Find Unlinked files should ignore Thumbs.db, etc #8800

prashant1712 · 2022-05-15T19:58:46Z

Reads the .gitignore file in the root directory of the library path and obeys it according to the option selected in the UI dialog box.

Change in CHANGELOG.md described in a way that is understandable for the average user (if applicable)
Tests created for changes (if applicable)
Manually tested changed features in running JabRef (always required)
Screenshots added in PR description (for UI changes)
Checked developer's documentation: Is the information available and up to date? If not, I outlined it in this pull request.
Checked documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request to the documentation repository.

…hing for unlinked local files

…unlinkedFiles#373

…abref into unlinkedFiles#373

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

CHANGELOG.md

prashant1712 · 2022-05-16T11:23:42Z

Thank you for your suggestions. I will make the changes and commit it soon.

.gitignore

calixtus

Great work. Some minor remarks, but looks already very good!

.idea/runConfigurations/JabRef_Main.xml

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

src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml

calixtus · 2022-05-16T19:58:04Z

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

+    DEFAULT(Localization.lang("Default")),
+    INCLUDE_ALL(Localization.lang("Include All Files"));
+
+    private static FileIgnoreUnlinkedFiles instance;


Is this necessary? You already have a var in FileFilterUtils...

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

…abref into unlinkedFiles#373

Co-authored-by: Christoph <siedlerkiller@gmail.com>

prashant1712 · 2022-05-18T09:28:01Z

@calixtus Thank you for the review. We are just finishing on the testing of the changes. We will let you know when it's done.

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

Check for existing files before reading

prashant1712 · 2022-05-21T09:55:28Z

@Siedlerchr Thank you for your help. Really appreciate the refactoring to improve the code, helped us in understanding the code better. One small thing, you changed the code to read the .gitignore file from the system of the user which i don't think is appropriate in our case. I'm changing it back to read it from the source directory of Jabref. Do let us know your opinion on this.

Siedlerchr · 2022-05-21T13:41:02Z

Yeah, that's one thing I wasn't sure about. I thought it makes sense to check the folder you selected to search for the files and the subfolders if there is any gitignore file inside and use this then?

prashant1712 · 2022-05-22T04:47:56Z

Yeah, i'm not really sure what to do now. Which scenario are we going to take: Searching for the .gitignore file in the directory selected by the user or picking up the .gitignore file from the source directory of JabRef. We initially thought that it makes sense to ignore the extensions and file names mentioned in the .gitignore file of JabRef as it gives a consistent behaviour across all users but I'm quite confused right now and would really appreciate a solution to this.

Siedlerchr · 2022-05-22T15:27:27Z

Let's ask @koppor as it was his issue...

calixtus · 2022-05-23T13:17:54Z

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

+import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.DirectoryStream.Filter;
 import java.nio.file.Files;
 import java.nio.file.Path;


I just mentioned you are mixing pre-java7-io api and nio. Is there a special reason?

koppor · 2022-05-23T18:03:15Z

Yeah, i'm not really sure what to do now. Which scenario are we going to take: Searching for the .gitignore file in the directory selected by the user

Yes, do this.

In addition following files / directories are always ignored:

.git
Thumbs.db

This list is hard-coded in Java. No additional text file. No option for configuration.

prashant1712 · 2022-05-25T11:55:21Z

Understood. Thank you @koppor for the clarification. I'll make the changes accordingly.

Siedlerchr · 2022-05-30T18:40:28Z

Please also include .DS_Store (A kind of desktop.ini equivalent for mac) in the default ignored files

calixtus · 2022-06-04T12:43:49Z

Any update here?

prashant1712 · 2022-06-05T08:37:38Z

Hi @calixtus, i am recovering from a medical condition right now. Will complete the changes when i'm recovered. Thank you for understanding.

calixtus · 2022-06-05T21:45:47Z

Of course, get well soon.

Co-authored-by: Christoph <siedlerkiller@gmail.com> Co-authored-by: Carl Christian Snethlage <50491877 Co-authored-by: ThiloteE <73715071+ThiloteE@users.noreply.github.com>

koppor · 2022-06-20T21:28:19Z

@prashant1712 In each dev call, we choose a PR (more or less randomly) to finish it. Today, we worked 2 hours on this one. the intermediate result is there. However, the tests still fail. We need to continue here.

* upstream/main: Try to make reproducible builds (JabRef#8925) Link to new board (and refine text) Pass the data as a string (JabRef#8923) Add IntelliJ plugins to Gitpod configuration Add gradle support Fix extension name Remove obsolete closing bracket Add gitpod config (JabRef#8921) Fix javafx version not displayed in About Dialog (JabRef#8918) Redesign "Manage field names & content" dialog (JabRef#8892) Rework IACR fetcher (JabRef#8904) Bump h2-mvstore from 2.1.212 to 2.1.214 in /buildSrc (JabRef#8915) Bump unoloader from 7.3.3 to 7.3.4 (JabRef#8912) Bump libreoffice from 7.3.3 to 7.3.4 (JabRef#8913) Bump tika-core from 2.4.0 to 2.4.1 (JabRef#8914) Bump org.eclipse.jgit from 6.1.0.202203080745-r to 6.2.0.202206071550-r (JabRef#8916)

add some more tests Fix checsktyle

* upstream/main: Fix for Dark theme not readable (JabRef#8929) Find Unlinked files should ignore Thumbs.db, etc (JabRef#8800) Try to make reproducible builds (JabRef#8925) Link to new board (and refine text) Pass the data as a string (JabRef#8923) Add IntelliJ plugins to Gitpod configuration Add gradle support Fix extension name Remove obsolete closing bracket Add gitpod config (JabRef#8921) Fix javafx version not displayed in About Dialog (JabRef#8918) Redesign "Manage field names & content" dialog (JabRef#8892)

* upstream/main: fix merge conflict Squashed 'buildres/csl/csl-locales/' changes from 969d9567ac..55459cd79f Squashed 'buildres/csl/csl-styles/' changes from e740261..3d3573c Show pdf icon for mime type in maintable (#8935) Fix for Dark theme not readable (#8929) Find Unlinked files should ignore Thumbs.db, etc (#8800) Try to make reproducible builds (#8925) Link to new board (and refine text) Pass the data as a string (#8923) Add IntelliJ plugins to Gitpod configuration Add gradle support Fix extension name Remove obsolete closing bracket

* upstream/main: Disable ResearchGateTest on CI (JabRef#8955) Bump checkstyle from 10.1 to 10.3.1 (JabRef#8950) Bump checkstyle from 10.1 to 10.3.1 (JabRef#8950) Bump mariadb-java-client from 2.7.5 to 2.7.6 (JabRef#8953) Add notification when adding previous entries to new group configuration (JabRef#8919) Remember Sidepane width after restart (JabRef#8936) move "Warn about duplicates on import" preferences option (JabRef#8937) Fix theme switching exception (JabRef#8939) fix merge conflict Squashed 'buildres/csl/csl-locales/' changes from 969d9567ac..55459cd79f Squashed 'buildres/csl/csl-styles/' changes from e740261..3d3573c Show pdf icon for mime type in maintable (JabRef#8935) Fix for Dark theme not readable (JabRef#8929) Find Unlinked files should ignore Thumbs.db, etc (JabRef#8800) Try to make reproducible builds (JabRef#8925) Link to new board (and refine text)

prashant1712 and others added 11 commits May 2, 2022 17:45

added ui component to ignore unlinked files

3f85f67

ignore the files in ".gitignore" when searching for unlinked local files

05ae9ef

ignore the name of files and the extention in ".gitignore" when searc…

849bb4f

…hing for unlinked local files

Merge branch 'Ziheng' of https://github.com/prashant1712/jabref into …

c654ca5

…unlinkedFiles#373

linked ui to the logic & refactored the code

c0926a5

resolved conflicts

595e203

adding localization key

4be3ce4

Merge branch 'unlinkedFiles#373' of https://github.com/prashant1712/j…

8f3c80e

…abref into unlinkedFiles#373

Merge branch 'JabRef:main' into unlinkedFiles#373

165c4a7

changelog updated

713b954

Merge branch 'unlinkedFiles#373' of https://github.com/prashant1712/j…

c6cb911

…abref into unlinkedFiles#373

Siedlerchr reviewed May 15, 2022

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

Siedlerchr reviewed May 15, 2022

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CHANGELOG.md Outdated Show resolved Hide resolved

ThiloteE added search external files labels May 16, 2022

Update .gitignore

77cf185

calixtus reviewed May 16, 2022

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calixtus reviewed May 16, 2022

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calixtus requested changes May 16, 2022

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prashant1712 and others added 5 commits May 17, 2022 15:24

changes after review

65c1de5

Merge branch 'unlinkedFiles#373' of https://github.com/prashant1712/j…

3fe6eab

…abref into unlinkedFiles#373

Update CHANGELOG.md

68bdca8

Co-authored-by: Christoph <siedlerkiller@gmail.com>

Merge branch 'JabRef:main' into unlinkedFiles#373

0d88c52

remove any modification from JabRef_Main.xml

79be853

prashant1712 requested review from Siedlerchr and calixtus May 19, 2022 10:34

Siedlerchr reviewed May 19, 2022

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

Rrefactor and move

a10916e

Check for existing files before reading

Siedlerchr and others added 3 commits May 19, 2022 20:02

checkstyle

2dae7de

Update .gitignore

663f1b4

changing to read .gitignore from source directory of JabRef

dfefd35

using Path.of instead Paths

a78b739

adding test for filterForUnlinkedFiles

81e8d9d

calixtus reviewed May 23, 2022

View reviewed changes

koppor added the status: changes required Pull requests that are not yet complete label May 31, 2022

koppor and others added 2 commits June 20, 2022 20:57

Merge remote-tracking branch 'origin/main' into unlinkedFiles#373

1db7b6e

Rewrote .gitignore logic

0a066ea

Co-authored-by: Christoph <siedlerkiller@gmail.com> Co-authored-by: Carl Christian Snethlage <50491877 Co-authored-by: ThiloteE <73715071+ThiloteE@users.noreply.github.com>

Siedlerchr and others added 3 commits June 27, 2022 21:53

Fix tests by adding hashcode and equals

27d021f

add some more tests Fix checsktyle

Update FileNodeViewModel.java

9ede81d

koppor removed the status: changes required Pull requests that are not yet complete label Jun 27, 2022

calixtus approved these changes Jun 27, 2022

View reviewed changes

Fix indent

17ef36f

koppor merged commit 2d15917 into JabRef:main Jun 27, 2022

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Find Unlinked files should ignore Thumbs.db, etc #8800

Find Unlinked files should ignore Thumbs.db, etc #8800

prashant1712 commented May 15, 2022 •

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Find Unlinked files should ignore Thumbs.db, etc #8800

Find Unlinked files should ignore Thumbs.db, etc #8800

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