diff --git a/doc/release-notes/10339-workflow.md b/doc/release-notes/10339-workflow.md new file mode 100644 index 00000000000..90d08dabb1f --- /dev/null +++ b/doc/release-notes/10339-workflow.md @@ -0,0 +1,3 @@ +The computational workflow metadata block has been updated to present a clickable link for the External Code Repository URL field. + +Release notes should include the usual instructions, for those who have installed this optional block, to update the computational_workflow block. (PR#10441) \ No newline at end of file diff --git a/doc/sphinx-guides/source/developers/testing.rst b/doc/sphinx-guides/source/developers/testing.rst index 2ea85913d42..3910a40b118 100755 --- a/doc/sphinx-guides/source/developers/testing.rst +++ b/doc/sphinx-guides/source/developers/testing.rst @@ -142,6 +142,8 @@ Generally speaking, unit tests have been flagged as non-essential because they a You should not feel obligated to run these tests continuously but you can use the ``mvn`` command above to run them. To iterate on the unit test in Netbeans and execute it with "Run -> Test File", you must temporarily comment out the annotation flagging the test as non-essential. +.. _integration-tests: + Integration Tests ----------------- @@ -392,10 +394,10 @@ Run this as the "dataverse" user. Note that after deployment the file "/usr/local/payara6/glassfish/domains/domain1/config/jacoco.exec" exists and is empty. -Run API Tests -~~~~~~~~~~~~~ +Run API Tests to Determine Code Coverage +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Note that even though you see "docker-aio" in the command below, we assume you are not necessarily running the test suite within Docker. (Some day we'll probably move this script to another directory.) For this reason, we pass the URL with the normal port (8080) that app servers run on to the ``run-test-suite.sh`` script. +Note that if you are looking for how to run API tests generally, you should refer to :ref:`integration-tests`. Note that "/usr/local/payara6/glassfish/domains/domain1/config/jacoco.exec" will become non-empty after you stop and start Payara. You must stop and start Payara before every run of the integration test suite. @@ -405,7 +407,8 @@ Note that "/usr/local/payara6/glassfish/domains/domain1/config/jacoco.exec" will /usr/local/payara6/bin/asadmin start-domain git clone https://github.com/IQSS/dataverse.git cd dataverse - conf/docker-aio/run-test-suite.sh http://localhost:8080 + TESTS=$(#VALUE FALSE FALSE TRUE FALSE TRUE FALSE computationalworkflow workflowDocumentation Documentation A link (URL) to the documentation or text describing the Computational Workflow and its use textbox 2 FALSE FALSE TRUE FALSE TRUE FALSE computationalworkflow #controlledVocabulary DatasetField Value identifier displayOrder workflowType Common Workflow Language (CWL) workflowtype_cwl 1 diff --git a/src/main/java/edu/harvard/iq/dataverse/FileDownloadServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/FileDownloadServiceBean.java index de3f4d2ab56..c5073693ab2 100644 --- a/src/main/java/edu/harvard/iq/dataverse/FileDownloadServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/FileDownloadServiceBean.java @@ -382,28 +382,26 @@ public void explore(GuestbookResponse guestbookResponse, FileMetadata fmd, Exter } } - public void downloadDatasetCitationXML(Dataset dataset) { - downloadCitationXML(null, dataset, false); + public void downloadDatasetCitationXML(DatasetVersion version) { + // DatasetVersion-level citation: + DataCitation citation=null; + citation = new DataCitation(version); + String fileNameString; + fileNameString = "attachment;filename=" + getFileNameFromPid(citation.getPersistentId()) + ".xml"; + downloadXML(citation, fileNameString); } public void downloadDatafileCitationXML(FileMetadata fileMetadata) { - downloadCitationXML(fileMetadata, null, false); + downloadCitationXML(fileMetadata, false); } public void downloadDirectDatafileCitationXML(FileMetadata fileMetadata) { - downloadCitationXML(fileMetadata, null, true); + downloadCitationXML(fileMetadata, true); } - public void downloadCitationXML(FileMetadata fileMetadata, Dataset dataset, boolean direct) { - DataCitation citation=null; - if (dataset != null){ - citation = new DataCitation(dataset.getLatestVersion()); - } else { - citation= new DataCitation(fileMetadata, direct); - } - FacesContext ctx = FacesContext.getCurrentInstance(); - HttpServletResponse response = (HttpServletResponse) ctx.getExternalContext().getResponse(); - response.setContentType("text/xml"); + public void downloadCitationXML(FileMetadata fileMetadata, boolean direct) { + DataCitation citation=null; + citation= new DataCitation(fileMetadata, direct); String fileNameString; if (fileMetadata == null || fileMetadata.getLabel() == null) { // Dataset-level citation: @@ -412,43 +410,46 @@ public void downloadCitationXML(FileMetadata fileMetadata, Dataset dataset, bool // Datafile-level citation: fileNameString = "attachment;filename=" + getFileNameFromPid(citation.getPersistentId()) + "-" + FileUtil.getCiteDataFileFilename(citation.getFileTitle(), FileUtil.FileCitationExtension.ENDNOTE); } + downloadXML(citation, fileNameString); + } + + public void downloadXML(DataCitation citation, String fileNameString) { + FacesContext ctx = FacesContext.getCurrentInstance(); + HttpServletResponse response = (HttpServletResponse) ctx.getExternalContext().getResponse(); + response.setContentType("text/xml"); response.setHeader("Content-Disposition", fileNameString); + try { ServletOutputStream out = response.getOutputStream(); citation.writeAsEndNoteCitation(out); out.flush(); ctx.responseComplete(); } catch (IOException e) { - } } - - public void downloadDatasetCitationRIS(Dataset dataset) { - downloadCitationRIS(null, dataset, false); + public void downloadDatasetCitationRIS(DatasetVersion version) { + // DatasetVersion-level citation: + DataCitation citation=null; + citation = new DataCitation(version); + String fileNameString; + fileNameString = "attachment;filename=" + getFileNameFromPid(citation.getPersistentId()) + ".ris"; + downloadRIS(citation, fileNameString); } public void downloadDatafileCitationRIS(FileMetadata fileMetadata) { - downloadCitationRIS(fileMetadata, null, false); + downloadCitationRIS(fileMetadata, false); } public void downloadDirectDatafileCitationRIS(FileMetadata fileMetadata) { - downloadCitationRIS(fileMetadata, null, true); + downloadCitationRIS(fileMetadata, true); } - public void downloadCitationRIS(FileMetadata fileMetadata, Dataset dataset, boolean direct) { - DataCitation citation=null; - if (dataset != null){ - citation = new DataCitation(dataset.getLatestVersion()); - } else { - citation= new DataCitation(fileMetadata, direct); - } - - FacesContext ctx = FacesContext.getCurrentInstance(); - HttpServletResponse response = (HttpServletResponse) ctx.getExternalContext().getResponse(); - response.setContentType("application/download"); - + public void downloadCitationRIS(FileMetadata fileMetadata, boolean direct) { + DataCitation citation=null; + citation= new DataCitation(fileMetadata, direct); + String fileNameString; if (fileMetadata == null || fileMetadata.getLabel() == null) { // Dataset-level citation: @@ -457,6 +458,14 @@ public void downloadCitationRIS(FileMetadata fileMetadata, Dataset dataset, bool // Datafile-level citation: fileNameString = "attachment;filename=" + getFileNameFromPid(citation.getPersistentId()) + "-" + FileUtil.getCiteDataFileFilename(citation.getFileTitle(), FileUtil.FileCitationExtension.RIS); } + downloadRIS(citation, fileNameString); + } + + public void downloadRIS(DataCitation citation, String fileNameString) { + //SEK 12/3/2018 changing this to open the json in a new tab. + FacesContext ctx = FacesContext.getCurrentInstance(); + HttpServletResponse response = (HttpServletResponse) ctx.getExternalContext().getResponse(); + response.setContentType("application/download"); response.setHeader("Content-Disposition", fileNameString); try { @@ -468,38 +477,33 @@ public void downloadCitationRIS(FileMetadata fileMetadata, Dataset dataset, bool } } - + private String getFileNameFromPid(GlobalId id) { return id.asString(); } - public void downloadDatasetCitationBibtex(Dataset dataset) { - downloadCitationBibtex(null, dataset, false); + public void downloadDatasetCitationBibtex(DatasetVersion version) { + // DatasetVersion-level citation: + DataCitation citation=null; + citation = new DataCitation(version); + String fileNameString; + fileNameString = "inline;filename=" + getFileNameFromPid(citation.getPersistentId()) + ".bib"; + downloadBibtex(citation, fileNameString); } public void downloadDatafileCitationBibtex(FileMetadata fileMetadata) { - downloadCitationBibtex(fileMetadata, null, false); + downloadCitationBibtex(fileMetadata, false); } public void downloadDirectDatafileCitationBibtex(FileMetadata fileMetadata) { - downloadCitationBibtex(fileMetadata, null, true); + downloadCitationBibtex(fileMetadata, true); } - public void downloadCitationBibtex(FileMetadata fileMetadata, Dataset dataset, boolean direct) { - DataCitation citation=null; - if (dataset != null){ - citation = new DataCitation(dataset.getLatestVersion()); - } else { - citation= new DataCitation(fileMetadata, direct); - } - //SEK 12/3/2018 changing this to open the json in a new tab. - FacesContext ctx = FacesContext.getCurrentInstance(); - HttpServletResponse response = (HttpServletResponse) ctx.getExternalContext().getResponse(); - - //Fix for 6029 FireFox was failing to parse it when content type was set to json - response.setContentType("text/plain"); + public void downloadCitationBibtex(FileMetadata fileMetadata, boolean direct) { + DataCitation citation=null; + citation= new DataCitation(fileMetadata, direct); String fileNameString; if (fileMetadata == null || fileMetadata.getLabel() == null) { @@ -509,6 +513,16 @@ public void downloadCitationBibtex(FileMetadata fileMetadata, Dataset dataset, b // Datafile-level citation: fileNameString = "inline;filename=" + getFileNameFromPid(citation.getPersistentId()) + "-" + FileUtil.getCiteDataFileFilename(citation.getFileTitle(), FileUtil.FileCitationExtension.BIBTEX); } + downloadBibtex(citation, fileNameString); + } + + public void downloadBibtex(DataCitation citation, String fileNameString) { + //SEK 12/3/2018 changing this to open the json in a new tab. + FacesContext ctx = FacesContext.getCurrentInstance(); + HttpServletResponse response = (HttpServletResponse) ctx.getExternalContext().getResponse(); + + //Fix for 6029 FireFox was failing to parse it when content type was set to json + response.setContentType("text/plain"); response.setHeader("Content-Disposition", fileNameString); try { diff --git a/src/main/webapp/dataset-citation.xhtml b/src/main/webapp/dataset-citation.xhtml index b42dd5e563f..346e39dc463 100644 --- a/src/main/webapp/dataset-citation.xhtml +++ b/src/main/webapp/dataset-citation.xhtml @@ -33,13 +33,13 @@ diff --git a/src/main/webapp/file.xhtml b/src/main/webapp/file.xhtml index f69b5c35afd..ea7b51f9640 100644 --- a/src/main/webapp/file.xhtml +++ b/src/main/webapp/file.xhtml @@ -112,19 +112,19 @@
    • @@ -161,19 +161,19 @@