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Rewrite DOI parsing #99

Merged
merged 11 commits into from
Aug 14, 2015
Merged

Rewrite DOI parsing #99

merged 11 commits into from
Aug 14, 2015

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stefan-kolb
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I rewrote the DOI parser as it was hard to understand and missing quite a few valid DOIs.
It's not 100% but should be a lot better than before.

  • Clearer and more permissive Regex
  • Better URL encoding and decoding
  • More test coverage

Any comments before merging this into master are appreciated.

simonharrer
simonharrer reviewed Aug 13, 2015
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src/main/java/net/sf/jabref/util/DOI.java
private static final Pattern DOI_PATT = Pattern.compile("^(?:https?://[^\\s]+?)?" + DOI_EXP + "$", Pattern.CASE_INSENSITIVE);

// DOI
private String doi;
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I would recommend to make it final.

simonharrer
simonharrer reviewed Aug 13, 2015
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src/main/java/net/sf/jabref/util/DOI.java
}
// whitespace
value = value.trim();
return value.matches(DOI_EXP);
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would it make sense to use an instance of the DOI class for this method?

@koppor
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koppor commented Aug 14, 2015

I did a quick test with clean up entries and all things work (DOI in note field, DOI and some text in note field, DOI in URL field, existing DOI).

stefan-kolb added a commit that referenced this pull request Aug 14, 2015
@stefan-kolb
Merge pull request #99 from JabRef/doi-parser
a394b59 
Rewrite DOI parsing
@stefan-kolb stefan-kolb merged commit a394b59 into master Aug 14, 2015
@stefan-kolb stefan-kolb deleted the doi-parser branch August 14, 2015 09:21
@Siedlerchr Siedlerchr mentioned this pull request May 25, 2017
Closed
InAnYan added a commit that referenced this pull request Aug 3, 2024
@InAnYan
Fix #99 and partially #101
c245e73
github-merge-queue bot pushed a commit that referenced this pull request Aug 14, 2024
@InAnYan @koppor
AI chatting functionality (#11430)
8a0edc2 
* Fix the code from code review

* Fix from code review and create new AiChatTabWorking

* Improve chat history storage code

* More fix from code review

* Remove obsolete parameter

* Add JavaDoc comment

* Fix checkstyle

* Fix JavaDoc

* Fix more checkstyle

* More checkstyle fixes

* Fix code changes

* Improve the PR

* Rework ADR-0031 to enable to use another option

* Add many LOGGEr.trace statements

* Change "message window" to "context window"

* Fix compiler errors

* Fix issue list index issue of langchain4j

* Fix lint issue

* Update 0031-store-chats-alongside-database.md

* More tracing

* Refine logging

* Remove closing of AiChatLanguageModel (because it's not closable)

* Use external package for OpenAI API connection

* Provide a custom executor for RetrievalAugmentor

* Fix shutdown issue (I hope)

* Refactor classes

* Change BibDatabaseChatHistoryFile

* Revert BibDatabaseChatHistoryFile to old version because of langchain4j

* Make round corners for chat messages

* Refactor embeddings generation

* Refactor embeddings generation

* Refactor embeddings generation

* Fix CHANGELOG.md

* Remove jpro-mdfx

* Add comment

* Fix localizations

* Fix checkstyle and remove OpenAI from PRIVACY.md

* Remove unnecessary comments

* Fix privacy notice UI

* Introduce new ApiKeyMissingComponent

* Thanks Tobiaz Diez for writing such a good EntryEditorTab class

* Fix InAnYan/jabref issues

* Merge `build.gradle` and `settings.gradle` from main branch

* Update ADRs

* Implement rethought ADR for chat history

* Use OpenAI embedding model

* Use Deep Java embedding model

* Remove old langchain4j embedding models

* Fix checkstyle errors

* Fix checkstyle and remove old dependencies

* Fixes from code review

* Restructure

* Fix checkstyle errors

* Add API base URL parameter

* Fix localization

* Fix from code review + ADR

* Something broken

* Now MistralAI and Hugging Face work

* Fix base URL for other LLM providers

* Fix base URL for other LLM providers

* Refactor MVStore usage

* Load embedding model in background

* Bump langchain4j version

* Fix bug

* Fix checkstyle and localization

* Implement summarization

* Fix checkstyle and localization

* Improve PrivacyNoticeComponent

* Fix from code review

* Update localization

* Wrap text

* Add padding

* Fix markdown

* Use stuff algorithm

* Add GPT-4o-mini

* Make chat model editable

* Update context window size and summarization

* Fix checkstyle

* Update PrivacyNoticeComponent.fxml

* Update AI summary tab

* Fix localization

* Change order so that there is no diff

* Reorrder dependencies

* Add missing CHANGELOG.md entry

* Refine ADR-0033

* Refine ADR0034

* Fix typos

* Refine ADR-0036

* Fix ADR-0037

* Fix title case

* Fix changes in module-info.java

* Readd removed requires org.apache.httpcomponents.core5.httpcore5

* Revert change in JabRefGUI to avoid conflicts

* Remove empty lines

* Reorder entries in JabRef_en.properties

* Simplify SummariesStorage (and add test)

* Use region/endregion

* Fix position of comment

* Add comment why the event bus is needed

* Do not show exception to the user - just that an error is occurred (saves %0 in localization)

* Use "URL %0" without colon (consistency)

* Fix typos

* History has to be kept

* Remove empty lines

* Fix language (hopefully)

* Compilefix

* Simplify BibDatabaseChatHistoryManager

* Fix from code review

* Fix issue #103

* Rework embeddings cache clearing

* Fix #99 and partially #101

* Partially fixing shutdown issues and UI progress monitor issue

* Add "requires scala.library" and add "region:" / "endregion"

* More grouping (move de.saxsys.mvvmfx.validation up)

* Add alphabetical hint

* Fix InAnYan#101 and InAnYan#106

* Discard changes to settings.gradle

* Fix InAnYan#105

* Follow-up fix for InAnYan#103

* Follow-up fix for InAnYan#103

* Remove obsolete class

* Partially fix InAnYan#98

* We do need dependencies to the AI providers, don't we?

* Fix InAnYan#93

* Simplify code

* Partially fix InAnYan#92

* Fix checkstyle and localization

* Fix hyperlinks and text in ApiKeyMissingComponent

* Fixes from code review

* Fix InAnYan#120

* Remove "X% work done" messages

* Fix InAnYan#114

* Partially fix InAnYan#113

* Partially fix InAnYan#110

* Fix InAnYan#110

* Fix InAnYan#111

* Improve embedding model downloading notifications

* Fix InAnYan#124

* Fix InAnYan#122

* Fix wrong context window size when expert settings customization is turned off

* Attempt to fix InAnYan#95

* Finally fix InAnYan#105

* Fix InAnYan#108

* Attempt to fix InAnYan#98

* Fix for InAnYan#104

* Fix for InAnYan#98

* Fix for InAnYan#95 (comment)

* Fix for InAnYan#98 (comment)

* Fix for InAnYan#126

* Fix for InAnYan#115

* Fix for InAnYan#113

* Fix for InAnYan#91

* Fix for InAnYan#121

* Fix for InAnYan#112 and InAnYan#116

* Fix for InAnYan#125

* Fixes from commit comments

* Fix for InAnYan#115

* Fix for InAnYan#120

* Fix for InAnYan#132

* Fix for InAnYan#132

* Fix for InAnYan#104

* Fix for InAnYan#118

* Fix for InAnYan#114

* Fix for InAnYan#104

* Store error messages in chat history

* Make error be a ChatMessageComponent

* Implement delete messages InAnYan#136

* Fix for InAnYan#118

* Fix for InAnYan#92

* Fix checkstyle and localization. And refactoring

* Fix for InAnYan#92

* Fix for InAnYan#139

* Show "Delete message" button only when necessary

* Fix for InAnYan#83

* Update src/main/java/org/jabref/logic/ai/AiService.java

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>

* Update src/main/java/org/jabref/logic/ai/chathistory/BibDatabaseChatHistoryManager.java

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>

* Update src/main/java/org/jabref/logic/ai/AiService.java

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>

* Update src/main/java/org/jabref/gui/Base.css

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>

* Update src/main/java/org/jabref/gui/Base.css

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>

* Fix from code review

* Partial fix for InAnYan#125

* Update colors for error message

* Fix for InAnYan#145 and InAnYan#142

* Make progress for embedding model download

* Fix checkstyle and localization

* Add workaround to get FileHistoryMenuTest running again

* Small fixes

* Revert "Small fixes"

This reverts commit 85382a1.

* Introduce AiApiKeyProvider

* Fix IDE setup instructions

* Do not load API keys on startup

* Rely on keystore encryption

* Prevent mulitple rebuilds when muliple preferences are updated

* Fix localization to be more provider independent

* Fix method names

* Add poor man's solution to notify of API key changes

* Reduce calls to key store (and fix key saving)

* Fix for InAnYan#148 and partially InAnYan#146

* Revert "Fix for InAnYan#148 and partially InAnYan#146"

This reverts commit 5fa3bb5.

* Fix for scrolling down when deleting a message

* Sort EmbeddingModel enum variants

* Fix GenerateSummaryTask progress indication

* Fix dark mode

* Add notice for embedding models size

---------

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
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3 participants
@stefan-kolb @koppor @simonharrer