToExplicitGroupCommand(req, findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), req, grpAliasInOwner), - new TreeSet<>(roleAssingeeIdentifiers))))); - } catch (WrappedResponse wr) { - return wr.refineResponse( "Adding role assignees to group " + dvIdtf + "/" + grpAliasInOwner ); - } + new TreeSet<>(roleAssingeeIdentifiers)))))); } @PUT @@ -636,18 +542,10 @@ public Response addRoleAssingee( @PathParam("identifier") String dvIdtf, public Response deleteRoleAssingee( @PathParam("identifier") String dvIdtf, @PathParam("aliasInOwner") String grpAliasInOwner, @PathParam("roleAssigneeIdentifier") String roleAssigneeIdentifier ) { - - try { - final DataverseRequest req = createDataverseRequest(findUserOrDie()); - return okResponse( - json( - execCommand( + return response( req ->ok(json(execCommand( new RemoveRoleAssigneesFromExplicitGroupCommand(req, findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), req, grpAliasInOwner), - Collections.singleton(roleAssigneeIdentifier))))); - } catch (WrappedResponse wr) { - return wr.refineResponse( "Adding role assignees to group " + dvIdtf + "/" + grpAliasInOwner ); - } + Collections.singleton(roleAssigneeIdentifier)))))); } private ExplicitGroup findExplicitGroupOrDie( DvObject dv, DataverseRequest req, String groupIdtf ) throws WrappedResponse { @@ -660,11 +558,10 @@ private ExplicitGroup findExplicitGroupOrDie( DvObject dv, DataverseRequest req, @Path("{identifier}/links") public Response listLinks(@PathParam("identifier") String dvIdtf ) { try { - - Dataverse dv = findDataverseOrDie(dvIdtf); User u = findUserOrDie(); + Dataverse dv = findDataverseOrDie(dvIdtf); if (!u.isSuperuser()) { - return errorResponse(Status.FORBIDDEN, "Not a superuser"); + return error(Status.FORBIDDEN, "Not a superuser"); } List dvsThisDvHasLinkedToList = dataverseSvc.findDataversesThisIdHasLinkedTo(dv.getId()); @@ -689,7 +586,7 @@ public Response listLinks(@PathParam("identifier") String dvIdtf ) { response.add("dataverses that the " + dv.getAlias() + " dataverse has linked to", dvsThisDvHasLinkedToBuilder); response.add("dataverses that link to the " + dv.getAlias(), dvsThatLinkToThisDvBuilder); response.add("datasets that the " + dv.getAlias() + " has linked to", datasetsThisDvHasLinkedToBuilder); - return okResponse(response); + return ok(response); } catch (WrappedResponse wr) { return wr.getResponse(); diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Groups.java b/src/main/java/edu/harvard/iq/dataverse/api/Groups.java index 0f414724a4c..671f3f3fb84 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Groups.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Groups.java @@ -45,16 +45,16 @@ public Response createIpGroups( JsonObject dto ){ IpGroup grp = new JsonParser().parseIpGroup(dto); if ( grp.getPersistedGroupAlias()== null ) { - return errorResponse(Response.Status.BAD_REQUEST, "Must provide valid group alias"); + return error(Response.Status.BAD_REQUEST, "Must provide valid group alias"); } grp.setProvider( groupSvc.getIpGroupProvider() ); grp = ipGroupPrv.store(grp); - return createdResponse("/groups/ip/" + grp.getPersistedGroupAlias(), json(grp) ); + return created("/groups/ip/" + grp.getPersistedGroupAlias(), json(grp) ); } catch ( Exception e ) { logger.log( Level.WARNING, "Error while storing a new IP group: " + e.getMessage(), e); - return errorResponse(Response.Status.INTERNAL_SERVER_ERROR, "Error: " + e.getMessage() ); + return error(Response.Status.INTERNAL_SERVER_ERROR, "Error: " + e.getMessage() ); } } @@ -68,7 +68,7 @@ public Response listIpGroups() { for ( IpGroup g : ipGroupPrv.findGlobalGroups() ) { arrBld.add( json(g) ); } - return okResponse( arrBld ); + return ok( arrBld ); } @GET @@ -81,7 +81,7 @@ public Response getIpGroup( @PathParam("groupIdtf") String groupIdtf ) { grp = ipGroupPrv.get(groupIdtf); } - return (grp == null) ? notFound( "Group " + groupIdtf + " not found") : okResponse(json(grp)); + return (grp == null) ? notFound( "Group " + groupIdtf + " not found") : ok(json(grp)); } @DELETE @@ -98,7 +98,7 @@ public Response deleteIpGroup( @PathParam("groupIdtf") String groupIdtf ) { try { ipGroupPrv.deleteGroup(grp); - return okResponse("Group " + grp.getAlias() + " deleted."); + return ok("Group " + grp.getAlias() + " deleted."); } catch ( Exception topExp ) { // get to the cause (unwraps EJB exception wrappers). Throwable e = topExp; @@ -107,7 +107,7 @@ public Response deleteIpGroup( @PathParam("groupIdtf") String groupIdtf ) { } if ( e instanceof IllegalArgumentException ) { - return errorResponse(Response.Status.BAD_REQUEST, e.getMessage()); + return error(Response.Status.BAD_REQUEST, e.getMessage()); } else { throw topExp; } @@ -121,7 +121,7 @@ public Response listShibGroups() { for (ShibGroup g : shibGroupPrv.findGlobalGroups()) { arrBld.add(json(g)); } - return okResponse(arrBld); + return ok(arrBld); } @POST @@ -130,24 +130,24 @@ public Response createShibGroup(JsonObject shibGroupInput) { String expectedNameKey = "name"; JsonString name = shibGroupInput.getJsonString(expectedNameKey); if (name == null) { - return errorResponse(Response.Status.BAD_REQUEST, "required field missing: " + expectedNameKey); + return error(Response.Status.BAD_REQUEST, "required field missing: " + expectedNameKey); } String expectedAttributeKey = "attribute"; JsonString attribute = shibGroupInput.getJsonString(expectedAttributeKey); if (attribute == null) { - return errorResponse(Response.Status.BAD_REQUEST, "required field missing: " + expectedAttributeKey); + return error(Response.Status.BAD_REQUEST, "required field missing: " + expectedAttributeKey); } String expectedPatternKey = "pattern"; JsonString pattern = shibGroupInput.getJsonString(expectedPatternKey); if (pattern == null) { - return errorResponse(Response.Status.BAD_REQUEST, "required field missing: " + expectedPatternKey); + return error(Response.Status.BAD_REQUEST, "required field missing: " + expectedPatternKey); } ShibGroup shibGroupToPersist = new ShibGroup(name.getString(), attribute.getString(), pattern.getString(), shibGroupPrv); ShibGroup persitedShibGroup = shibGroupPrv.persist(shibGroupToPersist); if (persitedShibGroup != null) { - return okResponse("Shibboleth group persisted: " + persitedShibGroup); + return ok("Shibboleth group persisted: " + persitedShibGroup); } else { - return errorResponse(Response.Status.BAD_REQUEST, "Could not persist Shibboleth group"); + return error(Response.Status.BAD_REQUEST, "Could not persist Shibboleth group"); } } @@ -160,15 +160,15 @@ public Response deleteShibGroup( @PathParam("primaryKey") String id ) { try { deleted = shibGroupPrv.delete(doomed); } catch (Exception ex) { - return errorResponse(Response.Status.BAD_REQUEST, ex.getMessage()); + return error(Response.Status.BAD_REQUEST, ex.getMessage()); } if (deleted) { - return okResponse("Shibboleth group " + id + " deleted"); + return ok("Shibboleth group " + id + " deleted"); } else { - return errorResponse(Response.Status.BAD_REQUEST, "Could not delete Shibboleth group with an id of " + id); + return error(Response.Status.BAD_REQUEST, "Could not delete Shibboleth group with an id of " + id); } } else { - return errorResponse(Response.Status.BAD_REQUEST, "Could not find Shibboleth group with an id of " + id); + return error(Response.Status.BAD_REQUEST, "Could not find Shibboleth group with an id of " + id); } } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/HarvestingClients.java b/src/main/java/edu/harvard/iq/dataverse/api/HarvestingClients.java index 8df72e4f9ca..08336869f49 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/HarvestingClients.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/HarvestingClients.java @@ -62,12 +62,12 @@ public Response harvestingClients(@QueryParam("key") String apiKey) throws IOExc try { harvestingClients = harvestingClientService.getAllHarvestingClients(); } catch (Exception ex) { - return errorResponse( Response.Status.INTERNAL_SERVER_ERROR, "Caught an exception looking up configured harvesting clients; " + ex.getMessage() ); + return error( Response.Status.INTERNAL_SERVER_ERROR, "Caught an exception looking up configured harvesting clients; " + ex.getMessage() ); } if (harvestingClients == null) { // returning an empty list: - return okResponse(jsonObjectBuilder().add("harvestingClients","")); + return ok(jsonObjectBuilder().add("harvestingClients","")); } JsonArrayBuilder hcArr = Json.createArrayBuilder(); @@ -93,7 +93,7 @@ public Response harvestingClients(@QueryParam("key") String apiKey) throws IOExc } } - return okResponse(jsonObjectBuilder().add("harvestingClients", hcArr)); + return ok(jsonObjectBuilder().add("harvestingClients", hcArr)); } @GET @@ -105,11 +105,11 @@ public Response harvestingClient(@PathParam("nickName") String nickName, @QueryP harvestingClient = harvestingClientService.findByNickname(nickName); } catch (Exception ex) { logger.warning("Exception caught looking up harvesting client " + nickName + ": " + ex.getMessage()); - return errorResponse( Response.Status.BAD_REQUEST, "Internal error: failed to look up harvesting client " + nickName + "."); + return error( Response.Status.BAD_REQUEST, "Internal error: failed to look up harvesting client " + nickName + "."); } if (harvestingClient == null) { - return errorResponse(Response.Status.NOT_FOUND, "Harvesting client " + nickName + " not found."); + return error(Response.Status.NOT_FOUND, "Harvesting client " + nickName + " not found."); } HarvestingClient retrievedHarvestingClient = null; @@ -128,15 +128,15 @@ public Response harvestingClient(@PathParam("nickName") String nickName, @QueryP } if (retrievedHarvestingClient == null) { - return errorResponse( Response.Status.BAD_REQUEST, + return error( Response.Status.BAD_REQUEST, "Internal error: failed to retrieve harvesting client " + nickName + "."); } try { - return okResponse(harvestingConfigAsJson(retrievedHarvestingClient)); + return ok(harvestingConfigAsJson(retrievedHarvestingClient)); } catch (Exception ex) { logger.warning("Unknown exception caught while trying to format harvesting client config as json: "+ex.getMessage()); - return errorResponse( Response.Status.BAD_REQUEST, + return error( Response.Status.BAD_REQUEST, "Internal error: failed to produce output for harvesting client " + nickName + "."); } } @@ -155,7 +155,7 @@ public Response createHarvestingClient(String jsonBody, @PathParam("nickName") S Dataverse ownerDataverse = dataverseService.findByAlias(dataverseAlias); if (ownerDataverse == null) { - return errorResponse(Response.Status.BAD_REQUEST, "No such dataverse: " + dataverseAlias); + return error(Response.Status.BAD_REQUEST, "No such dataverse: " + dataverseAlias); } harvestingClient.setDataverse(ownerDataverse); @@ -166,10 +166,10 @@ public Response createHarvestingClient(String jsonBody, @PathParam("nickName") S DataverseRequest req = createDataverseRequest(findUserOrDie()); HarvestingClient managedHarvestingClient = execCommand( new CreateHarvestingClientCommand(req, harvestingClient)); - return createdResponse( "/harvest/clients/" + nickName, harvestingConfigAsJson(managedHarvestingClient)); + return created( "/harvest/clients/" + nickName, harvestingConfigAsJson(managedHarvestingClient)); } catch (JsonParseException ex) { - return errorResponse( Response.Status.BAD_REQUEST, "Error parsing harvesting client: " + ex.getMessage() ); + return error( Response.Status.BAD_REQUEST, "Error parsing harvesting client: " + ex.getMessage() ); } catch (WrappedResponse ex) { return ex.getResponse(); @@ -190,7 +190,7 @@ public Response modifyHarvestingClient(String jsonBody, @PathParam("nickName") S } if (harvestingClient == null) { - return errorResponse( Response.Status.NOT_FOUND, "Harvesting client " + nickName + " not found."); + return error( Response.Status.NOT_FOUND, "Harvesting client " + nickName + " not found."); } String ownerDataverseAlias = harvestingClient.getDataverse().getAlias(); @@ -204,13 +204,13 @@ public Response modifyHarvestingClient(String jsonBody, @PathParam("nickName") S if (newDataverseAlias != null && !newDataverseAlias.equals("") && !newDataverseAlias.equals(ownerDataverseAlias)) { - return errorResponse(Response.Status.BAD_REQUEST, "Bad \"dataverseAlias\" supplied. Harvesting client "+nickName+" belongs to the dataverse "+ownerDataverseAlias); + return error(Response.Status.BAD_REQUEST, "Bad \"dataverseAlias\" supplied. Harvesting client "+nickName+" belongs to the dataverse "+ownerDataverseAlias); } HarvestingClient managedHarvestingClient = execCommand( new UpdateHarvestingClientCommand(req, harvestingClient)); - return createdResponse( "/datasets/" + nickName, harvestingConfigAsJson(managedHarvestingClient)); + return created( "/datasets/" + nickName, harvestingConfigAsJson(managedHarvestingClient)); } catch (JsonParseException ex) { - return errorResponse( Response.Status.BAD_REQUEST, "Error parsing harvesting client: " + ex.getMessage() ); + return error( Response.Status.BAD_REQUEST, "Error parsing harvesting client: " + ex.getMessage() ); } catch (WrappedResponse ex) { return ex.getResponse(); @@ -237,24 +237,24 @@ public Response startHarvestingJob(@PathParam("nickName") String clientNickname, try { authenticatedUser = findAuthenticatedUserOrDie(); } catch (WrappedResponse wr) { - return errorResponse(Response.Status.UNAUTHORIZED, "Authentication required to use this API method"); + return error(Response.Status.UNAUTHORIZED, "Authentication required to use this API method"); } if (authenticatedUser == null || !authenticatedUser.isSuperuser()) { - return errorResponse(Response.Status.FORBIDDEN, "Only the Dataverse Admin user can run harvesting jobs"); + return error(Response.Status.FORBIDDEN, "Only the Dataverse Admin user can run harvesting jobs"); } HarvestingClient harvestingClient = harvestingClientService.findByNickname(clientNickname); if (harvestingClient == null) { - return errorResponse(Response.Status.NOT_FOUND, "No such dataverse: "+clientNickname); + return error(Response.Status.NOT_FOUND, "No such dataverse: "+clientNickname); } DataverseRequest dataverseRequest = createDataverseRequest(authenticatedUser); harvesterService.doAsyncHarvest(dataverseRequest, harvestingClient); } catch (Exception e) { - return this.errorResponse(Response.Status.BAD_REQUEST, "Exception thrown when running harvesting client\""+clientNickname+"\" via REST API; " + e.getMessage()); + return this.error(Response.Status.BAD_REQUEST, "Exception thrown when running harvesting client\""+clientNickname+"\" via REST API; " + e.getMessage()); } return this.accepted(); } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/HarvestingServer.java b/src/main/java/edu/harvard/iq/dataverse/api/HarvestingServer.java index f54190597b2..6d7cf218e35 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/HarvestingServer.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/HarvestingServer.java @@ -63,12 +63,12 @@ public Response oaiSets(@QueryParam("key") String apiKey) throws IOException { try { oaiSets = oaiSetService.findAll(); } catch (Exception ex) { - return errorResponse(Response.Status.INTERNAL_SERVER_ERROR, "Caught an exception looking up available OAI sets; " + ex.getMessage()); + return error(Response.Status.INTERNAL_SERVER_ERROR, "Caught an exception looking up available OAI sets; " + ex.getMessage()); } if (oaiSets == null) { // returning an empty list: - return okResponse(jsonObjectBuilder().add("oaisets", "")); + return ok(jsonObjectBuilder().add("oaisets", "")); } JsonArrayBuilder hcArr = Json.createArrayBuilder(); @@ -77,7 +77,7 @@ public Response oaiSets(@QueryParam("key") String apiKey) throws IOException { hcArr.add(oaiSetAsJson(set)); } - return okResponse(jsonObjectBuilder().add("oaisets", hcArr)); + return ok(jsonObjectBuilder().add("oaisets", hcArr)); } @GET @@ -89,18 +89,18 @@ public Response oaiSet(@PathParam("specname") String spec, @QueryParam("key") St set = oaiSetService.findBySpec(spec); } catch (Exception ex) { logger.warning("Exception caught looking up OAI set " + spec + ": " + ex.getMessage()); - return errorResponse( Response.Status.BAD_REQUEST, "Internal error: failed to look up OAI set " + spec + "."); + return error( Response.Status.BAD_REQUEST, "Internal error: failed to look up OAI set " + spec + "."); } if (set == null) { - return errorResponse(Response.Status.NOT_FOUND, "OAI set " + spec + " not found."); + return error(Response.Status.NOT_FOUND, "OAI set " + spec + " not found."); } try { - return okResponse(oaiSetAsJson(set)); + return ok(oaiSetAsJson(set)); } catch (Exception ex) { logger.warning("Unknown exception caught while trying to format OAI set " + spec + " as json: "+ex.getMessage()); - return errorResponse( Response.Status.BAD_REQUEST, + return error( Response.Status.BAD_REQUEST, "Internal error: failed to produce output for OAI set " + spec + "."); } } @@ -120,7 +120,7 @@ public Response createOaiSet(String jsonBody, @PathParam("specname") String spec oaiSetService.save(set); - return createdResponse( "/harvest/server/oaisets" + spec, oaiSetAsJson(set)); + return created( "/harvest/server/oaisets" + spec, oaiSetAsJson(set)); //} catch (JsonParseException ex) { // return errorResponse( Response.Status.BAD_REQUEST, "Error parsing OAI set: " + ex.getMessage() ); @@ -135,7 +135,7 @@ public Response createOaiSet(String jsonBody, @PathParam("specname") String spec public Response modifyOaiSet(String jsonBody, @PathParam("specname") String spec, @QueryParam("key") String apiKey) throws IOException, JsonParseException { // TODO: // ... - return createdResponse("/harvest/server/oaisets" + spec, null); + return created("/harvest/server/oaisets" + spec, null); } @DELETE @@ -146,21 +146,21 @@ public Response deleteOaiSet(@PathParam("specname") String spec, @QueryParam("ke set = oaiSetService.findBySpec(spec); } catch (Exception ex) { logger.warning("Exception caught looking up OAI set " + spec + ": " + ex.getMessage()); - return errorResponse( Response.Status.BAD_REQUEST, "Internal error: failed to look up OAI set " + spec + "."); + return error( Response.Status.BAD_REQUEST, "Internal error: failed to look up OAI set " + spec + "."); } if (set == null) { - return errorResponse(Response.Status.NOT_FOUND, "OAI set " + spec + " not found."); + return error(Response.Status.NOT_FOUND, "OAI set " + spec + " not found."); } try { oaiSetService.setDeleteInProgress(set.getId()); oaiSetService.remove(set.getId()); } catch (Exception ex) { - return errorResponse( Response.Status.BAD_REQUEST, "Internal error: failed to delete OAI set " + spec + "; " + ex.getMessage()); + return error( Response.Status.BAD_REQUEST, "Internal error: failed to delete OAI set " + spec + "; " + ex.getMessage()); } - return okResponse("OAI Set " + spec + " deleted"); + return ok("OAI Set " + spec + " deleted"); } @@ -172,10 +172,10 @@ public Response oaiSetListDatasets(@PathParam("specname") String spec, @QueryPar set = oaiSetService.findBySpec(spec); } catch (Exception ex) { logger.warning("Exception caught looking up OAI set " + spec + ": " + ex.getMessage()); - return errorResponse( Response.Status.BAD_REQUEST, "Internal error: failed to look up OAI set " + spec + "."); + return error( Response.Status.BAD_REQUEST, "Internal error: failed to look up OAI set " + spec + "."); } - return okResponse(""); + return ok(""); } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Index.java b/src/main/java/edu/harvard/iq/dataverse/api/Index.java index e217b146dd6..b9724a81ef3 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Index.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Index.java @@ -112,7 +112,7 @@ private Response indexAllOrSubset(Long numPartitionsSelected, Long partitionIdTo long numPartitions = 1; if (numPartitionsSelected != null) { if (numPartitionsSelected < 1) { - return errorResponse(Status.BAD_REQUEST, "numPartitions must be 1 or higher but was " + numPartitionsSelected); + return error(Status.BAD_REQUEST, "numPartitions must be 1 or higher but was " + numPartitionsSelected); } else { numPartitions = numPartitionsSelected; } @@ -122,7 +122,7 @@ private Response indexAllOrSubset(Long numPartitionsSelected, Long partitionIdTo availablePartitionIds.add(i); } - Response invalidParitionIdSelection = errorResponse(Status.BAD_REQUEST, "You specified " + numPartitions + " partition(s) and your selected partitionId was " + partitionIdToProcess + " but you must select from these availableParitionIds: " + availablePartitionIds); + Response invalidParitionIdSelection = error(Status.BAD_REQUEST, "You specified " + numPartitions + " partition(s) and your selected partitionId was " + partitionIdToProcess + " but you must select from these availableParitionIds: " + availablePartitionIds); if (partitionIdToProcess != null) { long selected = partitionIdToProcess; if (!availablePartitionIds.contains(selected)) { @@ -151,7 +151,7 @@ private Response indexAllOrSubset(Long numPartitionsSelected, Long partitionIdTo if (previewOnly) { preview.add("args", args); preview.add("availablePartitionIds", availablePartitionIdsBuilder); - return okResponse(preview); + return ok(preview); } JsonObjectBuilder response = Json.createObjectBuilder(); @@ -167,7 +167,7 @@ private Response indexAllOrSubset(Long numPartitionsSelected, Long partitionIdTo int datasetCount = workloadPreview.getInt("datasetCount"); String status = "indexAllOrSubset has begun of " + dataverseCount + " dataverses and " + datasetCount + " datasets."; response.add("message", status); - return okResponse(response); + return ok(response); } catch (EJBException ex) { Throwable cause = ex; StringBuilder sb = new StringBuilder(); @@ -195,9 +195,9 @@ private Response indexAllOrSubset(Long numPartitionsSelected, Long partitionIdTo } } if (sb.toString().equals("javax.ejb.EJBException: Transaction aborted javax.transaction.RollbackException java.lang.IllegalStateException ")) { - return okResponse("indexing went as well as can be expected... got java.lang.IllegalStateException but some indexing may have happened anyway"); + return ok("indexing went as well as can be expected... got java.lang.IllegalStateException but some indexing may have happened anyway"); } else { - return errorResponse(Status.INTERNAL_SERVER_ERROR, sb.toString()); + return error(Status.INTERNAL_SERVER_ERROR, sb.toString()); } } } @@ -207,9 +207,9 @@ private Response indexAllOrSubset(Long numPartitionsSelected, Long partitionIdTo public Response clearSolrIndex() { try { JsonObjectBuilder response = SolrIndexService.deleteAllFromSolrAndResetIndexTimes(); - return okResponse(response); + return ok(response); } catch (SolrServerException | IOException ex) { - return errorResponse(Status.INTERNAL_SERVER_ERROR, ex.getLocalizedMessage()); + return error(Status.INTERNAL_SERVER_ERROR, ex.getLocalizedMessage()); } } @@ -224,7 +224,7 @@ public Response indexTypeById(@PathParam("type") String type, @PathParam("id") L * @todo Can we display the result of indexing to the user? */ Future indexDataverseFuture = indexService.indexDataverse(dataverse); - return okResponse("starting reindex of dataverse " + id); + return ok("starting reindex of dataverse " + id); } else { String response = indexService.removeSolrDocFromIndex(IndexServiceBean.solrDocIdentifierDataverse + id); return notFound("Could not find dataverse with id of " + id + ". Result from deletion attempt: " + response); @@ -234,7 +234,7 @@ public Response indexTypeById(@PathParam("type") String type, @PathParam("id") L if (dataset != null) { boolean doNormalSolrDocCleanUp = true; Future indexDatasetFuture = indexService.indexDataset(dataset, doNormalSolrDocCleanUp); - return okResponse("starting reindex of dataset " + id); + return ok("starting reindex of dataset " + id); } else { /** * @todo what about published, deaccessioned, etc.? Need @@ -251,9 +251,9 @@ public Response indexTypeById(@PathParam("type") String type, @PathParam("id") L */ boolean doNormalSolrDocCleanUp = true; Future indexDatasetFuture = indexService.indexDataset(datasetThatOwnsTheFile, doNormalSolrDocCleanUp); - return okResponse("started reindexing " + type + "/" + id); + return ok("started reindexing " + type + "/" + id); } else { - return errorResponse(Status.BAD_REQUEST, "illegal type: " + type); + return error(Status.BAD_REQUEST, "illegal type: " + type); } } catch (EJBException ex) { Throwable cause = ex; @@ -282,7 +282,7 @@ public Response indexTypeById(@PathParam("type") String type, @PathParam("id") L } } } - return errorResponse(Status.INTERNAL_SERVER_ERROR, sb.toString()); + return error(Status.INTERNAL_SERVER_ERROR, sb.toString()); } } @@ -290,13 +290,13 @@ public Response indexTypeById(@PathParam("type") String type, @PathParam("id") L @Path("dataset") public Response indexDatasetByPersistentId(@QueryParam("persistentId") String persistentId) { if (persistentId == null) { - return errorResponse(Status.BAD_REQUEST, "No persistent id given."); + return error(Status.BAD_REQUEST, "No persistent id given."); } Dataset dataset = null; try { dataset = datasetService.findByGlobalId(persistentId); } catch (Exception ex) { - return errorResponse(Status.BAD_REQUEST, "Problem looking up dataset with persistent id \"" + persistentId + "\". Error: " + ex.getMessage()); + return error(Status.BAD_REQUEST, "Problem looking up dataset with persistent id \"" + persistentId + "\". Error: " + ex.getMessage()); } if (dataset != null) { boolean doNormalSolrDocCleanUp = true; @@ -313,9 +313,9 @@ public Response indexDatasetByPersistentId(@QueryParam("persistentId") String pe versions.add(versionObject); } data.add("versions", versions); - return okResponse(data); + return ok(data); } else { - return errorResponse(Status.BAD_REQUEST, "Could not find dataset with persistent id " + persistentId); + return error(Status.BAD_REQUEST, "Could not find dataset with persistent id " + persistentId); } } @@ -335,14 +335,14 @@ public Response indexMod(@QueryParam("partitions") long partitions, @QueryParam( response.add("partitions", partitions); response.add("which", which); response.add("mine", mine.toString()); - return okResponse(response); + return ok(response); } @GET @Path("perms") public Response indexAllPermissions() { IndexResponse indexResponse = solrIndexService.indexAllPermissions(); - return okResponse(indexResponse.getMessage()); + return ok(indexResponse.getMessage()); } @GET @@ -350,10 +350,10 @@ public Response indexAllPermissions() { public Response indexPermissions(@PathParam("id") Long id) { DvObject dvObject = dvObjectService.findDvObject(id); if (dvObject == null) { - return errorResponse(Status.BAD_REQUEST, "Could not find DvObject based on id " + id); + return error(Status.BAD_REQUEST, "Could not find DvObject based on id " + id); } else { IndexResponse indexResponse = solrIndexService.indexPermissionsForOneDvObject(dvObject); - return okResponse(indexResponse.getMessage()); + return ok(indexResponse.getMessage()); } } @@ -366,7 +366,7 @@ public Response indexStatus() { try { contentInSolrButNotDatabase = getContentInSolrButNotDatabase(); } catch (SearchException ex) { - return errorResponse(Response.Status.INTERNAL_SERVER_ERROR, "Can not determine index status. " + ex.getLocalizedMessage() + ". Is Solr down? Exception: " + ex.getCause().getLocalizedMessage()); + return error(Response.Status.INTERNAL_SERVER_ERROR, "Can not determine index status. " + ex.getLocalizedMessage() + ". Is Solr down? Exception: " + ex.getCause().getLocalizedMessage()); } JsonObjectBuilder permissionsInDatabaseButStaleInOrMissingFromSolr = getPermissionsInDatabaseButStaleInOrMissingFromSolr(); @@ -378,7 +378,7 @@ public Response indexStatus() { .add("permissionsInDatabaseButStaleInOrMissingFromIndex", permissionsInDatabaseButStaleInOrMissingFromSolr) .add("permissionsInIndexButNotDatabase", permissionsInSolrButNotDatabase); - return okResponse(data); + return ok(data); } private JsonObjectBuilder getContentInDatabaseButStaleInOrMissingFromSolr() { @@ -560,7 +560,7 @@ public Response searchDebug( User user = findUserByApiToken(apiToken); if (user == null) { - return errorResponse(Response.Status.UNAUTHORIZED, "Invalid apikey '" + apiToken + "'"); + return error(Response.Status.UNAUTHORIZED, "Invalid apikey '" + apiToken + "'"); } Dataverse subtreeScope = dataverseService.findRootDataverse(); @@ -574,7 +574,7 @@ public Response searchDebug( try { solrQueryResponse = searchService.search(createDataverseRequest(user), subtreeScope, query, filterQueries, sortField, sortOrder, paginationStart, dataRelatedToMe, numResultsPerPage); } catch (SearchException ex) { - return errorResponse(Response.Status.INTERNAL_SERVER_ERROR, ex.getLocalizedMessage() + ": " + ex.getCause().getLocalizedMessage()); + return error(Response.Status.INTERNAL_SERVER_ERROR, ex.getLocalizedMessage() + ": " + ex.getCause().getLocalizedMessage()); } JsonArrayBuilder itemsArrayBuilder = Json.createArrayBuilder(); @@ -583,7 +583,7 @@ public Response searchDebug( itemsArrayBuilder.add(solrSearchResult.getType() + ":" + solrSearchResult.getNameSort()); } - return okResponse(itemsArrayBuilder); + return ok(itemsArrayBuilder); } /** @@ -597,12 +597,12 @@ public Response searchPermsDebug( User user = findUserByApiToken(apiToken); if (user == null) { - return errorResponse(Response.Status.UNAUTHORIZED, "Invalid apikey '" + apiToken + "'"); + return error(Response.Status.UNAUTHORIZED, "Invalid apikey '" + apiToken + "'"); } DvObject dvObjectToLookUp = dvObjectService.findDvObject(dvObjectId); if (dvObjectToLookUp == null) { - return errorResponse(Status.BAD_REQUEST, "Could not find DvObject based on id " + dvObjectId); + return error(Status.BAD_REQUEST, "Could not find DvObject based on id " + dvObjectId); } List solrDocs = SolrIndexService.determineSolrDocs(dvObjectToLookUp); @@ -637,21 +637,21 @@ public Response searchPermsDebug( data.add("timestamps", timestamps); data.add("roleAssignments", roleAssignmentsData); - return okResponse(data); + return ok(data); } @DELETE @Path("timestamps") public Response deleteAllTimestamps() { int numItemsCleared = dvObjectService.clearAllIndexTimes(); - return okResponse("cleared: " + numItemsCleared); + return ok("cleared: " + numItemsCleared); } @DELETE @Path("timestamps/{dvObjectId}") public Response deleteTimestamp(@PathParam("dvObjectId") long dvObjectId) { int numItemsCleared = dvObjectService.clearIndexTimes(dvObjectId); - return okResponse("cleared: " + numItemsCleared); + return ok("cleared: " + numItemsCleared); } @GET @@ -659,7 +659,7 @@ public Response deleteTimestamp(@PathParam("dvObjectId") long dvObjectId) { public Response filesearch(@QueryParam("persistentId") String persistentId, @QueryParam("semanticVersion") String semanticVersion, @QueryParam("q") String userSuppliedQuery) { Dataset dataset = datasetService.findByGlobalId(persistentId); if (dataset == null) { - return errorResponse(Status.BAD_REQUEST, "Could not find dataset with persistent id " + persistentId); + return error(Status.BAD_REQUEST, "Could not find dataset with persistent id " + persistentId); } User user = GuestUser.get(); try { @@ -671,12 +671,12 @@ public Response filesearch(@QueryParam("persistentId") String persistentId, @Que } RetrieveDatasetVersionResponse datasetVersionResponse = datasetVersionService.retrieveDatasetVersionByPersistentId(persistentId, semanticVersion); if (datasetVersionResponse == null) { - return errorResponse(Status.BAD_REQUEST, "Problem searching for files. Could not find dataset version based on " + persistentId + " and " + semanticVersion); + return error(Status.BAD_REQUEST, "Problem searching for files. Could not find dataset version based on " + persistentId + " and " + semanticVersion); } DatasetVersion datasetVersion = datasetVersionResponse.getDatasetVersion(); FileView fileView = searchFilesService.getFileView(datasetVersion, user, userSuppliedQuery); if (fileView == null) { - return errorResponse(Status.BAD_REQUEST, "Problem searching for files. Null returned from getFileView."); + return error(Status.BAD_REQUEST, "Problem searching for files. Null returned from getFileView."); } JsonArrayBuilder filesFound = Json.createArrayBuilder(); JsonArrayBuilder cards = Json.createArrayBuilder(); @@ -714,7 +714,7 @@ public Response filesearch(@QueryParam("persistentId") String persistentId, @Que data.add("filterQueries", filterQueries); data.add("allDataverVersionIds", allDatasetVersionIds); data.add("semanticVersion", datasetVersion.getSemanticVersion()); - return okResponse(data); + return ok(data); } @GET @@ -730,12 +730,12 @@ public Response getFileMetadataByDatasetId( try { fileMetadatasFound = dataFileService.findFileMetadataByDatasetVersionId(datasetIdToLookUp, maxResults, sortField, sortOrder); } catch (Exception ex) { - return errorResponse(Status.BAD_REQUEST, "error: " + ex.getCause().getMessage() + ex); + return error(Status.BAD_REQUEST, "error: " + ex.getCause().getMessage() + ex); } for (FileMetadata fileMetadata : fileMetadatasFound) { data.add(fileMetadata.getLabel()); } - return okResponse(data); + return ok(data); } } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Info.java b/src/main/java/edu/harvard/iq/dataverse/api/Info.java index 24122b7c28d..d1360458326 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Info.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Info.java @@ -18,7 +18,7 @@ public class Info extends AbstractApiBean { public Response getDatasetPublishPopupCustomText() { String setting = settingsService.getValueForKey(SettingsServiceBean.Key.DatasetPublishPopupCustomText); if (setting != null) { - return okResponse(Json.createObjectBuilder().add("message", setting)); + return ok(Json.createObjectBuilder().add("message", setting)); } else { return notFound("Setting " + SettingsServiceBean.Key.DatasetPublishPopupCustomText + " not found"); } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Mail.java b/src/main/java/edu/harvard/iq/dataverse/api/Mail.java index 4f135af1054..3b5050b480b 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Mail.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Mail.java @@ -24,7 +24,7 @@ public Response sendMail() { ActionLogRecord alr = new ActionLogRecord(ActionLogRecord.ActionType.Admin, "sendMail"); // mailService.bulkSendNotifications(); actionLogSvc.log(alr); - return okResponse("bulk send notification is deprecated"); + return ok("bulk send notification is deprecated"); } } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/MetadataBlocks.java b/src/main/java/edu/harvard/iq/dataverse/api/MetadataBlocks.java index e0376f71412..7debb502dc6 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/MetadataBlocks.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/MetadataBlocks.java @@ -29,7 +29,7 @@ public Response list() { bld.add( brief.json(block) ); } - return okResponse(bld); + return ok(bld); } @Path("{identifier}") @@ -37,7 +37,7 @@ public Response list() { public Response getBlock( @PathParam("identifier") String idtf ) { MetadataBlock b = findMetadataBlock(idtf); - return (b != null ) ? okResponse(json(b)) : notFound("Can't find metadata block '" + idtf + "'"); + return (b != null ) ? ok(json(b)) : notFound("Can't find metadata block '" + idtf + "'"); } } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Roles.java b/src/main/java/edu/harvard/iq/dataverse/api/Roles.java index 4b439dc6262..d58c84bb3a4 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Roles.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Roles.java @@ -1,17 +1,13 @@ package edu.harvard.iq.dataverse.api; import edu.harvard.iq.dataverse.api.dto.RoleDTO; -import edu.harvard.iq.dataverse.Dataverse; import edu.harvard.iq.dataverse.authorization.DataverseRole; -import edu.harvard.iq.dataverse.DataverseServiceBean; import edu.harvard.iq.dataverse.authorization.Permission; -import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUserServiceBean; -import javax.ejb.EJB; +import edu.harvard.iq.dataverse.authorization.users.User; import javax.ws.rs.GET; import javax.ws.rs.POST; import javax.ws.rs.Path; import javax.ws.rs.PathParam; - import static edu.harvard.iq.dataverse.util.json.JsonPrinter.*; import edu.harvard.iq.dataverse.engine.command.impl.CreateRoleCommand; import edu.harvard.iq.dataverse.engine.command.impl.DeleteRoleCommand; @@ -19,7 +15,6 @@ import javax.ws.rs.DELETE; import javax.ws.rs.QueryParam; import javax.ws.rs.core.Response; -import javax.ws.rs.core.Response.Status; /** * Util API for managing roles. Might not make it to the production version. @@ -29,57 +24,43 @@ @Path("roles") public class Roles extends AbstractApiBean { - @EJB - BuiltinUserServiceBean usersSvc; - - @EJB - DataverseServiceBean dvSvc; - @GET @Path("{id}") public Response viewRole( @PathParam("id") Long id) { - try { - DataverseRole role = rolesSvc.find(id); - if ( role == null ) { - return notFound("role with id " + id + " not found"); - } else { - return ( permissionSvc.userOn(findUserOrDie(), role.getOwner()).has(Permission.ManageDataversePermissions) ) - ? okResponse( json(role) ) : permissionError("Permission required to view roles."); - } - } catch (WrappedResponse ex) { - return ex.getResponse(); - } + return response( ()-> { + final User user = findUserOrDie(); + final DataverseRole role = findRoleOrDie(id); + return ( permissionSvc.userOn(user, role.getOwner()).has(Permission.ManageDataversePermissions) ) + ? ok( json(role) ) : permissionError("Permission required to view roles."); + }); } @DELETE @Path("{id}") public Response deleteRole( @PathParam("id") Long id ) { - DataverseRole role = rolesSvc.find(id); - if ( role == null ) { - return notFound( "role with id " + id + " not found"); - } else { - try { - execCommand( new DeleteRoleCommand(createDataverseRequest(findUserOrDie()), role) ); - return okResponse("role " + id + " deleted."); - - } catch (WrappedResponse ex) { - return ex.refineResponse( "Cannot delete role " + id + "." ); - } - } + try { + execCommand( new DeleteRoleCommand(createDataverseRequest(findUserOrDie()), findRoleOrDie(id)) ); + return ok("role " + id + " deleted."); + + } catch (WrappedResponse ex) { + return ex.refineResponse( "Cannot delete role " + id + "." ); + } } @POST public Response createNewRole( RoleDTO roleDto, - @QueryParam("dvo") String dvoIdtf ) { - - Dataverse d = findDataverse(dvoIdtf); - if ( d == null ) return errorResponse( Status.BAD_REQUEST, "no dataverse with id " + dvoIdtf ); - - try { - return okResponse(json(execCommand(new CreateRoleCommand(roleDto.asRole(), createDataverseRequest(findUserOrDie()), d)))); - } catch ( WrappedResponse ce ) { - return ce.refineResponse("Role creation failed."); - } + @QueryParam("dvo") String dvoIdtf ) { + return response( ()-> ok(json(execCommand( + new CreateRoleCommand(roleDto.asRole(), + createDataverseRequest(findUserOrDie()), + findDataverseOrDie(dvoIdtf)))))); } - + + private DataverseRole findRoleOrDie( long id ) throws WrappedResponse { + DataverseRole role = rolesSvc.find(id); + if ( role != null ) { + return role; + } + throw new WrappedResponse(notFound( "role with id " + id + " not found")); + } } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/SavedSearches.java b/src/main/java/edu/harvard/iq/dataverse/api/SavedSearches.java index 2f093392f61..7ead0d23711 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/SavedSearches.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/SavedSearches.java @@ -42,7 +42,7 @@ public Response meta() { endpoints.add("GET /id"); endpoints.add("POST"); endpoints.add("DELETE /id"); - return okResponse(endpoints); + return ok(endpoints); } @GET @@ -56,7 +56,7 @@ public Response list() { } JsonObjectBuilder response = Json.createObjectBuilder(); response.add("saved searches", savedSearchesBuilder); - return okResponse(response); + return ok(response); } @GET @@ -65,9 +65,9 @@ public Response show(@PathParam("id") long id) { SavedSearch savedSearch = savedSearchSvc.find(id); if (savedSearch != null) { JsonObjectBuilder response = toJson(savedSearch); - return okResponse(response); + return ok(response); } else { - return errorResponse(NOT_FOUND, "Could not find saved search id " + id); + return error(NOT_FOUND, "Could not find saved search id " + id); } } @@ -92,7 +92,7 @@ private JsonObjectBuilder toJson(SavedSearch savedSearch) { public Response add(JsonObject body) { if (body == null) { - return errorResponse(BAD_REQUEST, "JSON is expected."); + return error(BAD_REQUEST, "JSON is expected."); } String keyForAuthenticatedUserId = "creatorId"; @@ -100,16 +100,16 @@ public Response add(JsonObject body) { try { creatorIdToLookUp = body.getInt(keyForAuthenticatedUserId); } catch (NullPointerException ex) { - return errorResponse(BAD_REQUEST, "Required field missing: " + keyForAuthenticatedUserId); + return error(BAD_REQUEST, "Required field missing: " + keyForAuthenticatedUserId); } catch (ClassCastException ex) { - return errorResponse(BAD_REQUEST, "A number is required for " + keyForAuthenticatedUserId); + return error(BAD_REQUEST, "A number is required for " + keyForAuthenticatedUserId); } catch (Exception ex) { - return errorResponse(BAD_REQUEST, "Problem with " + keyForAuthenticatedUserId + ": " + ex); + return error(BAD_REQUEST, "Problem with " + keyForAuthenticatedUserId + ": " + ex); } AuthenticatedUser creator = authSvc.findByID(creatorIdToLookUp); if (creator == null) { - return errorResponse(Response.Status.NOT_FOUND, "Could not find user based on " + keyForAuthenticatedUserId + ": " + creatorIdToLookUp); + return error(Response.Status.NOT_FOUND, "Could not find user based on " + keyForAuthenticatedUserId + ": " + creatorIdToLookUp); } String keyForQuery = "query"; @@ -117,7 +117,7 @@ public Response add(JsonObject body) { try { query = body.getString(keyForQuery); } catch (NullPointerException ex) { - return errorResponse(BAD_REQUEST, "Required field missing: " + keyForQuery); + return error(BAD_REQUEST, "Required field missing: " + keyForQuery); } String keyForDefinitionPointId = "definitionPointId"; @@ -125,15 +125,15 @@ public Response add(JsonObject body) { try { dataverseIdToLookup = body.getInt(keyForDefinitionPointId); } catch (NullPointerException ex) { - return errorResponse(BAD_REQUEST, "Required field missing: " + keyForDefinitionPointId); + return error(BAD_REQUEST, "Required field missing: " + keyForDefinitionPointId); } catch (ClassCastException ex) { - return errorResponse(BAD_REQUEST, "A number is required for " + keyForDefinitionPointId); + return error(BAD_REQUEST, "A number is required for " + keyForDefinitionPointId); } catch (Exception ex) { - return errorResponse(BAD_REQUEST, "Problem with " + keyForDefinitionPointId + ": " + ex); + return error(BAD_REQUEST, "Problem with " + keyForDefinitionPointId + ": " + ex); } Dataverse definitionPoint = dataverseSvc.find(dataverseIdToLookup); if (definitionPoint == null) { - return errorResponse(NOT_FOUND, "Could not find a dataverse based on id " + dataverseIdToLookup); + return error(NOT_FOUND, "Could not find a dataverse based on id " + dataverseIdToLookup); } SavedSearch toPersist = new SavedSearch(query, definitionPoint, creator); @@ -150,7 +150,7 @@ public Response add(JsonObject body) { } catch (NullPointerException ex) { // filter queries are not required, keep going } catch (Exception ex) { - return errorResponse(BAD_REQUEST, "Problem getting filter queries: " + ex); + return error(BAD_REQUEST, "Problem getting filter queries: " + ex); } if (!savedSearchFilterQuerys.isEmpty()) { @@ -159,7 +159,7 @@ public Response add(JsonObject body) { try { SavedSearch persistedSavedSearch = savedSearchSvc.add(toPersist); - return okResponse("Added: " + persistedSavedSearch); + return ok("Added: " + persistedSavedSearch); } catch (EJBException ex) { StringBuilder errors = new StringBuilder(); Throwable throwable = ex.getCause(); @@ -167,7 +167,7 @@ public Response add(JsonObject body) { errors.append(throwable).append(" "); throwable = throwable.getCause(); } - return errorResponse(BAD_REQUEST, "Problem adding saved search: " + errors); + return error(BAD_REQUEST, "Problem adding saved search: " + errors); } } @@ -176,17 +176,17 @@ public Response add(JsonObject body) { public Response delete(@PathParam("id") long doomedId) { boolean disabled = true; if (disabled) { - return errorResponse(BAD_REQUEST, "Saved Searches can not safely be deleted because links can not safely be deleted. See https://github.com/IQSS/dataverse/issues/1364 for details."); + return error(BAD_REQUEST, "Saved Searches can not safely be deleted because links can not safely be deleted. See https://github.com/IQSS/dataverse/issues/1364 for details."); } SavedSearch doomed = savedSearchSvc.find(doomedId); if (doomed == null) { - return errorResponse(NOT_FOUND, "Could not find saved search id " + doomedId); + return error(NOT_FOUND, "Could not find saved search id " + doomedId); } boolean wasDeleted = savedSearchSvc.delete(doomedId); if (wasDeleted) { - return okResponse(Json.createObjectBuilder().add("Deleted", doomedId)); + return ok(Json.createObjectBuilder().add("Deleted", doomedId)); } else { - return errorResponse(INTERNAL_SERVER_ERROR, "Problem deleting id " + doomedId); + return error(INTERNAL_SERVER_ERROR, "Problem deleting id " + doomedId); } } @@ -196,11 +196,11 @@ public Response makeLinksForAllSavedSearches(@QueryParam("debug") boolean debug) JsonObjectBuilder makeLinksResponse; try { makeLinksResponse = savedSearchSvc.makeLinksForAllSavedSearches(debug); - return okResponse(makeLinksResponse); + return ok(makeLinksResponse); } catch (CommandException ex) { - return errorResponse(BAD_REQUEST, ex.getLocalizedMessage()); + return error(BAD_REQUEST, ex.getLocalizedMessage()); } catch (SearchException ex) { - return errorResponse(INTERNAL_SERVER_ERROR, ex.getLocalizedMessage()); + return error(INTERNAL_SERVER_ERROR, ex.getLocalizedMessage()); } } @@ -209,16 +209,16 @@ public Response makeLinksForAllSavedSearches(@QueryParam("debug") boolean debug) public Response makeLinksForSingleSavedSearch(@PathParam("id") long savedSearchIdToLookUp, @QueryParam("debug") boolean debug) { SavedSearch savedSearchToMakeLinksFor = savedSearchSvc.find(savedSearchIdToLookUp); if (savedSearchToMakeLinksFor == null) { - return errorResponse(BAD_REQUEST, "Count not find saved search id " + savedSearchIdToLookUp); + return error(BAD_REQUEST, "Count not find saved search id " + savedSearchIdToLookUp); } try { DataverseRequest dataverseRequest = new DataverseRequest(savedSearchToMakeLinksFor.getCreator(), SavedSearchServiceBean.getHttpServletRequest()); JsonObjectBuilder response = savedSearchSvc.makeLinksForSingleSavedSearch(dataverseRequest, savedSearchToMakeLinksFor, debug); - return okResponse(response); + return ok(response); } catch (CommandException ex) { - return errorResponse(BAD_REQUEST, ex.getLocalizedMessage()); + return error(BAD_REQUEST, ex.getLocalizedMessage()); } catch (SearchException ex) { - return errorResponse(INTERNAL_SERVER_ERROR, ex.getLocalizedMessage()); + return error(INTERNAL_SERVER_ERROR, ex.getLocalizedMessage()); } } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Search.java b/src/main/java/edu/harvard/iq/dataverse/api/Search.java index 9b8dfeb2045..f7bd6672035 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Search.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Search.java @@ -101,7 +101,7 @@ public Response search( filterQueries.add(filterDownToSubtree); } } catch (Exception ex) { - return errorResponse(Response.Status.BAD_REQUEST, ex.getLocalizedMessage()); + return error(Response.Status.BAD_REQUEST, ex.getLocalizedMessage()); } // users can't change these (yet anyway) @@ -132,7 +132,7 @@ public Response search( } String message = "Exception running search for [" + query + "] with filterQueries " + filterQueries + " and paginationStart [" + paginationStart + "]: " + sb.toString(); logger.info(message); - return errorResponse(Response.Status.INTERNAL_SERVER_ERROR, message); + return error(Response.Status.INTERNAL_SERVER_ERROR, message); } JsonArrayBuilder itemsArrayBuilder = Json.createArrayBuilder(); @@ -183,12 +183,12 @@ public Response search( * @todo You get here if you pass only ":" as a query, for * example. Should we return more or better information? */ - return errorResponse(Response.Status.BAD_REQUEST, solrQueryResponse.getError()); + return error(Response.Status.BAD_REQUEST, solrQueryResponse.getError()); } response.setHeader("Access-Control-Allow-Origin", "*"); - return okResponse(value); + return ok(value); } else { - return errorResponse(Response.Status.BAD_REQUEST, "q parameter is missing"); + return error(Response.Status.BAD_REQUEST, "q parameter is missing"); } } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/TestApi.java b/src/main/java/edu/harvard/iq/dataverse/api/TestApi.java index 0cebd7dd716..8cacdc5ac4d 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/TestApi.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/TestApi.java @@ -51,7 +51,7 @@ public class TestApi extends AbstractApiBean { @Path("echo/{whatever}") @GET public Response echo( @PathParam("whatever") String body ) { - return okResponse(body); + return ok(body); } @Path("permissions/{dvo}") @@ -67,14 +67,14 @@ public Response findPermissonsOn(@PathParam("dvo") String dvo) { JsonObjectBuilder bld = Json.createObjectBuilder(); bld.add("user", aUser.getIdentifier() ); bld.add("permissions", json(permissionSvc.permissionsFor(createDataverseRequest(aUser), dvObj)) ); - return okResponse(bld); + return ok(bld); } catch (WrappedResponse wr) { return wr.getResponse(); } } catch (Exception e) { logger.log( Level.SEVERE, "Error while testing permissions", e ); - return errorResponse(Response.Status.INTERNAL_SERVER_ERROR, e.getMessage()); + return error(Response.Status.INTERNAL_SERVER_ERROR, e.getMessage()); } } @@ -83,7 +83,7 @@ public Response findPermissonsOn(@PathParam("dvo") String dvo) { public Response findRoleAssignee(@PathParam("idtf") String idtf) { RoleAssignee ra = roleAssigneeSvc.getRoleAssignee(idtf); return (ra == null) ? notFound("Role Assignee '" + idtf + "' not found.") - : okResponse(json(ra.getDisplayInfo())); + : ok(json(ra.getDisplayInfo())); } @Path("bcrypt/encrypt/{word}") @@ -107,7 +107,7 @@ public String test( @PathParam("w1") String w1 ) { @GET public Response testUserLookup() { try { - return okResponse( json(findAuthenticatedUserOrDie()) ); + return ok( json(findAuthenticatedUserOrDie()) ); } catch (WrappedResponse ex) { return ex.getResponse(); } @@ -122,7 +122,7 @@ public Response explicitGroupMembership( @PathParam("identifier") String idtf) { } Set groups = explicitGroups.findGroups(roleAssignee); logger.log(Level.INFO, "Groups for {0}: {1}", new Object[]{roleAssignee, groups}); - return okResponse( groups.stream().map( g->json(g).build()).collect(toJsonArray()) ); + return ok( groups.stream().map( g->json(g) ).collect(toJsonArray()) ); } @Path("ipGroups/containing/{address}") @@ -137,7 +137,7 @@ public Response getIpGroupsContaining( @PathParam("address") String addrStr ) { r.add("groups", ipGroupsSvc.findAllIncludingIp(addr).stream() .map( IpGroup::toString ) .collect(stringsToJsonArray())); - return okResponse( r ); + return ok( r ); } catch ( IllegalArgumentException iae ) { return badRequest(addrStr + " is not a valid address: " + iae.getMessage()); diff --git a/src/main/java/edu/harvard/iq/dataverse/api/WorldMapRelatedData.java b/src/main/java/edu/harvard/iq/dataverse/api/WorldMapRelatedData.java index 616d5c6ccce..c0e9c8f3edd 100755 --- a/src/main/java/edu/harvard/iq/dataverse/api/WorldMapRelatedData.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/WorldMapRelatedData.java @@ -149,7 +149,7 @@ public Response checkWorldMapAPI(@Context HttpServletRequest request logger.info("Failed to retrieve image. Error:" + e2); } - return okResponse( "Looks good " + identifier + " " + mapLayerMetadata.getLayerName()); + return ok( "Looks good " + identifier + " " + mapLayerMetadata.getLayerName()); } @@ -201,7 +201,7 @@ private Response mapDataFileTokenOnlyOption(@Context HttpServletRequest request } } if (user==null){ - return errorResponse(Response.Status.FORBIDDEN, "Not logged in"); + return error(Response.Status.FORBIDDEN, "Not logged in"); } @@ -214,27 +214,27 @@ private Response mapDataFileTokenOnlyOption(@Context HttpServletRequest request // Check if the user exists AuthenticatedUser dvUser = dataverseUserService.findByID(dvuser_id); if ( dvUser == null ){ - return errorResponse(Response.Status.FORBIDDEN, "Invalid user"); + return error(Response.Status.FORBIDDEN, "Invalid user"); } // Check if this file exists DataFile dfile = dataFileService.find(datafile_id); if (dfile==null){ - return errorResponse(Response.Status.NOT_FOUND, "DataFile not found for id: " + datafile_id); + return error(Response.Status.NOT_FOUND, "DataFile not found for id: " + datafile_id); } /* Is the dataset public? */ if (!dfile.getOwner().isReleased()){ - return errorResponse(Response.Status.FORBIDDEN, "Mapping is only permitted for public datasets/files"); + return error(Response.Status.FORBIDDEN, "Mapping is only permitted for public datasets/files"); } // Does this user have permission to edit metadata for this file? if (!permissionService.request(createDataverseRequest(dvUser)).on(dfile.getOwner()).has(Permission.EditDataset)){ String errMsg = "The user does not have permission to edit metadata for this file."; - return errorResponse(Response.Status.FORBIDDEN, errMsg); + return error(Response.Status.FORBIDDEN, errMsg); } WorldMapToken token = tokenServiceBean.getNewToken(dfile, dvUser); @@ -243,7 +243,7 @@ private Response mapDataFileTokenOnlyOption(@Context HttpServletRequest request // Return only the token in a JSON object final JsonObjectBuilder jsonInfo = Json.createObjectBuilder(); jsonInfo.add(WorldMapToken.GEOCONNECT_TOKEN_KEY, token.getToken()); - return okResponse(jsonInfo); + return ok(jsonInfo); } // Redirect to geoconnect url @@ -256,7 +256,7 @@ private Response mapDataFileTokenOnlyOption(@Context HttpServletRequest request try { redirect_uri = new URI(redirect_url_str); } catch (URISyntaxException ex) { - return errorResponse(Response.Status.NOT_FOUND, "Faile to create URI from: " + redirect_url_str); + return error(Response.Status.NOT_FOUND, "Faile to create URI from: " + redirect_url_str); } // Response. return Response.seeOther(redirect_uri).build(); @@ -354,7 +354,7 @@ public Response getWorldMapDatafileInfo(String jsonTokenData, @Context HttpServl jsonTokenInfo = Json.createReader(rdr).readObject(); } catch ( JsonParsingException jpe ) { logger.log(Level.SEVERE, "Json: " + jsonTokenData); - return errorResponse( Response.Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage() ); + return error( Response.Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage() ); } logger.info("(1a) jsonTokenInfo: " + jsonTokenInfo); @@ -362,7 +362,7 @@ public Response getWorldMapDatafileInfo(String jsonTokenData, @Context HttpServl String worldmapTokenParam = this.retrieveTokenValueFromJson(jsonTokenInfo); logger.info("(1b) token from JSON: " + worldmapTokenParam); if (worldmapTokenParam==null){ - return errorResponse(Response.Status.BAD_REQUEST, "Token not found in JSON request."); + return error(Response.Status.BAD_REQUEST, "Token not found in JSON request."); } // Retrieve WorldMapToken and make sure it is valid @@ -371,7 +371,7 @@ public Response getWorldMapDatafileInfo(String jsonTokenData, @Context HttpServl logger.info("(2) token retrieved from db: " + wmToken); if (wmToken==null){ - return errorResponse(Response.Status.UNAUTHORIZED, "No access. Invalid token."); + return error(Response.Status.UNAUTHORIZED, "No access. Invalid token."); } // Make sure the token's User still has permissions to access the file @@ -379,7 +379,7 @@ public Response getWorldMapDatafileInfo(String jsonTokenData, @Context HttpServl logger.info("(3) check permissions"); if (!(tokenServiceBean.canTokenUserEditFile(wmToken))){ tokenServiceBean.expireToken(wmToken); - return errorResponse(Response.Status.UNAUTHORIZED, "No access. Invalid token."); + return error(Response.Status.UNAUTHORIZED, "No access. Invalid token."); } @@ -389,24 +389,24 @@ public Response getWorldMapDatafileInfo(String jsonTokenData, @Context HttpServl // AuthenticatedUser dvUser = wmToken.getDataverseUser(); if (dvUser == null) { - return errorResponse(Response.Status.NOT_FOUND, "DataverseUser not found for token"); + return error(Response.Status.NOT_FOUND, "DataverseUser not found for token"); } DataFile dfile = wmToken.getDatafile(); if (dfile == null) { - return errorResponse(Response.Status.NOT_FOUND, "DataFile not found for token"); + return error(Response.Status.NOT_FOUND, "DataFile not found for token"); } // (1a) Retrieve FileMetadata FileMetadata dfile_meta = dfile.getFileMetadata(); if (dfile_meta==null){ - return errorResponse(Response.Status.NOT_FOUND, "FileMetadata not found"); + return error(Response.Status.NOT_FOUND, "FileMetadata not found"); } // (2) Now get the dataset and the latest DatasetVersion Dataset dset = dfile.getOwner(); if (dset==null){ - return errorResponse(Response.Status.NOT_FOUND, "Owning Dataset for this DataFile not found"); + return error(Response.Status.NOT_FOUND, "Owning Dataset for this DataFile not found"); } // (2a) latest DatasetVersion @@ -414,13 +414,13 @@ public Response getWorldMapDatafileInfo(String jsonTokenData, @Context HttpServl // DatasetVersion dset_version = dset.getLatestVersion(); if (dset_version==null){ - return errorResponse(Response.Status.NOT_FOUND, "Latest DatasetVersion for this DataFile not found"); + return error(Response.Status.NOT_FOUND, "Latest DatasetVersion for this DataFile not found"); } // (3) get Dataverse Dataverse dverse = dset.getOwner(); if (dverse==null){ - return errorResponse(Response.Status.NOT_FOUND, "Dataverse for this DataFile's Dataset not found"); + return error(Response.Status.NOT_FOUND, "Dataverse for this DataFile's Dataset not found"); } // (4) Roll it all up in a JSON response @@ -437,7 +437,7 @@ public Response getWorldMapDatafileInfo(String jsonTokenData, @Context HttpServl jsonData.add("mapping_type", "tabular"); }else{ logger.log(Level.SEVERE, "This was neither a Shapefile nor a Tabular data file. DataFile id: " + dfile.getId()); - return errorResponse( Response.Status.BAD_REQUEST, "Sorry! This file does not have mapping data. Please contact the Dataverse administrator. DataFile id: " + dfile.getId()); + return error( Response.Status.BAD_REQUEST, "Sorry! This file does not have mapping data. Please contact the Dataverse administrator. DataFile id: " + dfile.getId()); } @@ -504,7 +504,7 @@ public Response getWorldMapDatafileInfo(String jsonTokenData, @Context HttpServl jsonData.add("datafile_content_type", dfile.getContentType()); jsonData.add("datafile_create_datetime", dfile.getCreateDate().toString()); - return okResponse(jsonData); + return ok(jsonData); } @@ -532,7 +532,7 @@ public Response updateWorldMapLayerData(String jsonLayerData){ //---------------------------------- if (jsonLayerData==null){ logger.log(Level.SEVERE, "jsonLayerData is null"); - return errorResponse( Response.Status.BAD_REQUEST, "No JSON data"); + return error( Response.Status.BAD_REQUEST, "No JSON data"); } // (1) Parse JSON @@ -542,27 +542,27 @@ public Response updateWorldMapLayerData(String jsonLayerData){ jsonInfo = Json.createReader(rdr).readObject(); } catch ( JsonParsingException jpe ) { logger.log(Level.SEVERE, "Json: " + jsonLayerData); - return errorResponse( Response.Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage() ); + return error( Response.Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage() ); } // Retrieve token string String worldmapTokenParam = this.retrieveTokenValueFromJson(jsonInfo); if (worldmapTokenParam==null){ - return errorResponse(Response.Status.BAD_REQUEST, "Token not found in JSON request."); + return error(Response.Status.BAD_REQUEST, "Token not found in JSON request."); } // Retrieve WorldMapToken and make sure it is valid // WorldMapToken wmToken = this.tokenServiceBean.retrieveAndRefreshValidToken(worldmapTokenParam); if (wmToken==null){ - return errorResponse(Response.Status.UNAUTHORIZED, "No access. Invalid token."); + return error(Response.Status.UNAUTHORIZED, "No access. Invalid token."); } // Make sure the token's User still has permissions to access the file // if (!(tokenServiceBean.canTokenUserEditFile(wmToken))){ tokenServiceBean.expireToken(wmToken); - return errorResponse(Response.Status.UNAUTHORIZED, "No access. Invalid token."); + return error(Response.Status.UNAUTHORIZED, "No access. Invalid token."); } @@ -570,26 +570,26 @@ public Response updateWorldMapLayerData(String jsonLayerData){ // for (String attr : MapLayerMetadata.MANDATORY_JSON_FIELDS ){ if (!jsonInfo.containsKey(attr)){ - return errorResponse( Response.Status.BAD_REQUEST, "Error parsing Json. Key not found [" + attr + "]\nRequired keys are: " + MapLayerMetadata.MANDATORY_JSON_FIELDS ); + return error( Response.Status.BAD_REQUEST, "Error parsing Json. Key not found [" + attr + "]\nRequired keys are: " + MapLayerMetadata.MANDATORY_JSON_FIELDS ); } } // (3) Attempt to retrieve DataverseUser AuthenticatedUser dvUser = wmToken.getDataverseUser(); if (dvUser == null) { - return errorResponse(Response.Status.NOT_FOUND, "DataverseUser not found for token"); + return error(Response.Status.NOT_FOUND, "DataverseUser not found for token"); } // (4) Attempt to retrieve DataFile DataFile dfile = wmToken.getDatafile(); if (dfile==null){ - return errorResponse(Response.Status.NOT_FOUND, "DataFile not found for token"); + return error(Response.Status.NOT_FOUND, "DataFile not found for token"); } // check permissions! if (!permissionService.request( createDataverseRequest(dvUser) ).on(dfile.getOwner()).has(Permission.EditDataset)){ String errMsg = "The user does not have permission to edit metadata for this file. (MapLayerMetadata)"; - return errorResponse(Response.Status.FORBIDDEN, errMsg); + return error(Response.Status.FORBIDDEN, errMsg); } @@ -639,7 +639,7 @@ public Response updateWorldMapLayerData(String jsonLayerData){ MapLayerMetadata savedMapLayerMetadata = mapLayerMetadataService.save(mapLayerMetadata); if (savedMapLayerMetadata==null){ logger.log(Level.SEVERE, "Json: " + jsonLayerData); - return errorResponse( Response.Status.BAD_REQUEST, "Failed to save map layer! Original JSON: "); + return error( Response.Status.BAD_REQUEST, "Failed to save map layer! Original JSON: "); } @@ -658,7 +658,7 @@ public Response updateWorldMapLayerData(String jsonLayerData){ Logger.getLogger(WorldMapRelatedData.class.getName()).log(Level.SEVERE, null, ex); } - return okResponse("map layer object saved!"); + return ok("map layer object saved!"); } // end updateWorldMapLayerData @@ -684,7 +684,7 @@ public Response deleteWorldMapLayerData(String jsonData){ //----------------------------------*/ if (jsonData==null){ logger.log(Level.SEVERE, "jsonData is null"); - return errorResponse( Response.Status.BAD_REQUEST, "No JSON data"); + return error( Response.Status.BAD_REQUEST, "No JSON data"); } // (1) Parse JSON // @@ -693,44 +693,44 @@ public Response deleteWorldMapLayerData(String jsonData){ jsonInfo = Json.createReader(rdr).readObject(); } catch ( JsonParsingException jpe ) { logger.log(Level.SEVERE, "Json: " + jsonData); - return errorResponse( Response.Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage() ); + return error( Response.Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage() ); } // (2) Retrieve token string String worldmapTokenParam = this.retrieveTokenValueFromJson(jsonInfo); if (worldmapTokenParam==null){ - return errorResponse(Response.Status.BAD_REQUEST, "Token not found in JSON request."); + return error(Response.Status.BAD_REQUEST, "Token not found in JSON request."); } // (3) Retrieve WorldMapToken and make sure it is valid // WorldMapToken wmToken = this.tokenServiceBean.retrieveAndRefreshValidToken(worldmapTokenParam); if (wmToken==null){ - return errorResponse(Response.Status.UNAUTHORIZED, "No access. Invalid token."); + return error(Response.Status.UNAUTHORIZED, "No access. Invalid token."); } // (4) Make sure the token's User still has permissions to access the file // if (!(tokenServiceBean.canTokenUserEditFile(wmToken))){ tokenServiceBean.expireToken(wmToken); - return errorResponse(Response.Status.UNAUTHORIZED, "No access. Invalid token."); + return error(Response.Status.UNAUTHORIZED, "No access. Invalid token."); } // (5) Attempt to retrieve DataFile and mapLayerMetadata DataFile dfile = wmToken.getDatafile(); MapLayerMetadata mapLayerMetadata = this.mapLayerMetadataService.findMetadataByDatafile(dfile); if (mapLayerMetadata==null){ - return errorResponse(Response.Status.EXPECTATION_FAILED, "No map layer metadata found."); + return error(Response.Status.EXPECTATION_FAILED, "No map layer metadata found."); } // (6) Delete the mapLayerMetadata // (note: permissions checked here for a second time by the mapLayerMetadataService call) // if (!(this.mapLayerMetadataService.deleteMapLayerMetadataObject(mapLayerMetadata, wmToken.getDataverseUser()))){ - return errorResponse(Response.Status.PRECONDITION_FAILED, "Failed to delete layer"); + return error(Response.Status.PRECONDITION_FAILED, "Failed to delete layer"); }; - return okResponse("Map layer metadata deleted."); + return ok("Map layer metadata deleted."); } // end deleteWorldMapLayerData @@ -753,7 +753,7 @@ public Response deleteWorldMapToken(String jsonData){ //----------------------------------*/ if (jsonData==null){ logger.log(Level.SEVERE, "jsonData is null"); - return errorResponse( Response.Status.BAD_REQUEST, "No JSON data"); + return error( Response.Status.BAD_REQUEST, "No JSON data"); } // (1) Parse JSON // @@ -762,26 +762,26 @@ public Response deleteWorldMapToken(String jsonData){ jsonInfo = Json.createReader(rdr).readObject(); } catch ( JsonParsingException jpe ) { logger.log(Level.SEVERE, "Json: " + jsonData); - return errorResponse( Response.Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage() ); + return error( Response.Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage() ); } // (2) Retrieve token string String worldmapTokenParam = this.retrieveTokenValueFromJson(jsonInfo); if (worldmapTokenParam==null){ - return errorResponse(Response.Status.BAD_REQUEST, "Token not found in JSON request."); + return error(Response.Status.BAD_REQUEST, "Token not found in JSON request."); } // (3) Retrieve WorldMapToken // WorldMapToken wmToken = this.tokenServiceBean.findByName(worldmapTokenParam); if (wmToken==null){ - return errorResponse(Response.Status.NOT_FOUND, "Token not found."); + return error(Response.Status.NOT_FOUND, "Token not found."); } // (4) Delete the token // tokenServiceBean.deleteToken(wmToken); - return okResponse("Token has been deleted."); + return ok("Token has been deleted."); } // end deleteWorldMapLayerData diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java index c3fbb45c4ad..0024aa75767 100644 --- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java +++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java @@ -1,5 +1,6 @@ package edu.harvard.iq.dataverse.util.json; +import edu.emory.mathcs.backport.java.util.Collections; import edu.harvard.iq.dataverse.ControlledVocabularyValue; import edu.harvard.iq.dataverse.DataFile; import edu.harvard.iq.dataverse.Dataset; @@ -12,6 +13,7 @@ import edu.harvard.iq.dataverse.Dataverse; import edu.harvard.iq.dataverse.DataverseContact; import edu.harvard.iq.dataverse.DataverseFacet; +import edu.harvard.iq.dataverse.DataverseTheme; import edu.harvard.iq.dataverse.authorization.DataverseRole; import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUser; import edu.harvard.iq.dataverse.FileMetadata; @@ -33,6 +35,7 @@ import edu.harvard.iq.dataverse.util.DatasetFieldWalker; import edu.harvard.iq.dataverse.util.StringUtil; import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder; +import java.util.ArrayList; import java.util.Set; import javax.json.Json; import javax.json.JsonArrayBuilder; @@ -47,6 +50,7 @@ import java.util.EnumSet; import java.util.LinkedList; import java.util.Map; +import java.util.Optional; import java.util.function.BiConsumer; import java.util.function.BinaryOperator; import java.util.function.Function; @@ -55,7 +59,6 @@ import static java.util.stream.Collectors.toList; import javax.json.JsonArray; import javax.json.JsonObject; -import javax.json.JsonValue; /** * Convert objects to Json. @@ -217,14 +220,26 @@ public static JsonObjectBuilder json(Dataverse dv) { } public static JsonArrayBuilder json(List dataverseContacts) { - JsonArrayBuilder bld = Json.createArrayBuilder(); - for (DataverseContact dc : dataverseContacts) { - bld.add(jsonObjectBuilder() - .add("displayOrder", dc.getDisplayOrder()) - .add("contactEmail", dc.getContactEmail()) - ); + return dataverseContacts.stream() + .map( dc -> jsonObjectBuilder() + .add("displayOrder", dc.getDisplayOrder()) + .add("contactEmail", dc.getContactEmail()) + ).collect( toJsonArray() ); + } + + public static JsonObjectBuilder json( DataverseTheme theme ) { + final NullSafeJsonBuilder baseObject = jsonObjectBuilder() + .add("id", theme.getId() ) + .add("logo", theme.getLogo()) + .add("tagline", theme.getTagline()) + .add("linkUrl", theme.getLinkUrl()) + .add("linkColor", theme.getLinkColor()) + .add("textColor", theme.getTextColor()) + .add("backgroundColor", theme.getBackgroundColor()); + if ( theme.getLogoAlignment() != null ) { + baseObject.add("logoBackgroundColor", theme.getLogoBackgroundColor()); } - return bld; + return baseObject; } public static JsonObjectBuilder json(BuiltinUser user) { @@ -251,19 +266,6 @@ public static JsonObjectBuilder json(Dataset ds) { .add("publicationDate", ds.getPublicationDateFormattedYYYYMMDD()); } - private static String getRootDataverseNameforCitation(Dataset dataset) { - Dataverse root = dataset.getOwner(); - while (root.getOwner() != null) { - root = root.getOwner(); - } - String rootDataverseName = root.getName(); - if (!StringUtil.isEmpty(rootDataverseName)) { - return rootDataverseName + " Dataverse"; - } else { - return ""; - } - } - public static JsonObjectBuilder json(DatasetVersion dsv) { JsonObjectBuilder bld = jsonObjectBuilder() .add("id", dsv.getId()) @@ -304,7 +306,20 @@ public static JsonObjectBuilder json(DatasetVersion dsv) { return bld; } - + + private static String getRootDataverseNameforCitation(Dataset dataset) { + Dataverse root = dataset.getOwner(); + while (root.getOwner() != null) { + root = root.getOwner(); + } + String rootDataverseName = root.getName(); + if (!StringUtil.isEmpty(rootDataverseName)) { + return rootDataverseName + " Dataverse"; + } else { + return ""; + } + } + private static String getLicenseInfo(DatasetVersion dsv) { if (dsv.getTermsOfUseAndAccess().getLicense() != null && dsv.getTermsOfUseAndAccess().getLicense().equals(TermsOfUseAndAccess.License.CC0)) { return "CC0 Waiver"; @@ -585,10 +600,8 @@ public static JsonObjectBuilder json(PrivateUrl privateUrl) { .add("roleAssignment", json(privateUrl.getRoleAssignment())); } - public static JsonObjectBuilder json(T j ) { - if (j instanceof ExplicitGroup) { - ExplicitGroup eg = (ExplicitGroup) j; - JsonArrayBuilder ras = Json.createArrayBuilder(); + public static JsonObjectBuilder json( ExplicitGroup eg ) { + JsonArrayBuilder ras = Json.createArrayBuilder(); for (String u : eg.getContainedRoleAssgineeIdentifiers()) { ras.add(u); } @@ -599,24 +612,15 @@ public static JsonObjectBuilder json(T j ) { .add("description", eg.getDescription()) .add("displayName", eg.getDisplayName()) .add("containedRoleAssignees", ras); - - } else { // implication: (j instanceof DataverseFacet) - DataverseFacet f = (DataverseFacet) j; - return jsonObjectBuilder() - .add("id", String.valueOf(f.getId())) // TODO should just be id I think - .add("name", f.getDatasetFieldType().getDisplayName()); - } } - - public static JsonArrayBuilder json(Collection jc) { - JsonArrayBuilder bld = Json.createArrayBuilder(); - for (T j : jc) { - bld.add(json(j)); - } - return bld; + + public static JsonObjectBuilder json( DataverseFacet aFacet ) { + return jsonObjectBuilder() + .add("id", String.valueOf(aFacet.getId())) // TODO should just be id I think + .add("name", aFacet.getDatasetFieldType().getDisplayName()); } - - public static Collector stringsToJsonArray() { + + public static Collector stringsToJsonArray() { return new Collector() { @Override @@ -651,37 +655,39 @@ public Set characteristics() { }; } - public static Collector toJsonArray() { - return new Collector() { + public static Collector, JsonArrayBuilder> toJsonArray() { + return new Collector, JsonArrayBuilder>() { @Override - public Supplier supplier() { - return () -> Json.createArrayBuilder(); + public Supplier> supplier() { + return () -> new ArrayList<>(); } @Override - public BiConsumer accumulator() { - return (JsonArrayBuilder b, JsonValue s) -> b.add(s); + public BiConsumer, JsonObjectBuilder> accumulator() { + return (t, u) ->t.add(u); } @Override - public BinaryOperator combiner() { + public BinaryOperator> combiner() { return (jab1, jab2) -> { - JsonArrayBuilder retVal = Json.createArrayBuilder(); - jab1.build().forEach(retVal::add); - jab2.build().forEach(retVal::add); - return retVal; + jab1.addAll(jab2); + return jab1; }; } @Override - public Function finisher() { - return Function.identity(); + public Function, JsonArrayBuilder> finisher() { + return (l) -> { + JsonArrayBuilder bld = Json.createArrayBuilder(); + l.forEach( bld::add ); + return bld; + }; } @Override public Set characteristics() { - return EnumSet.of(Collector.Characteristics.IDENTITY_FINISH); + return Collections.emptySet(); } }; } From 231e3ff00b9d173138701601a64993219f103854 Mon Sep 17 00:00:00 2001 From: Michael Bar-Sinai Date: Mon, 26 Sep 2016 01:21:28 +0300 Subject: [PATCH 013/172] Updated Datasets, Roles and some Groups and Admins to the new infrastructure --- .../edu/harvard/iq/dataverse/api/Admin.java | 15 +- .../harvard/iq/dataverse/api/Datasets.java | 363 ++++++++---------- .../edu/harvard/iq/dataverse/api/Groups.java | 8 +- .../iq/dataverse/api/MetadataBlocks.java | 13 +- .../edu/harvard/iq/dataverse/api/Roles.java | 14 +- 5 files changed, 167 insertions(+), 246 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Admin.java b/src/main/java/edu/harvard/iq/dataverse/api/Admin.java index b1ecae4635a..3c946885521 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Admin.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Admin.java @@ -9,7 +9,6 @@ import edu.harvard.iq.dataverse.authorization.UserIdentifier; import edu.harvard.iq.dataverse.authorization.exceptions.AuthenticationProviderFactoryNotFoundException; import edu.harvard.iq.dataverse.authorization.exceptions.AuthorizationSetupException; -import edu.harvard.iq.dataverse.authorization.providers.AuthenticationProviderFactory; import edu.harvard.iq.dataverse.authorization.providers.AuthenticationProviderRow; import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUser; import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUserServiceBean; @@ -36,7 +35,6 @@ import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder; import static edu.harvard.iq.dataverse.util.json.JsonPrinter.*; import java.io.StringReader; -import java.util.List; import java.util.Map; import java.util.logging.Level; import java.util.logging.Logger; @@ -101,14 +99,13 @@ public Response deleteSetting( @PathParam("name") String name ) { @Path("authenticationProviderFactories") @GET public Response listAuthProviderFactories() { - JsonArrayBuilder arb = Json.createArrayBuilder(); - for ( AuthenticationProviderFactory f : authSvc.listProviderFactories() ){ - arb.add( jsonObjectBuilder() + return ok(authSvc.listProviderFactories() + .stream() + .map( f -> jsonObjectBuilder() .add("alias", f.getAlias() ) - .add("info", f.getInfo() )); - } - - return ok(arb); + .add("info", f.getInfo() ) ) + .collect( toJsonArray() ) + ); } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index dfe9a32056b..5e5670ab57a 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -108,19 +108,13 @@ private interface DsVersionHandler { @GET @Path("{id}") public Response getDataset(@PathParam("id") String id) { - - try { - final DataverseRequest r = createDataverseRequest(findUserOrDie()); - - Dataset retrieved = execCommand(new GetDatasetCommand(r, findDatasetOrDie(id))); - DatasetVersion latest = execCommand(new GetLatestAccessibleDatasetVersionCommand(r, retrieved)); + return response( req -> { + final Dataset retrieved = execCommand(new GetDatasetCommand(req, findDatasetOrDie(id))); + final DatasetVersion latest = execCommand(new GetLatestAccessibleDatasetVersionCommand(req, retrieved)); final JsonObjectBuilder jsonbuilder = json(retrieved); return ok(jsonbuilder.add("latestVersion", (latest != null) ? json(latest) : null)); - } catch (WrappedResponse ex) { - return ex.refineResponse("GETting dataset " + id + " failed."); - } - + }); } // TODO: @@ -171,58 +165,46 @@ public Response exportDataset(@QueryParam("persistentId") String persistentId, @ @DELETE @Path("{id}") public Response deleteDataset( @PathParam("id") String id) { - - try { - execCommand( new DeleteDatasetCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id))); + return response( req -> { + execCommand( new DeleteDatasetCommand(req, findDatasetOrDie(id))); return ok("Dataset " + id + " deleted"); - - } catch (WrappedResponse ex) { - return ex.refineResponse( "Failed to delete dataset " + id ); - } - + }); } @DELETE @Path("{id}/destroy") public Response destroyDataset( @PathParam("id") String id) { - try { - execCommand( new DestroyDatasetCommand(findDatasetOrDie(id), createDataverseRequest(findUserOrDie()) )); + return response( req -> { + execCommand( new DestroyDatasetCommand(findDatasetOrDie(id), req) ); return ok("Dataset " + id + " destroyed"); - - } catch (WrappedResponse ex) { - return ex.refineResponse( "Failed to detroy dataset " + id ); - } + }); } @PUT @Path("{id}/citationdate") public Response setCitationDate( @PathParam("id") String id, String dsfTypeName) { - try { - if ( dsfTypeName.trim().isEmpty() ){ - throw new WrappedResponse( badRequest("Please provide a dataset field type in the requst body.") ); - } - DatasetFieldType dsfType = null; - if (!":publicationDate".equals(dsfTypeName)) { - dsfType = datasetFieldSvc.findByName(dsfTypeName); - if (dsfType == null) { - throw new WrappedResponse( badRequest("Dataset Field Type Name " + dsfTypeName + " not found.") ); - } + return response( req -> { + if ( dsfTypeName.trim().isEmpty() ){ + return badRequest("Please provide a dataset field type in the requst body."); + } + DatasetFieldType dsfType = null; + if (!":publicationDate".equals(dsfTypeName)) { + dsfType = datasetFieldSvc.findByName(dsfTypeName); + if (dsfType == null) { + return badRequest("Dataset Field Type Name " + dsfTypeName + " not found."); } - - execCommand(new SetDatasetCitationDateCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id), dsfType)); - - return ok("Citation Date for dataset " + id + " set to: " + (dsfType != null ? dsfType.getDisplayName() : "default")); - - } catch (WrappedResponse ex) { - return ex.refineResponse("Unable to set citation date for dataset " + id + "."); } + + execCommand(new SetDatasetCitationDateCommand(req, findDatasetOrDie(id), dsfType)); + return ok("Citation Date for dataset " + id + " set to: " + (dsfType != null ? dsfType.getDisplayName() : "default")); + }); } @DELETE @Path("{id}/citationdate") public Response useDefaultCitationDate( @PathParam("id") String id) { - return response( ()->{ - execCommand(new SetDatasetCitationDateCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id), null)); + return response( req -> { + execCommand(new SetDatasetCitationDateCommand(req, findDatasetOrDie(id), null)); return ok("Citation Date for dataset " + id + " set to default"); }); } @@ -230,11 +212,10 @@ public Response useDefaultCitationDate( @PathParam("id") String id) { @GET @Path("{id}/versions") public Response listVersions( @PathParam("id") String id ) { - return response( ()->{ + return response( req -> { return ok( execCommand( - new ListVersionsCommand(createDataverseRequest(findUserOrDie()), - findDatasetOrDie(id)) ) + new ListVersionsCommand(req, findDatasetOrDie(id)) ) .stream() .map( d -> json(d) ) .collect(toJsonArray()));}); @@ -243,44 +224,27 @@ public Response listVersions( @PathParam("id") String id ) { @GET @Path("{id}/versions/{versionId}") public Response getVersion( @PathParam("id") String datasetId, @PathParam("versionId") String versionId) { - - try { - DatasetVersion dsv = getDatasetVersionOrDie(createDataverseRequest(findUserOrDie()), versionId, findDatasetOrDie(datasetId)); - + return response( req -> { + DatasetVersion dsv = getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId)); return (dsv == null || dsv.getId() == null) ? notFound("Dataset version not found") : ok(json(dsv)); - - } catch (WrappedResponse ex) { - return ex.getResponse(); - } + }); } @GET @Path("{id}/versions/{versionId}/files") public Response getVersionFiles( @PathParam("id") String datasetId, @PathParam("versionId") String versionId) { - try { - return ok( jsonFileMetadatas( - getDatasetVersionOrDie(createDataverseRequest(findUserOrDie()), - versionId, - findDatasetOrDie(datasetId)).getFileMetadatas())); - } catch (WrappedResponse ex) { - return ex.getResponse(); - } + return response( req -> ok( jsonFileMetadatas( + getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId)).getFileMetadatas())) ); } @GET @Path("{id}/versions/{versionId}/metadata") public Response getVersionMetadata( @PathParam("id") String datasetId, @PathParam("versionId") String versionId) { - - try { - return ok( + return response( req -> ok( jsonByBlocks( - getDatasetVersionOrDie( createDataverseRequest(findUserOrDie()), versionId, findDatasetOrDie(datasetId) ) - .getDatasetFields())); - - } catch (WrappedResponse ex) { - return ex.getResponse(); - } + getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId) ) + .getDatasetFields()))); } @GET @@ -289,8 +253,8 @@ public Response getVersionMetadataBlock( @PathParam("id") String datasetId, @PathParam("versionNumber") String versionNumber, @PathParam("block") String blockName ) { - try { - DatasetVersion dsv = getDatasetVersionOrDie(createDataverseRequest(findUserOrDie()), versionNumber, findDatasetOrDie(datasetId) ); + return response( req -> { + DatasetVersion dsv = getDatasetVersionOrDie(req, versionNumber, findDatasetOrDie(datasetId) ); Map> fieldsByBlock = DatasetField.groupByBlock(dsv.getDatasetFields()); for ( Map.Entry> p : fieldsByBlock.entrySet() ) { @@ -299,11 +263,7 @@ public Response getVersionMetadataBlock( @PathParam("id") String datasetId, } } return notFound("metadata block named " + blockName + " not found"); - - } catch (WrappedResponse ex) { - return ex.getResponse(); - } - + }); } @DELETE @@ -312,45 +272,36 @@ public Response deleteDraftVersion( @PathParam("id") String id, @PathParam("ver if ( ! ":draft".equals(versionId) ) { return badRequest("Only the :draft version can be deleted"); } - - try { - execCommand( new DeleteDatasetVersionCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id)) ); + + return response( req -> { + execCommand( new DeleteDatasetVersionCommand(req, findDatasetOrDie(id)) ); return ok("Draft version of dataset " + id + " deleted"); - } catch (WrappedResponse ex) { - return ex.getResponse(); - } + }); } @GET @Path("{id}/modifyRegistration") public Response updateDatasetTargetURL(@PathParam("id") String id ) { - - try { - execCommand(new UpdateDatasetTargetURLCommand(findDatasetOrDie(id), createDataverseRequest(findUserOrDie()))); + return response( req -> { + execCommand(new UpdateDatasetTargetURLCommand(findDatasetOrDie(id), req)); return ok("Dataset " + id + " target url updated"); - - } catch (WrappedResponse ex) { - return ex.getResponse(); - } - + }); } @GET @Path("/modifyRegistrationAll") public Response updateDatasetTargetURLAll() { - List allDatasets = datasetService.findAll(); - - for (Dataset ds : allDatasets){ - - try { - execCommand(new UpdateDatasetTargetURLCommand(findDatasetOrDie(ds.getId().toString()), createDataverseRequest(findUserOrDie()))); - } catch (WrappedResponse ex) { - Logger.getLogger(Datasets.class.getName()).log(Level.SEVERE, null, ex); - } - - } - return ok("Update All Dataset target url completed"); + return response( req -> { + datasetService.findAll().forEach( ds -> { + try { + execCommand(new UpdateDatasetTargetURLCommand(findDatasetOrDie(ds.getId().toString()), req)); + } catch (WrappedResponse ex) { + Logger.getLogger(Datasets.class.getName()).log(Level.SEVERE, null, ex); + } + }); + return ok("Update All Dataset target url completed"); + }); } @PUT @@ -450,91 +401,6 @@ public Response getLinks(@PathParam("id") String idSupplied ) { } } - - private T handleVersion( String versionId, DsVersionHandler hdl ) - throws WrappedResponse { - switch (versionId) { - case ":latest": return hdl.handleLatest(); - case ":draft": return hdl.handleDraft(); - case ":latest-published": return hdl.handleLatestPublished(); - default: - try { - String[] versions = versionId.split("\\."); - switch (versions.length) { - case 1: - return hdl.handleSpecific(Long.parseLong(versions[0]), (long)0.0); - case 2: - return hdl.handleSpecific( Long.parseLong(versions[0]), Long.parseLong(versions[1]) ); - default: - throw new WrappedResponse(error( Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'")); - } - } catch ( NumberFormatException nfe ) { - throw new WrappedResponse( error( Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'") ); - } - } - } - - private DatasetVersion getDatasetVersionOrDie( final DataverseRequest req, String versionNumber, final Dataset ds ) throws WrappedResponse { - DatasetVersion dsv = execCommand( handleVersion(versionNumber, new DsVersionHandler>(){ - - @Override - public Command handleLatest() { - return new GetLatestAccessibleDatasetVersionCommand(req, ds); - } - - @Override - public Command handleDraft() { - return new GetDraftDatasetVersionCommand(req, ds); - } - - @Override - public Command handleSpecific(long major, long minor) { - return new GetSpecificPublishedDatasetVersionCommand(req, ds, major, minor); - } - - @Override - public Command handleLatestPublished() { - return new GetLatestPublishedDatasetVersionCommand(req, ds); - } - })); - if ( dsv == null || dsv.getId() == null ) { - throw new WrappedResponse( notFound("Dataset version " + versionNumber + " of dataset " + ds.getId() + " not found") ); - } - return dsv; - } - - Dataset findDatasetOrDie( String id ) throws WrappedResponse { - Dataset dataset; - if ( id.equals(PERSISTENT_ID_KEY) ) { - String persistentId = getRequestParameter(PERSISTENT_ID_KEY.substring(1)); - if ( persistentId == null ) { - throw new WrappedResponse( - badRequest("When accessing a dataset based on persistent id, " - + "a " + PERSISTENT_ID_KEY.substring(1) + " query parameter " - + "must be present")); - } - dataset = datasetService.findByGlobalId(persistentId); - if (dataset == null) { - throw new WrappedResponse( notFound("dataset " + persistentId + " not found") ); - } - return dataset; - - } else { - try { - dataset = datasetService.find( Long.parseLong(id) ); - if (dataset == null) { - throw new WrappedResponse( notFound("dataset " + id + " not found") ); - } - return dataset; - } catch ( NumberFormatException nfe ) { - throw new WrappedResponse( - badRequest("Bad dataset id number: '" + id + "'")); - } - } - - } - - /** * @todo Implement this for real as part of * https://github.com/IQSS/dataverse/issues/2579 @@ -615,52 +481,127 @@ public Response createAssignment(String userOrGroup, @PathParam("identifier") St @GET @Path("{identifier}/assignments") public Response getAssignments(@PathParam("identifier") String id) { - return response( ()-> + return response( req -> ok( execCommand( - new ListRoleAssignments(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id))) + new ListRoleAssignments(req, findDatasetOrDie(id))) .stream().map(ra->json(ra)).collect(toJsonArray())) ); } @GET @Path("{id}/privateUrl") public Response getPrivateUrlData(@PathParam("id") String idSupplied) { - try { - PrivateUrl privateUrl = execCommand(new GetPrivateUrlCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied))); - if (privateUrl != null) { - return ok(json(privateUrl)); - } else { - return error(Response.Status.NOT_FOUND, "Private URL not found."); - } - } catch (WrappedResponse wr) { - return wr.getResponse(); - } + return response( req -> { + PrivateUrl privateUrl = execCommand(new GetPrivateUrlCommand(req, findDatasetOrDie(idSupplied))); + return (privateUrl != null) ? ok(json(privateUrl)) + : error(Response.Status.NOT_FOUND, "Private URL not found."); + }); } @POST @Path("{id}/privateUrl") public Response createPrivateUrl(@PathParam("id") String idSupplied) { - return response( ()-> + return response( req -> ok(json(execCommand( - new CreatePrivateUrlCommand(createDataverseRequest(findUserOrDie()), - findDatasetOrDie(idSupplied)))))); + new CreatePrivateUrlCommand(req, findDatasetOrDie(idSupplied)))))); } @DELETE @Path("{id}/privateUrl") public Response deletePrivateUrl(@PathParam("id") String idSupplied) { - try { - User user = findUserOrDie(); + return response( req -> { Dataset dataset = findDatasetOrDie(idSupplied); - PrivateUrl privateUrl = execCommand(new GetPrivateUrlCommand(createDataverseRequest(user), dataset)); + PrivateUrl privateUrl = execCommand(new GetPrivateUrlCommand(req, dataset)); if (privateUrl != null) { - execCommand(new DeletePrivateUrlCommand(createDataverseRequest(user), dataset)); + execCommand(new DeletePrivateUrlCommand(req, dataset)); return ok("Private URL deleted."); } else { - return error(Response.Status.NOT_FOUND, "No Private URL to delete."); + return notFound("No Private URL to delete."); + } + }); + } + + private Dataset findDatasetOrDie( String id ) throws WrappedResponse { + Dataset dataset; + if ( id.equals(PERSISTENT_ID_KEY) ) { + String persistentId = getRequestParameter(PERSISTENT_ID_KEY.substring(1)); + if ( persistentId == null ) { + throw new WrappedResponse( + badRequest("When accessing a dataset based on persistent id, " + + "a " + PERSISTENT_ID_KEY.substring(1) + " query parameter " + + "must be present")); + } + dataset = datasetService.findByGlobalId(persistentId); + if (dataset == null) { + throw new WrappedResponse( notFound("dataset " + persistentId + " not found") ); + } + return dataset; + + } else { + try { + dataset = datasetService.find( Long.parseLong(id) ); + if (dataset == null) { + throw new WrappedResponse( notFound("dataset " + id + " not found") ); + } + return dataset; + } catch ( NumberFormatException nfe ) { + throw new WrappedResponse( + badRequest("Bad dataset id number: '" + id + "'")); } - } catch (WrappedResponse wr) { - return wr.getResponse(); } + } + + + private T handleVersion( String versionId, DsVersionHandler hdl ) + throws WrappedResponse { + switch (versionId) { + case ":latest": return hdl.handleLatest(); + case ":draft": return hdl.handleDraft(); + case ":latest-published": return hdl.handleLatestPublished(); + default: + try { + String[] versions = versionId.split("\\."); + switch (versions.length) { + case 1: + return hdl.handleSpecific(Long.parseLong(versions[0]), (long)0.0); + case 2: + return hdl.handleSpecific( Long.parseLong(versions[0]), Long.parseLong(versions[1]) ); + default: + throw new WrappedResponse(error( Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'")); + } + } catch ( NumberFormatException nfe ) { + throw new WrappedResponse( error( Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'") ); + } + } + } + + private DatasetVersion getDatasetVersionOrDie( final DataverseRequest req, String versionNumber, final Dataset ds ) throws WrappedResponse { + DatasetVersion dsv = execCommand( handleVersion(versionNumber, new DsVersionHandler>(){ + + @Override + public Command handleLatest() { + return new GetLatestAccessibleDatasetVersionCommand(req, ds); + } + + @Override + public Command handleDraft() { + return new GetDraftDatasetVersionCommand(req, ds); + } + + @Override + public Command handleSpecific(long major, long minor) { + return new GetSpecificPublishedDatasetVersionCommand(req, ds, major, minor); + } + @Override + public Command handleLatestPublished() { + return new GetLatestPublishedDatasetVersionCommand(req, ds); + } + })); + if ( dsv == null || dsv.getId() == null ) { + throw new WrappedResponse( notFound("Dataset version " + versionNumber + " of dataset " + ds.getId() + " not found") ); + } + return dsv; + } + } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Groups.java b/src/main/java/edu/harvard/iq/dataverse/api/Groups.java index 671f3f3fb84..41be1ab438d 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Groups.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Groups.java @@ -63,12 +63,8 @@ public Response createIpGroups( JsonObject dto ){ @GET @Path("ip") public Response listIpGroups() { - - JsonArrayBuilder arrBld = Json.createArrayBuilder(); - for ( IpGroup g : ipGroupPrv.findGlobalGroups() ) { - arrBld.add( json(g) ); - } - return ok( arrBld ); + return ok( ipGroupPrv.findGlobalGroups() + .stream().map(g->json(g)).collect(toJsonArray()) ); } @GET diff --git a/src/main/java/edu/harvard/iq/dataverse/api/MetadataBlocks.java b/src/main/java/edu/harvard/iq/dataverse/api/MetadataBlocks.java index 7debb502dc6..26564eaef56 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/MetadataBlocks.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/MetadataBlocks.java @@ -5,14 +5,10 @@ import javax.ws.rs.Path; import javax.ws.rs.Produces; import javax.ws.rs.core.Response; -import javax.json.Json; -import javax.json.JsonArrayBuilder; import static edu.harvard.iq.dataverse.util.json.JsonPrinter.brief; -import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json; import javax.ws.rs.PathParam; import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json; -import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json; -import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json; +import static edu.harvard.iq.dataverse.util.json.JsonPrinter.toJsonArray; /** * Api bean for managing metadata blocks. @@ -24,12 +20,7 @@ public class MetadataBlocks extends AbstractApiBean { @GET public Response list() { - JsonArrayBuilder bld = Json.createArrayBuilder(); - for ( MetadataBlock block : metadataBlockSvc.listMetadataBlocks() ) { - bld.add( brief.json(block) ); - } - - return ok(bld); + return ok(metadataBlockSvc.listMetadataBlocks().stream().map(brief::json).collect(toJsonArray())); } @Path("{identifier}") diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Roles.java b/src/main/java/edu/harvard/iq/dataverse/api/Roles.java index d58c84bb3a4..b3f75e00c5a 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Roles.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Roles.java @@ -38,22 +38,18 @@ public Response viewRole( @PathParam("id") Long id) { @DELETE @Path("{id}") public Response deleteRole( @PathParam("id") Long id ) { - try { - execCommand( new DeleteRoleCommand(createDataverseRequest(findUserOrDie()), findRoleOrDie(id)) ); + return response( req -> { + execCommand( new DeleteRoleCommand(req, findRoleOrDie(id)) ); return ok("role " + id + " deleted."); - - } catch (WrappedResponse ex) { - return ex.refineResponse( "Cannot delete role " + id + "." ); - } + }); } @POST public Response createNewRole( RoleDTO roleDto, @QueryParam("dvo") String dvoIdtf ) { - return response( ()-> ok(json(execCommand( + return response( req -> ok(json(execCommand( new CreateRoleCommand(roleDto.asRole(), - createDataverseRequest(findUserOrDie()), - findDataverseOrDie(dvoIdtf)))))); + req,findDataverseOrDie(dvoIdtf)))))); } private DataverseRole findRoleOrDie( long id ) throws WrappedResponse { From c83f555648f29735c0197b30a8f02048ae450682 Mon Sep 17 00:00:00 2001 From: Michael Bar-Sinai Date: Mon, 26 Sep 2016 01:28:44 +0300 Subject: [PATCH 014/172] Resolved merge conflicts with develop --- .../java/edu/harvard/iq/dataverse/api/Groups.java | 12 ++---------- .../authorization/groups/impl/ipaddress/IpGroup.java | 3 --- 2 files changed, 2 insertions(+), 13 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Groups.java b/src/main/java/edu/harvard/iq/dataverse/api/Groups.java index ea98173e851..2641e36939f 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Groups.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Groups.java @@ -55,18 +55,10 @@ void postConstruct() { public Response postIpGroup( JsonObject dto ){ try { IpGroup grp = new JsonParser().parseIpGroup(dto); -<<<<<<< HEAD - - if ( grp.getPersistedGroupAlias()== null ) { - return error(Response.Status.BAD_REQUEST, "Must provide valid group alias"); - } - grp.setProvider( groupSvc.getIpGroupProvider() ); -======= grp.setGroupProvider( ipGroupPrv ); grp.setPersistedGroupAlias( ipGroupPrv.findAvailableName( grp.getPersistedGroupAlias()==null ? "ipGroup" : grp.getPersistedGroupAlias())); ->>>>>>> develop grp = ipGroupPrv.store(grp); return created("/groups/ip/" + grp.getPersistedGroupAlias(), json(grp) ); @@ -99,11 +91,11 @@ public Response putIpGroups( @PathParam("groupName") String groupName, JsonObjec grp.setGroupProvider( ipGroupPrv ); grp.setPersistedGroupAlias( groupName ); grp = ipGroupPrv.store(grp); - return createdResponse("/groups/ip/" + grp.getPersistedGroupAlias(), json(grp) ); + return created("/groups/ip/" + grp.getPersistedGroupAlias(), json(grp) ); } catch ( Exception e ) { logger.log( Level.WARNING, "Error while storing a new IP group: " + e.getMessage(), e); - return errorResponse(Response.Status.INTERNAL_SERVER_ERROR, "Error: " + e.getMessage() ); + return error(Response.Status.INTERNAL_SERVER_ERROR, "Error: " + e.getMessage() ); } } diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/IpGroup.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/IpGroup.java index b4b801ad668..d6ee006bc52 100644 --- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/IpGroup.java +++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/IpGroup.java @@ -157,12 +157,9 @@ public String toString() { return "[IpGroup alias:" + getPersistedGroupAlias() +" id:" + getId() + " ranges:" + getIpv4Ranges() + "," + getIpv6Ranges() + "]"; } -<<<<<<< HEAD -======= private void updateRangeOwnership( Collection ranges ) { for ( IpAddressRange rng : ranges ) { rng.setOwner(this); } } ->>>>>>> develop } From e8d19b36fb51c321a80cc0dff482cbcd6ba3a35c Mon Sep 17 00:00:00 2001 From: Philip Durbin Date: Tue, 27 Sep 2016 09:46:22 -0400 Subject: [PATCH 015/172] Put maintenance page back in branch #2588 This reverts commit be727595f7797f6b9290f31b65595e49fb710d4c. --- .../etc/maintenance/HarvardShield_RGB.png | Bin 0 -> 15728 bytes 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ze960#8m*x8A%EAw(*zeL9V02-P|v>9NURKAjk=md^>xrOfJ&D*)}uvAs>Tf)A&q5=WOLSMynk#~=g)=N zHZDUvODQZ%4n`avDeOPb@`8i`P3Q=2ZPJ)=BJ;QIlf!z3y!o|@b1t>NF3BdOSvhRk zjbgu!{h>rcX(eMQ`@10N zJ2GXiET(6}sx0oWrHk)ZZW@uBvL*qFeCW)+j zqRp_QqWX_1kUO36-n}XdZzX7vY(v8Tdhiid3aqUcR+f^+RAF2_GwL?q$xoUkP**UW z85=u1giK87o=tUPg?Y{<9FA;$*k16AXwrdVH44NDsqT%F(Xr=+mzACTO+Iijr3#{P z1BGHColy(3v}pJvWD0~krgex<&!)vik?vtS<+C$X4`dWsN;xZT5R-$)Ze0=)@4#`Y zG}Bi?SU{|YyFGQpF=9cW3r%#sxU` + + + + Harvard Dataverse + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    +
    + +
    + Harvard Dataverse +
    +
    + A collaboration with Harvard Library, Harvard University IT, and IQSS +
    +
    +
    +
    +
    +
    +

    We apologize for the service interruption.

    +

    The Harvard Dataverse is currently undergoing maintenance. At this time both the application and APIs are not able to be used. However, the datasets stored in the Harvard Dataverse are fine and not impacted by this maintenance.

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    If you have any comments, questions or concerns, please reach out to support@dataverse.org.

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    + + + diff --git a/doc/sphinx-guides/source/installation/administration.rst b/doc/sphinx-guides/source/installation/administration.rst index 59cf11652a3..b2f908bd8f1 100644 --- a/doc/sphinx-guides/source/installation/administration.rst +++ b/doc/sphinx-guides/source/installation/administration.rst @@ -67,6 +67,13 @@ https://github.com/IQSS/dataverse/issues/2595 contains some information on enabl There is a database table called ``actionlogrecord`` that captures events that may be of interest. See https://github.com/IQSS/dataverse/issues/2729 for more discussion around this table. +Maintenance +---------- + +When you have scheduled down time for your production servers, we provide a `sample maintenance page <../_static/installation/files/etc/maintenance/maintenance.xhtml>`_ for you to use. To download, right-click and select "Save Link As". + +The maintenance page is intended to be a static page served by Apache to provide users with a nicer, more informative experience when the site is unavailable. + User Administration ------------------- From 5c3b88e8626401128f16213a408052560be10a5f Mon Sep 17 00:00:00 2001 From: Michael Bar-Sinai Date: Tue, 27 Sep 2016 17:48:33 +0300 Subject: [PATCH 016/172] Updated docs and expected return code in DataversesIT --- .../providers/builtin/BuiltinUserServiceBean.java | 6 ++---- .../engine/command/impl/DestroyDatasetCommand.java | 3 +-- .../java/edu/harvard/iq/dataverse/api/DataversesIT.java | 5 +++-- 3 files changed, 6 insertions(+), 8 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/BuiltinUserServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/BuiltinUserServiceBean.java index 760b7a2986d..d5459a2fb75 100644 --- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/BuiltinUserServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/BuiltinUserServiceBean.java @@ -46,16 +46,14 @@ public String encryptPassword(String plainText) { } public BuiltinUser save(BuiltinUser dataverseUser) { - /** - * Trim the email address no matter what the user entered or is entered + /* Trim the email address no matter what the user entered or is entered * on their behalf in the case of Shibboleth assertions. * * @todo Why doesn't Bean Validation report that leading and trailing * whitespace in an email address is a problem? */ dataverseUser.setEmail(dataverseUser.getEmail().trim()); - /** - * We throw a proper IllegalArgumentException here because otherwise + /* We throw a proper IllegalArgumentException here because otherwise * from the API you get a 500 response and "Can't save user: null". */ ValidatorFactory factory = Validation.buildDefaultValidatorFactory(); diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java index 1f27ba0a199..12ac09af935 100644 --- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java +++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java @@ -8,7 +8,6 @@ import edu.harvard.iq.dataverse.RoleAssignment; import edu.harvard.iq.dataverse.authorization.Permission; import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser; -import edu.harvard.iq.dataverse.authorization.users.User; import edu.harvard.iq.dataverse.engine.command.AbstractVoidCommand; import edu.harvard.iq.dataverse.engine.command.CommandContext; import edu.harvard.iq.dataverse.engine.command.DataverseRequest; @@ -25,7 +24,7 @@ import java.util.logging.Logger; /** - * Same as {@link DeleteDatasetCommand}, but does not stop it the dataset is + * Same as {@link DeleteDatasetCommand}, but does not stop if the dataset is * published. This command is reserved for super-users, if at all. * * @author michael diff --git a/src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java b/src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java index 2d243e9bb50..6508f46d7fb 100644 --- a/src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java +++ b/src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java @@ -3,6 +3,7 @@ import com.jayway.restassured.RestAssured; import com.jayway.restassured.response.Response; import java.util.logging.Logger; +import javax.ws.rs.core.Response.Status; import org.junit.AfterClass; import org.junit.BeforeClass; import org.junit.Test; @@ -49,8 +50,8 @@ public void testAttemptToCreateDuplicateAlias() throws Exception { logger.info("Attempting to creating dataverse with alias '" + dataverseAlias2 + "' (uppercase version of existing '" + dataverseAlias1 + "' dataverse, should fail)..."); Response attemptToCreateDataverseWithDuplicateAlias = UtilIT.createDataverse(dataverseAlias2, apiToken1); attemptToCreateDataverseWithDuplicateAlias.prettyPrint(); - assertEquals(400, attemptToCreateDataverseWithDuplicateAlias.getStatusCode()); - + assertEquals(403, attemptToCreateDataverseWithDuplicateAlias.getStatusCode()); + logger.info("Deleting dataverse " + dataverseAlias1); Response deleteDataverse1Response = UtilIT.deleteDataverse(dataverseAlias1, apiToken1); deleteDataverse1Response.prettyPrint(); From d315204aa08c0141141b78cc547b05d77c1e9098 Mon Sep 17 00:00:00 2001 From: "Calvin Winkowski (Telnoratti)" Date: Tue, 27 Sep 2016 12:43:45 -0400 Subject: [PATCH 017/172] Use CONFIG_DEFAULTS for postgres user. --- scripts/installer/install | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/installer/install b/scripts/installer/install index 744f86f0997..8e1008ec997 100755 --- a/scripts/installer/install +++ b/scripts/installer/install @@ -830,7 +830,7 @@ else my $psql_command = $psql_exec - . "/createdb -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -U dvnapp " + . "/createdb -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -U $CONFIG_DEFAULTS{'POSTGRES_USER'} " . $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} . " --owner=" . $CONFIG_DEFAULTS{'POSTGRES_USER'}; From efa4372d026d0043cdbadc82bc127e6cd118e157 Mon Sep 17 00:00:00 2001 From: Michael Bar-Sinai Date: Thu, 29 Sep 2016 00:02:14 +0300 Subject: [PATCH 018/172] Updated integration tests. Updated some Admin methods to use new infrastructure --- .../edu/harvard/iq/dataverse/api/Admin.java | 19 ++++++------------- .../harvard/iq/dataverse/api/DatasetsIT.java | 4 ++-- 2 files changed, 8 insertions(+), 15 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Admin.java b/src/main/java/edu/harvard/iq/dataverse/api/Admin.java index 3c946885521..c519d00080e 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Admin.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Admin.java @@ -31,7 +31,6 @@ import javax.ws.rs.Path; import javax.ws.rs.PathParam; import javax.ws.rs.core.Response; - import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder; import static edu.harvard.iq.dataverse.util.json.JsonPrinter.*; import java.io.StringReader; @@ -112,13 +111,8 @@ public Response listAuthProviderFactories() { @Path("authenticationProviders") @GET public Response listAuthProviders() { - JsonArrayBuilder arb = Json.createArrayBuilder(); - for ( AuthenticationProviderRow r : - em.createNamedQuery("AuthenticationProviderRow.findAll", AuthenticationProviderRow.class).getResultList() ){ - arb.add( json(r) ); - } - - return ok(arb); + return ok(em.createNamedQuery("AuthenticationProviderRow.findAll", AuthenticationProviderRow.class).getResultList() + .stream().map( r->json(r) ).collect( toJsonArray() )); } @Path("authenticationProviders") @@ -157,13 +151,13 @@ public Response showProvider( @PathParam("id") String id ) { public Response enableAuthenticationProvider( @PathParam("id")String id, String body ) { if ( ! Util.isBoolean(body) ) { - return error(Response.Status.BAD_REQUEST, "Illegal value '" + body + "'. Try 'true' or 'false'"); + return error(Response.Status.BAD_REQUEST, "Illegal value '" + body + "'. Use 'true' or 'false'"); } boolean enable = Util.isTrue(body); AuthenticationProviderRow row = em.find(AuthenticationProviderRow.class, id); if ( row == null ) { - return error( Status.NOT_FOUND, "Can't find authentication provider with id '" + id + "'"); + return notFound("Can't find authentication provider with id '" + id + "'"); } row.setEnabled(enable); @@ -179,11 +173,10 @@ public Response enableAuthenticationProvider( @PathParam("id")String id, String return ok(String.format("Authentication Provider %s enabled", row.getId())); } catch (AuthenticationProviderFactoryNotFoundException ex) { - return error(Response.Status.BAD_REQUEST, - String.format("Can't instantiate provider, as there's no factory with alias %s", row.getFactoryAlias())); + return notFound(String.format("Can't instantiate provider, as there's no factory with alias %s", row.getFactoryAlias())); } catch (AuthorizationSetupException ex) { logger.log(Level.WARNING, "Error instantiating authentication provider: " + ex.getMessage(), ex); - return error(Response.Status.BAD_REQUEST, + return error(Status.INTERNAL_SERVER_ERROR, String.format("Can't instantiate provider: %s", ex.getMessage())); } diff --git a/src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java b/src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java index 57114710ca7..ba122ebc23f 100644 --- a/src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java +++ b/src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java @@ -303,7 +303,7 @@ public void testPrivateUrl() { Response tryToCreatePrivateUrlWhenExisting = UtilIT.privateUrlCreate(datasetId, apiToken); tryToCreatePrivateUrlWhenExisting.prettyPrint(); - assertEquals(BAD_REQUEST.getStatusCode(), tryToCreatePrivateUrlWhenExisting.getStatusCode()); + assertEquals(FORBIDDEN.getStatusCode(), tryToCreatePrivateUrlWhenExisting.getStatusCode()); Response publishDataverse = UtilIT.publishDataverseViaSword(dataverseAlias, apiToken); assertEquals(OK.getStatusCode(), publishDataverse.getStatusCode()); @@ -322,7 +322,7 @@ public void testPrivateUrl() { Response tryToCreatePrivateUrlToPublishedVersion = UtilIT.privateUrlCreate(datasetId, apiToken); tryToCreatePrivateUrlToPublishedVersion.prettyPrint(); - assertEquals(BAD_REQUEST.getStatusCode(), tryToCreatePrivateUrlToPublishedVersion.getStatusCode()); + assertEquals(FORBIDDEN.getStatusCode(), tryToCreatePrivateUrlToPublishedVersion.getStatusCode()); String newTitle = "I am changing the title"; Response updatedMetadataResponse = UtilIT.updateDatasetTitleViaSword(dataset1PersistentId, newTitle, apiToken); From 9b5f7aff4937c113d1a641288679d1ed70f206d5 Mon Sep 17 00:00:00 2001 From: Philip Durbin Date: Thu, 29 Sep 2016 12:41:04 -0400 Subject: [PATCH 019/172] stupid EJB timer. kill it #3336 #3358 --- scripts/database/homebrew/delete-all | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/database/homebrew/delete-all b/scripts/database/homebrew/delete-all index 9a2d0239b45..2d2c2110c6b 100755 --- a/scripts/database/homebrew/delete-all +++ b/scripts/database/homebrew/delete-all @@ -1,5 +1,6 @@ #!/bin/sh /Applications/NetBeans/glassfish4/glassfish/bin/asadmin stop-domain +rm -rf /Applications/NetBeans/glassfish4/glassfish/domains/domain1/generated scripts/database/homebrew/drop-database scripts/search/clear rm -rf ~/dataverse/files From e8a9116cab0ccaddde378687425e229ec690f2b2 Mon Sep 17 00:00:00 2001 From: Stephen Kraffmiller Date: Thu, 6 Oct 2016 10:04:58 -0400 Subject: [PATCH 020/172] #2465 File Landing Page move download button logic and processing out of Dataset Page --- .../edu/harvard/iq/dataverse/DataFile.java | 81 +- .../iq/dataverse/DataFileServiceBean.java | 38 +- .../edu/harvard/iq/dataverse/DatasetPage.java | 985 +++--------------- .../iq/dataverse/EditDatafilesPage.java | 4 +- .../iq/dataverse/FileDownloadHelper.java | 187 ++++ .../iq/dataverse/FileDownloadServiceBean.java | 378 +++++++ .../edu/harvard/iq/dataverse/FilePage.java | 155 ++- .../iq/dataverse/GuestbookResponse.java | 45 +- .../GuestbookResponseServiceBean.java | 273 ++++- .../iq/dataverse/NavigationWrapper.java | 2 +- .../iq/dataverse/api/DownloadInstance.java | 37 + .../dataverse/api/DownloadInstanceWriter.java | 16 + .../datasetutility/TwoRavensHelper.java | 253 +++++ .../WorldMapPermissionHelper.java | 598 +++++++++++ src/main/webapp/dataset-citation.xhtml | 6 +- src/main/webapp/dataset.xhtml | 191 +--- src/main/webapp/editFilesFragment.xhtml | 15 +- .../file-download-button-fragment.xhtml | 237 +++++ .../webapp/file-download-popup-fragment.xhtml | 153 +++ src/main/webapp/file.xhtml | 65 +- src/main/webapp/filesFragment.xhtml | 255 +---- .../filesFragmentWorldMapTestQuery.xhtml | 2 +- src/main/webapp/subset/gui_subset.xhtml | 4 +- 23 files changed, 2665 insertions(+), 1315 deletions(-) create mode 100644 src/main/java/edu/harvard/iq/dataverse/FileDownloadHelper.java create mode 100644 src/main/java/edu/harvard/iq/dataverse/FileDownloadServiceBean.java create mode 100644 src/main/java/edu/harvard/iq/dataverse/datasetutility/TwoRavensHelper.java create mode 100644 src/main/java/edu/harvard/iq/dataverse/datasetutility/WorldMapPermissionHelper.java create mode 100644 src/main/webapp/file-download-button-fragment.xhtml create mode 100644 src/main/webapp/file-download-popup-fragment.xhtml diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFile.java b/src/main/java/edu/harvard/iq/dataverse/DataFile.java index 057faf4211e..a55c043e3ad 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataFile.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataFile.java @@ -7,6 +7,7 @@ import edu.harvard.iq.dataverse.dataaccess.DataFileIO; import edu.harvard.iq.dataverse.ingest.IngestReport; import edu.harvard.iq.dataverse.ingest.IngestRequest; +import edu.harvard.iq.dataverse.util.BundleUtil; import edu.harvard.iq.dataverse.util.FileUtil; import edu.harvard.iq.dataverse.util.ShapefileHandler; import java.io.IOException; @@ -16,12 +17,14 @@ import java.nio.file.Path; import java.nio.file.Paths; import java.nio.file.Files; -import java.util.Comparator; +import java.util.Arrays; import javax.persistence.Entity; import javax.persistence.OneToMany; import javax.persistence.OneToOne; import javax.persistence.CascadeType; import javax.persistence.Column; +import javax.persistence.EnumType; +import javax.persistence.Enumerated; import javax.persistence.Index; import javax.persistence.JoinColumn; import javax.persistence.JoinTable; @@ -62,9 +65,56 @@ public class DataFile extends DvObject implements Comparable { @Column( nullable = false ) private String fileSystemName; - - @Column( nullable = false ) - private String md5; + + /** + * End users will see "SHA-1" (with a hyphen) rather than "SHA1" in the GUI + * and API but in the "datafile" table we persist "SHA1" (no hyphen) for + * type safety (using keys of the enum). In the "setting" table, we persist + * "SHA-1" (with a hyphen) to match the GUI and the "Algorithm Name" list at + * https://docs.oracle.com/javase/8/docs/technotes/guides/security/StandardNames.html#MessageDigest + * + * The list of types should be limited to the list above in the technote + * because the string gets passed into MessageDigest.getInstance() and you + * can't just pass in any old string. + */ + public enum ChecksumType { + + MD5("MD5"), + SHA1("SHA-1"); + + private final String text; + + private ChecksumType(final String text) { + this.text = text; + } + + public static ChecksumType fromString(String text) { + if (text != null) { + for (ChecksumType checksumType : ChecksumType.values()) { + if (text.equals(checksumType.text)) { + return checksumType; + } + } + } + throw new IllegalArgumentException("ChecksumType must be one of these values: " + Arrays.asList(ChecksumType.values()) + "."); + } + + @Override + public String toString() { + return text; + } + } + + @Column(nullable = false) + @Enumerated(EnumType.STRING) + private ChecksumType checksumType; + + /** + * Examples include "f622da34d54bdc8ee541d6916ac1c16f" as an MD5 value or + * "3a484dfdb1b429c2e15eb2a735f1f5e4d5b04ec6" as a SHA-1 value" + */ + @Column(nullable = false) + private String checksumValue; @Column(nullable=true) private Long filesize; // Number of bytes in file. Allows 0 and null, negative numbers not permitted @@ -370,15 +420,26 @@ public void setRestricted(boolean restricted) { this.restricted = restricted; } + public ChecksumType getChecksumType() { + return checksumType; + } - public String getmd5() { - return this.md5; + public void setChecksumType(ChecksumType checksumType) { + this.checksumType = checksumType; } - - public void setmd5(String md5) { - this.md5 = md5; + + public String getChecksumValue() { + return this.checksumValue; } - + + public void setChecksumValue(String checksumValue) { + this.checksumValue = checksumValue; + } + + public String getOriginalChecksumType() { + return BundleUtil.getStringFromBundle("file.originalChecksumType", Arrays.asList(this.checksumType.toString()) ); + } + public DataFileIO getAccessObject() throws IOException { DataFileIO dataAccess = DataAccess.createDataAccessObject(this); diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java index c2ecce1543e..49fc1df55c8 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java @@ -255,7 +255,7 @@ public DataFile findCheapAndEasy(Long id) { Object[] result = null; try { - result = (Object[]) em.createNativeQuery("SELECT t0.ID, t0.CREATEDATE, t0.INDEXTIME, t0.MODIFICATIONTIME, t0.PERMISSIONINDEXTIME, t0.PERMISSIONMODIFICATIONTIME, t0.PUBLICATIONDATE, t0.CREATOR_ID, t0.RELEASEUSER_ID, t0.PREVIEWIMAGEAVAILABLE, t1.CONTENTTYPE, t1.FILESYSTEMNAME, t1.FILESIZE, t1.INGESTSTATUS, t1.MD5, t1.RESTRICTED, t3.ID, t3.AUTHORITY, t3.IDENTIFIER FROM DVOBJECT t0, DATAFILE t1, DVOBJECT t2, DATASET t3 WHERE ((t0.ID = " + id + ") AND (t0.OWNER_ID = t2.ID) AND (t2.ID = t3.ID) AND (t1.ID = t0.ID))").getSingleResult(); + result = (Object[]) em.createNativeQuery("SELECT t0.ID, t0.CREATEDATE, t0.INDEXTIME, t0.MODIFICATIONTIME, t0.PERMISSIONINDEXTIME, t0.PERMISSIONMODIFICATIONTIME, t0.PUBLICATIONDATE, t0.CREATOR_ID, t0.RELEASEUSER_ID, t0.PREVIEWIMAGEAVAILABLE, t1.CONTENTTYPE, t1.FILESYSTEMNAME, t1.FILESIZE, t1.INGESTSTATUS, t1.CHECKSUMVALUE, t1.RESTRICTED, t3.ID, t3.AUTHORITY, t3.IDENTIFIER, t1.CHECKSUMTYPE FROM DVOBJECT t0, DATAFILE t1, DVOBJECT t2, DATASET t3 WHERE ((t0.ID = " + id + ") AND (t0.OWNER_ID = t2.ID) AND (t2.ID = t3.ID) AND (t1.ID = t0.ID))").getSingleResult(); } catch (Exception ex) { return null; } @@ -346,14 +346,14 @@ public DataFile findCheapAndEasy(Long id) { String md5 = (String) result[14]; if (md5 != null) { - dataFile.setmd5(md5); + dataFile.setChecksumValue(md5); } Boolean restricted = (Boolean) result[15]; if (restricted != null) { dataFile.setRestricted(restricted); } - + Dataset owner = new Dataset(); @@ -362,6 +362,17 @@ public DataFile findCheapAndEasy(Long id) { owner.setId((Long)result[16]); owner.setAuthority((String)result[17]); owner.setIdentifier((String)result[18]); + + String checksumType = (String) result[19]; + if (checksumType != null) { + try { + // In the database we store "SHA1" rather than "SHA-1". + DataFile.ChecksumType typeFromStringInDatabase = DataFile.ChecksumType.valueOf(checksumType); + dataFile.setChecksumType(typeFromStringInDatabase); + } catch (IllegalArgumentException ex) { + logger.info("Exception trying to convert " + checksumType + " to enum: " + ex); + } + } dataFile.setOwner(owner); @@ -461,11 +472,11 @@ public void findFileMetadataOptimizedExperimental(Dataset owner, DatasetVersion } dataTagsResults = null; - logger.fine("Retrieved "+i+" data tags."); + logger.fine("Retrieved "+i+" data tags."); i = 0; - List fileResults = em.createNativeQuery("SELECT t0.ID, t0.CREATEDATE, t0.INDEXTIME, t0.MODIFICATIONTIME, t0.PERMISSIONINDEXTIME, t0.PERMISSIONMODIFICATIONTIME, t0.PUBLICATIONDATE, t0.CREATOR_ID, t0.RELEASEUSER_ID, t1.CONTENTTYPE, t1.FILESYSTEMNAME, t1.FILESIZE, t1.INGESTSTATUS, t1.MD5, t1.RESTRICTED FROM DVOBJECT t0, DATAFILE t1 WHERE ((t0.OWNER_ID = " + owner.getId() + ") AND ((t1.ID = t0.ID) AND (t0.DTYPE = 'DataFile')))").getResultList(); + List fileResults = em.createNativeQuery("SELECT t0.ID, t0.CREATEDATE, t0.INDEXTIME, t0.MODIFICATIONTIME, t0.PERMISSIONINDEXTIME, t0.PERMISSIONMODIFICATIONTIME, t0.PUBLICATIONDATE, t0.CREATOR_ID, t0.RELEASEUSER_ID, t1.CONTENTTYPE, t1.FILESYSTEMNAME, t1.FILESIZE, t1.INGESTSTATUS, t1.CHECKSUMVALUE, t1.RESTRICTED, t1.CHECKSUMTYPE FROM DVOBJECT t0, DATAFILE t1 WHERE ((t0.OWNER_ID = " + owner.getId() + ") AND ((t1.ID = t0.ID) AND (t0.DTYPE = 'DataFile')))").getResultList(); for (Object[] result : fileResults) { Integer file_id = (Integer) result[0]; @@ -544,13 +555,24 @@ public void findFileMetadataOptimizedExperimental(Dataset owner, DatasetVersion String md5 = (String) result[13]; if (md5 != null) { - dataFile.setmd5(md5); + dataFile.setChecksumValue(md5); } Boolean restricted = (Boolean) result[14]; if (restricted != null) { dataFile.setRestricted(restricted); } + + String checksumType = (String) result[15]; + if (checksumType != null) { + try { + // In the database we store "SHA1" rather than "SHA-1". + DataFile.ChecksumType typeFromStringInDatabase = DataFile.ChecksumType.valueOf(checksumType); + dataFile.setChecksumType(typeFromStringInDatabase); + } catch (IllegalArgumentException ex) { + logger.info("Exception trying to convert " + checksumType + " to enum: " + ex); + } + } // TODO: // - if ingest status is "bad", look up the ingest report; @@ -1080,7 +1102,7 @@ public boolean isFileClassDocument (DataFile file) { return false; } - // "Documents": PDF, assorted MS docs, etc. + // "Documents": PDF, assorted MS docs, etc. String contentType = file.getContentType(); int scIndex = 0; @@ -1199,4 +1221,4 @@ public void populateFileSearchCard(SolrSearchResult solrSearchResult) { solrSearchResult.setEntity(this.findCheapAndEasy(solrSearchResult.getEntityId())); } -} +} \ No newline at end of file diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java index 55811ac8b1a..10dd7f36847 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java @@ -78,11 +78,14 @@ import java.util.HashSet; import javax.faces.model.SelectItem; import java.util.logging.Level; +import edu.harvard.iq.dataverse.datasetutility.TwoRavensHelper; +import edu.harvard.iq.dataverse.datasetutility.WorldMapPermissionHelper; import javax.faces.component.UIComponent; import javax.faces.component.UIInput; import javax.faces.event.AjaxBehaviorEvent; +import javax.faces.context.ExternalContext; import org.apache.commons.lang.StringEscapeUtils; import org.primefaces.component.tabview.TabView; @@ -148,6 +151,8 @@ public enum DisplayMode { @EJB GuestbookResponseServiceBean guestbookResponseService; @EJB + FileDownloadServiceBean fileDownloadService; + @EJB DataverseLinkingServiceBean dvLinkingService; @EJB DatasetLinkingServiceBean dsLinkingService; @@ -186,6 +191,7 @@ public enum DisplayMode { private List