WIP Restapi #628

Siedlerchr · 2022-09-21T19:05:36Z

This ports the code of https://github.com/UST-QuAntiL/PlanQK-Library to JabRef's core.

src/main/resources/xjc/medline/dtd/pubmed_190101.dtd

src/main/resources/xjc/medline/dtd/mathml3-qname1.mod

src/main/java/org/jabref/logic/shared/restserver/rest/base/Library.java

src/main/java/org/jabref/logic/shared/restserver/rest/model/StudyDTO.java

src/main/java/org/jabref/logic/shared/restserver/core/repository/LibraryService.java

.../java/org/jabref/logic/shared/restserver/core/serialization/BibEntryJacksonDeserializer.java

src/main/java/org/jabref/logic/shared/restserver/core/serialization/BibEntryMapper.java

TODO fix javafx inject errors

src/main/java/org/jabref/gui/EntryTypeView.java

* upstream/afterburner: Update afterburner to jakarta # Conflicts: # build.gradle

* upstream/main: (42 commits) Place subgroups w.r.t. alphabetical ordering (JabRef#9228) DOAB Fetcher now fetches ISBN and imprint fields where possible (JabRef#9229) ISSUE-9145: implement isbn fetcher (JabRef#9205) Remove explicit javafx jmod stuff (JabRef#9245) New Crowdin updates (JabRef#9239) Support Arabic language (JabRef#9243) Process CLI arguments before starting gui (JabRef#9217) Update README Decision Records link (JabRef#9241) Opening a file removes duplicate keywords and triggers lib changed (JabRef#9216) New Crowdin updates (JabRef#9237) Add Ukrainian as language (JabRef#9236) Add ADR-0026 on using Swing's FileChooser (JabRef#9235) Log exception (JabRef#9227) Fix archunit (JabRef#9234) Bump tika-core from 2.4.1 to 2.5.0 (JabRef#9232) Check group type before showing dialog in edit group (JabRef#8909) Fix unexpected closing of preferences dialog (JabRef#9225) Fix typo in connection error message (JabRef#9226) Improve VSCode config (JabRef#9218) Searching for an entry on the web shouldn't take forever (JabRef#9199) ... # Conflicts: # build.gradle # lib/afterburner.fx.jar # src/main/java/org/jabref/cli/Launcher.java # src/main/java/org/jabref/gui/EntryTypeView.java # src/main/java/org/jabref/gui/auximport/FromAuxDialog.java # src/main/java/org/jabref/gui/bibtexextractor/ExtractBibtexDialog.java # src/main/java/org/jabref/gui/collab/ExternalChangesResolverDialog.java # src/main/java/org/jabref/gui/commonfxcontrols/CitationKeyPatternPanel.java # src/main/java/org/jabref/gui/contentselector/ContentSelectorDialogView.java # src/main/java/org/jabref/gui/customentrytypes/CustomizeEntryTypeDialogView.java # src/main/java/org/jabref/gui/documentviewer/DocumentViewerView.java # src/main/java/org/jabref/gui/edit/ManageKeywordsDialog.java # src/main/java/org/jabref/gui/entryeditor/EntryEditor.java # src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabView.java # src/main/java/org/jabref/gui/errorconsole/ErrorConsoleView.java # src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialogView.java # src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java # src/main/java/org/jabref/gui/help/AboutDialogView.java # src/main/java/org/jabref/gui/importer/ImportCustomEntryTypesDialog.java # src/main/java/org/jabref/gui/importer/ImportEntriesDialog.java # src/main/java/org/jabref/gui/integrity/IntegrityCheckDialog.java # src/main/java/org/jabref/gui/libraryproperties/AbstractPropertiesTabView.java # src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesView.java # src/main/java/org/jabref/gui/libraryproperties/constants/ConstantsPropertiesView.java # src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesView.java # src/main/java/org/jabref/gui/libraryproperties/keypattern/KeyPatternPropertiesView.java # src/main/java/org/jabref/gui/libraryproperties/saving/SavingPropertiesView.java # src/main/java/org/jabref/gui/linkedfile/LinkedFileEditDialogView.java # src/main/java/org/jabref/gui/openoffice/ManageCitationsDialogView.java # src/main/java/org/jabref/gui/openoffice/StyleSelectDialogView.java # src/main/java/org/jabref/gui/preferences/AbstractPreferenceTabView.java # src/main/java/org/jabref/gui/preferences/PreferencesDialogView.java # src/main/java/org/jabref/gui/preferences/customexporter/CustomExporterTab.java # src/main/java/org/jabref/gui/preferences/externalfiletypes/EditExternalFileTypeEntryDialog.java # src/main/java/org/jabref/gui/preferences/journals/JournalAbbreviationsTab.java # src/main/java/org/jabref/gui/preferences/keybindings/KeyBindingsTab.java # src/main/java/org/jabref/gui/preferences/preview/PreviewTab.java # src/main/java/org/jabref/gui/preferences/protectedterms/ProtectedTermsTab.java # src/main/java/org/jabref/gui/search/GlobalSearchResultDialog.java # src/main/java/org/jabref/gui/shared/SharedDatabaseLoginDialogView.java # src/main/java/org/jabref/gui/slr/ManageStudyDefinitionView.java # src/main/java/org/jabref/gui/texparser/ParseLatexDialogView.java # src/main/java/org/jabref/gui/texparser/ParseLatexResultView.java

src/main/java/org/jabref/logic/pdf/search/indexing/IndexingTaskManager.java.orig

Siedlerchr · 2023-01-05T13:08:42Z

Further idea: https://foojay.io/today/whats-new-in-jakarta-rest-3-1-in-jakarta-ee-10/
No cotainer necessary as it seems

koppor · 2023-01-05T13:11:26Z

Quoting from the article:

In the past, to run a Jakarta EE REST application required a full deployment to a compatible runtime like the Payara Platform or Payara Cloud. Jakarta REST 3.1 in Jakarta EE 10 introduced a new API to bootstrap REST resources outside of a container.

The simplest way to get a REST API deployed is to call the start() method on the jakarta.ws.rs. SeBootstrap class. This method returns a CompletionStage that you can then chain for different purposes.

koppor · 2023-01-05T13:11:53Z

Maybe, we just need to remove dependencies and call the start method? 1 hour pair programming?

Siedlerchr · 2023-01-05T13:21:28Z

https://github.com/jakartaee/rest/blob/master/examples/src/main/java/jaxrs/examples/bootstrap/BasicJavaSeBootstrapExample.java

* upstream/main: (244 commits) Use Set instead of List for custom journal abbreviations (JabRef#9515) Delete snap.yml (JabRef#9526) New Crowdin updates (JabRef#9523) Fix not on fx thread error when downloading file (JabRef#9522) Fix downloading in case of circular redirect (JabRef#9519) Typo: sucess -> success (JabRef#9520) New Crowdin updates (JabRef#9517) Add CHANGELOG.md entry for 9472 Fix journal abbbrev checker for curly braces (JabRef#9504) Remove journal_abbreviations_ieee_strings.csv from journal lists (JabRef#9511) Bump mockito-core from 4.10.0 to 4.11.0 (JabRef#9513) Bump lucene-core from 9.4.1 to 9.4.2 (JabRef#9512) Bump checkstyle from 10.5.0 to 10.6.0 (JabRef#9514) Create a better solution for define multi line fields (JabRef#9456) Check links once a month Really ignore CHANGELOG.md in link check Fix spaces Add missing dots Squashed 'buildres/csl/csl-styles/' changes from 84dba23..43566f2 try to repack deb file (JabRef#9506) ...

buildres/csl/csl-styles/rassegna-degli-archivi-di-stato-bibliografia-generale.csl

Siedlerchr · 2023-01-05T15:37:47Z

Fuu. I hat this complicated shit. Still needs a server implementation like jersey or whatever.

koppor · 2023-01-05T22:43:39Z

Trying to do two things

Use RestEasy as server (seems to be more "lightweight"
Switch from glassfish jaxb to Jackson

Found these helpful links:

Following is not supported by Jackson:

JAXBContext.newInstance("org.jabref.logic.importer.fileformat.mods");

There is ObjectMapper and XmlMapper.

However, polymorphism in XMLElements is not supported by JAXB. See FasterXML/jackson-modules-base#127.

Thus, I tried to rewrite the Importers to a StAX-based parsing. This is a huge job, but would make the code more "clean" and hopefully remove this xjc stuff. Was possibly a bad idea 5 years ago to go for the JAXB way and not directly parse the XML.

koppor · 2023-01-05T22:45:30Z

And now we have

reads package org.jboss.resteasy.concurrent from both resteasy.core.spi and resteasy.core

Siedlerchr · 2023-01-06T06:09:56Z

Yes. I encountered the split modules as well. I don't think this jaxb rewrite will help.
Jetty etc had also problems. In the end it's jlink again

koppor · 2023-01-06T15:03:18Z

Submitted RestEasy Issue https://issues.redhat.com/browse/RESTEASY-3272

# Conflicts: # build.gradle

buildres/csl/csl-styles/archives-of-medical-research.csl

- Add log if server cannot start - Refine root page

src/main/java/org/jabref/logic/shared/restserver/rest/Root.java

koppor · 2023-03-18T00:10:55Z

Fun with modules:

error: duplicate module on application module path
  module in jakarta.activation

* upstream/main: (26 commits) Remove bibtexml.xsd (We don't support BibTeXML any more) Rewrite code of MedlineImporter (JabRef#9673) Rename variable and add more documentation Fix checkstyle Add hanling of "field = {content\}" Add link to PR Add link to PR. JabRef writes a new backup file only if there is a change. Add debug output to log.txt Refine logging howto Change log level for non-found files during PDF indexing Initial ImportHandlerTest Streamline AppDirs paths add a clear history button in sub-menu Removed redundant list add for en.properties add Localization.lang for string correct changelog add test for getLastSearchHistory and change HashLinkedSet to ArrayList fix the checkstlye ...

Siedlerchr · 2023-03-18T19:48:52Z

I could fix the duplicate module stuff, but we stilll have method too large...

* upstream/main: Bump org.slf4j:slf4j-api from 2.0.6 to 2.0.7 in /buildSrc Bump org.slf4j:slf4j-api from 2.0.6 to 2.0.7 Bump org.apache.tika:tika-core from 2.6.0 to 2.7.0 Bump hmarr/auto-approve-action from 3.2.0 to 3.2.1 Bump actions/deploy-pages from 1 to 2 Bump org.eclipse.jgit:org.eclipse.jgit Bump org.mockito:mockito-core from 5.1.1 to 5.2.0

# Conflicts: # src/main/java/org/jabref/logic/layout/format/MarkdownFormatter.java

Add jaxrs copy over code

b29aaea

github-actions bot reviewed Sep 21, 2022

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try with jetty

c951839

TODO fix javafx inject errors

github-actions bot reviewed Sep 21, 2022

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src/main/java/org/jabref/gui/EntryTypeView.java Outdated Show resolved Hide resolved

Siedlerchr added 4 commits September 21, 2022 22:10

fcking inject (

96d917a

Update afterburner to jakarta

4b38bd1

Merge remote-tracking branch 'upstream/afterburner' into restApi

8f8dff9

* upstream/afterburner: Update afterburner to jakarta # Conflicts: # build.gradle

add another fcking injection stuff

03bcdd3

Siedlerchr mentioned this pull request Sep 21, 2022

Migrate from javax to jakarta JabRef/afterburner.fx#3

Merged

Siedlerchr added 2 commits September 22, 2022 20:23

test again

7ce929b

fix afterburner

809a579

Siedlerchr mentioned this pull request Oct 12, 2022

Add HTTP server for MS Office Word integration JabRef/jabref#9246

Closed

6 tasks

Siedlerchr added 2 commits October 13, 2022 22:36

Fix conflicts

9293da1

calixtus reviewed Oct 14, 2022

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src/main/java/org/jabref/logic/pdf/search/indexing/IndexingTaskManager.java.orig Outdated Show resolved Hide resolved

cleanup

698e88f

github-actions bot reviewed Jan 5, 2023

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buildres/csl/csl-styles/rassegna-degli-archivi-di-stato-bibliografia-generale.csl Outdated Show resolved Hide resolved

fix compile errors

bcca5cc

Switch to JBOSS RestEasy (and Jackson instead of Glassfish)

dd77dce

koppor added 2 commits January 6, 2023 14:25

Switch back to Glassfish for JAXB (instead of Jackson)

4640087

Switch from Glassfish to Jackson2 for JSON (but keep it for XML)

a6ee546

Remove one dependency

1b4c30d

koppor added 2 commits March 17, 2023 18:05

Merge remote-tracking branch 'origin/main' into restapi

67280b0

# Conflicts: # build.gradle

Remove two "nice-to-have" Markdown plugins (strikethrough, tasklist)

1bbb1db

github-actions bot reviewed Mar 17, 2023

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koppor added 7 commits March 17, 2023 19:29

Fix checkstyle

5c448de

Remove duoble dependency entry

6095223

Really remove Markdown extension

82492fd

Endless startup...

bf659ea

Get server to run

636873d

- Add log if server cannot start - Refine root page

Make use of JabRefDesktop for default directory

2f8302b

Streamline code of ServerPropertyService

1b1fa9d

github-actions bot reviewed Mar 18, 2023

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src/main/java/org/jabref/logic/shared/restserver/rest/Root.java Outdated Show resolved Hide resolved

koppor and others added 5 commits March 18, 2023 01:12

Fix checkstyle

cf14659

fix starting error

0c2c30c

fix jlink dupliate module

306d731

run in background thread

a0799b0

Siedlerchr and others added 4 commits March 20, 2023 17:39

remove tika

3b14255

Fix checkstyle

e734892

Merge branch 'main' into restapi

1aacc96

# Conflicts: # src/main/java/org/jabref/logic/layout/format/MarkdownFormatter.java

koppor mentioned this pull request Apr 8, 2023

Introduces test http server JabRef/jabref#9748

Merged

koppor closed this in JabRef/jabref#9748 Sep 4, 2023

koppor deleted the restapi branch January 9, 2024 20:59

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WIP Restapi #628

WIP Restapi #628

Siedlerchr commented Sep 21, 2022 •

edited by koppor

Siedlerchr commented Jan 5, 2023

koppor commented Jan 5, 2023

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koppor commented Mar 18, 2023

Siedlerchr commented Mar 18, 2023

WIP Restapi #628

WIP Restapi #628

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Siedlerchr commented Sep 21, 2022 • edited by koppor

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Siedlerchr commented Sep 21, 2022 •

edited by koppor