Fixes #3472: Files starting with BibTeX key of a similar entry are no longer found by mistake #3509

tobiasdiez · 2017-12-10T14:46:36Z

Fixes #3472.
The auto-link algorithm just checked if the file starts with the BibTeX key. This leads to a lot of false positives since "Einstein1902a.pdf" is found for the entry "Einstein1902" although this pdf probably belongs to a second paper by Einstein that was published in the same year.
This is fixed in this PR.
With the proposed implementation also the pdf file "Einstein1902aboutSomething.pdf" is no longer found (since there is really no possibility in telling the difference to "Einstein1902a - a second paper.pdf"). Thus the user is advised to add some non-letter character after the key.

Change in CHANGELOG.md described
Tests created for changes
Screenshots added (for bigger UI changes)
Manually tested changed features in running JabRef
Check documentation status (Issue created for outdated help page at help.jabref.org?)
If you changed the localization: Did you run gradle localizationUpdate?

… longer found by mistake

Siedlerchr · 2017-12-10T16:25:31Z

src/main/java/org/jabref/logic/util/io/FileFinder.java

- default List<Path> findAssociatedFiles(BibEntry entry, List<Path> directories, List<String> extensions) {
- Map<BibEntry, List<Path>> associatedFiles = findAssociatedFiles(Collections.singletonList(entry), directories, extensions);
- return associatedFiles.getOrDefault(entry, Collections.emptyList());
+ default Collection<Path> findAssociatedFiles(BibEntry entry, List<Path> directories, List<String> extensions) {


Why do you use the collection interface here? List interface defines a somehow ordered collection
I would really prefer list here
https://stackoverflow.com/a/3317408/3450689

The multimap only returns a collection because it actually is not implemented as a list (the sorting is random). But now we don't need multimaps anymore so we can go back to lists!

Siedlerchr · 2017-12-10T17:30:43Z

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

 if (!files.isEmpty()) {
- Path file = files.get(0);
+ Path file = files.iterator().next();


I see no advantage in using Collection here

Siedlerchr · 2017-12-10T17:40:23Z

src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java

+ this(databaseContext.getFileDirectoriesAsPaths(fileDirectoryPreferences), autoLinkPreferences, externalFileTypes);
+ }
+
+ public AutoSetFileLinksUtil(List<Path> directories, AutoLinkPreferences autoLinkPreferences, ExternalFileTypes externalFileTypes) {


I am against creating a second constructor. It was my initial idea in #3368 and guess who supposed the current alternative? 😆
See your comment #3368 (comment)

I don't understand what you mean. The linked comment is about the list of entries and not about how the AutoSetFileLinksUtil gets the things needed (like directories and preferences). I think, the current setup makes sense: on initialization, specify everything the auto set functionality needs to know. Why don't you like these constructors?

Ah sorry, I could not see all code in the line on my mobile, so I was a b9it confused. Forget about my remark,

No problem!

Siedlerchr · 2017-12-10T17:42:12Z

src/main/java/org/jabref/logic/util/io/CiteKeyBasedFileFinder.java

 Objects.requireNonNull(directories);
 Objects.requireNonNull(entries);

- Map<BibEntry, List<Path>> result = new HashMap<>();
+ Multimap<BibEntry, Path> result = ArrayListMultimap.create();


If you structure the code similar to the one in AutoSetLinks, you won't need a multimap:

for (BibEntry entry : entries) { List<LinkedFile> linkedFiles = util.findassociatedNotLinkedFiles(entry, databaseContext, Globals.prefs.getFileDirectoryPreferences(), Globals.prefs.getAutoLinkPreferences(), ExternalFileTypes.getInstance()); if (ce != null) { for (LinkedFile linkedFile : linkedFiles) {

Thanks! This is really good feedback. I just realized that the finder never gets a list of entries as argument but always a single entry. Thus the design can be simplified drastically without mulitmaps or maps to collections.

Siedlerchr · 2017-12-10T20:59:59Z

src/test/java/org/jabref/logic/util/io/RegExpBasedFileFinderTests.java

@@ -56,7 +57,7 @@ public void testFindFiles() {
 RegExpBasedFileFinder fileFinder = new RegExpBasedFileFinder("**/[bibtexkey].*\\\\.[extension]", ',');

 //when
- List<Path> result = fileFinder.findAssociatedFiles(localEntry, dirs, extensions);
+ Collection<Path> result = fileFinder.findAssociatedFiles(localEntry, dirs, extensions);


Here you can change them back to list again

koppor · 2017-12-11T07:17:12Z

How does this relate with the preferences?

Documentation at http://help.jabref.org/en/FileLinks#auto-linking-files

Are these settings still respected?

tobiasdiez · 2017-12-11T08:44:17Z

@koppor Yes, these settings are still valid. The fix applies only if you select the first option "Auto link files that start with the BibTeX key".

Siedlerchr · 2017-12-16T12:19:21Z

src/main/java/org/jabref/logic/util/io/CiteKeyBasedFileFinder.java

+ // The file name starts with the key, that's already a good start
+ // However, we do not want to match "JabRefa" for "JabRef" since this is probably a file belonging to another entry published in the same time / same name
+ char charAfterKey = filename.charAt(citeKey.length());
+ return !StringUtil.contains(BibtexKeyPatternUtil.CHARS, charAfterKey);


Better direclty use the java method: String.contains(Character.toString(c))

And also take a look at the codacy

Siedlerchr

Only one little thing left, otherwise good

tobiasdiez · 2017-12-23T12:58:53Z

@koppor Why did you removed the "ready-for-review" flag and marked this PR as WIP? I was and I am still waiting for a second review, otherwise this PR is ready from my point of view. The minor issues pointed-out by @Siedlerchr are now also fixed.

koppor · 2018-05-30T12:10:22Z

Think, because I watched this PR, liked it and just wanted others to focus on other PRs.

tobiasdiez added 2 commits December 10, 2017 14:42

Refactor auto link classes

26c4462

Fixes #3472: Files starting with BibTeX key of a similar entry are no…

456241c

… longer found by mistake

tobiasdiez added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Dec 10, 2017

Siedlerchr requested changes Dec 10, 2017

View reviewed changes

Simplify code

3784d90

Siedlerchr reviewed Dec 10, 2017

View reviewed changes

Implement feedback, fix tests and checkstyle

18a6688

Siedlerchr reviewed Dec 16, 2017

View reviewed changes

Siedlerchr approved these changes Dec 16, 2017

View reviewed changes

koppor changed the title ~~Fixes #3472: Files starting with BibTeX key of a similar entry are no longer found by mistake~~ [WIP] Fixes #3472: Files starting with BibTeX key of a similar entry are no longer found by mistake Dec 22, 2017

koppor removed the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Dec 22, 2017

tobiasdiez changed the title ~~[WIP] Fixes #3472: Files starting with BibTeX key of a similar entry are no longer found by mistake~~ Fixes #3472: Files starting with BibTeX key of a similar entry are no longer found by mistake Dec 23, 2017

tobiasdiez added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Dec 23, 2017

Minor changes

fb207b2

tobiasdiez added 5 commits December 23, 2017 13:59

Merge branch 'master' into fix3472

88cdb43

Merge branch 'fix3472' of https://github.com/JabRef/jabref into fix3472

8f30b75

Fix changelog

c45de80

Really fix changelog

e661b76

Fix build

9d03922

koppor merged commit f86e24d into master Dec 23, 2017

koppor deleted the fix3472 branch December 23, 2017 14:06

koppor mentioned this pull request May 30, 2018

Look up fulltext documents does not link existing PDFs #3874

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Fixes #3472: Files starting with BibTeX key of a similar entry are no longer found by mistake #3509

Fixes #3472: Files starting with BibTeX key of a similar entry are no longer found by mistake #3509

tobiasdiez commented Dec 10, 2017 •

edited

Loading

Siedlerchr Dec 10, 2017

tobiasdiez Dec 10, 2017

Siedlerchr Dec 10, 2017

Siedlerchr Dec 10, 2017

tobiasdiez Dec 10, 2017

Siedlerchr Dec 10, 2017

tobiasdiez Dec 10, 2017

Siedlerchr Dec 10, 2017

tobiasdiez Dec 10, 2017

Siedlerchr Dec 10, 2017

tobiasdiez Dec 10, 2017

koppor commented Dec 11, 2017

tobiasdiez commented Dec 11, 2017

Siedlerchr Dec 16, 2017

Siedlerchr Dec 16, 2017

Siedlerchr left a comment

tobiasdiez commented Dec 23, 2017

koppor commented May 30, 2018

Fixes #3472: Files starting with BibTeX key of a similar entry are no longer found by mistake #3509

Fixes #3472: Files starting with BibTeX key of a similar entry are no longer found by mistake #3509

Conversation

tobiasdiez commented Dec 10, 2017 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

koppor commented Dec 11, 2017

tobiasdiez commented Dec 11, 2017

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Siedlerchr left a comment

Choose a reason for hiding this comment

tobiasdiez commented Dec 23, 2017

koppor commented May 30, 2018

tobiasdiez commented Dec 10, 2017 •

edited

Loading