Fix issue: Auto-linking files with safe character replacements #9267 #9316

Rita-Zhou · 2022-10-27T08:08:34Z

Short Description

This aims to fix the issue where it is impossible to find the related file when the citation key involves some characters (e.g. :) that cannot be contained in the file name.
We fix this issue by searching the related file with the citation key where its unsafe characters are replaced with underscores _. (See #9267)

UI changes

Input a citation key with an unsafe character (colon ":")

Before

After

Note: The user should reopen the library to see the attachment

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.

…linking_files_with_safe_character_replacements

Siedlerchr · 2022-10-27T08:29:54Z

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

@@ -65,8 +65,13 @@ public List<Path> findAssociatedFiles(BibEntry entry, List<Path> directories, Li
        return result.stream().sorted().collect(Collectors.toList());
    }

+    public static String getSafeCiteKey(String citeKey) {
+        // replace the unsafe character with the underscore.
+        return citeKey.replaceAll("[:/*?<>|]", "_");


You should use the method FileNameCleaner.cleanFileName because this method is also called when the Filename is built from the citation key (when you have rename to pattern)

Thank you! I changed the citation key filter to FileNameCleaner!

Siedlerchr

Thanks, lgtm!

Siedlerchr · 2022-10-27T09:31:34Z

Thank you for the pull request. In future, please use the GitHub syntax Fixes #9304. Otherwise, GitHub does not automatically close the linked issue.

Siedlerchr · 2022-10-28T19:52:41Z

TODO: That looks good so far, but I am unsure atm if it is also necessary to have this for exact matches
Can you add a test case for this as well, if the preference option is "only exact key matches"?

xianghao-wang · 2022-10-29T04:18:31Z

TODO: That looks good so far, but I am unsure atm if it is also necessary to have this for exact matches Can you add a test case for this as well, if the preference option is "only exact key matches"?

Many thanks, I just now added a test for both "exact" and "startsWith" searches.

StartsWith match: check whether a file name starts with a string and this string's unsafe characters will be converted to _. Exact match: check whether a file name exactly matches a string without allowing character replacement.

A suggestion: I notice there are 3 searches for auto-linking files - 1. start with 2. exact 3. regex. I think it would be better to replace "startwith" with a new search called "fuzzy search" which can match part of the filename intelligently as suggested #9322 .

xianghao-wang · 2022-10-30T09:56:39Z

Sorry for forgetting to fix the code style and I just now fixed it.

calixtus

Looks good to me!

Siedlerchr · 2022-10-30T19:33:38Z

Thanks again for your PR!
I am unsure about the exact matching, but would leave it as it for now. If it's still an issue or requested by the users we can do a follow up.

…ok-info.com-JabRef#9145 * upstream/main: New Crowdin updates (JabRef#9333) Refresh example styles Squashed 'buildres/csl/csl-styles/' changes from 4eee79a..13fd98e Bump unirest-java from 3.13.11 to 3.13.12 (JabRef#9330) Bump checkstyle from 10.3.4 to 10.4 (JabRef#9331) Bump gittools/actions from 0.9.14 to 0.9.15 (JabRef#9332) Group context menu presents relevant options depending on number of subgroups (JabRef#9286) Removed BibTeX file type and included HTML and Markdown types (JabRef#9318) Fix issue: Auto-linking files with safe character replacements JabRef#9267 (JabRef#9316) Fix for issue 8806: Button highlights doesn't respect rounded corners (JabRef#9320) New Crowdin updates (JabRef#9324) Update CHANGELOG.md Try to relocate listener binding (JabRef#9238) Changed the messages after importing unlinked local files to past passive tense. (JabRef#9308) Changed the color of found text from red to high contrast (JabRef#9315) # Conflicts: # CHANGELOG.md

* upstream/main: (30 commits) New translations JabRef_en.properties (German) (JabRef#9336) Fix Abbreviation for Escaped Ampersand (JabRef#9288) Fix font size preference not updating in preference dialog 8386 (JabRef#9287) New Crowdin updates (JabRef#9333) Refresh example styles Squashed 'buildres/csl/csl-styles/' changes from 4eee79a..13fd98e Bump unirest-java from 3.13.11 to 3.13.12 (JabRef#9330) Bump checkstyle from 10.3.4 to 10.4 (JabRef#9331) Bump gittools/actions from 0.9.14 to 0.9.15 (JabRef#9332) Group context menu presents relevant options depending on number of subgroups (JabRef#9286) Removed BibTeX file type and included HTML and Markdown types (JabRef#9318) Fix issue: Auto-linking files with safe character replacements JabRef#9267 (JabRef#9316) Fix for issue 8806: Button highlights doesn't respect rounded corners (JabRef#9320) New Crowdin updates (JabRef#9324) Update CHANGELOG.md Try to relocate listener binding (JabRef#9238) Changed the messages after importing unlinked local files to past passive tense. (JabRef#9308) Changed the color of found text from red to high contrast (JabRef#9315) New Crowdin updates (JabRef#9317) Add skips for MacOS X build (JabRef#9305) ...

* upstream/main: New Crowdin updates (#9333) Refresh example styles Squashed 'buildres/csl/csl-styles/' changes from 4eee79a..13fd98e Bump unirest-java from 3.13.11 to 3.13.12 (#9330) Bump checkstyle from 10.3.4 to 10.4 (#9331) Bump gittools/actions from 0.9.14 to 0.9.15 (#9332) Group context menu presents relevant options depending on number of subgroups (#9286) Removed BibTeX file type and included HTML and Markdown types (#9318) Fix issue: Auto-linking files with safe character replacements #9267 (#9316) Fix for issue 8806: Button highlights doesn't respect rounded corners (#9320) New Crowdin updates (#9324) Update CHANGELOG.md Try to relocate listener binding (#9238) Changed the messages after importing unlinked local files to past passive tense. (#9308) Changed the color of found text from red to high contrast (#9315) New Crowdin updates (#9317) Add skips for MacOS X build (#9305) New Crowdin updates (#9248) Fix for issue 9304 (#9313) # Conflicts: # CHANGELOG.md

Rita-Zhou added 4 commits October 27, 2022 17:07

fix the safe character replacement and auto-linking the files

81feb69

Merge branch 'main' of https://github.com/Rita-Zhou/jabref into Auto-…

345da63

…linking_files_with_safe_character_replacements

Merge branch 'main' of https://github.com/Rita-Zhou/jabref into Auto-…

d86b3ed

…linking_files_with_safe_character_replacements

Test the unsafe citation key attach the file.

88c46ae

Siedlerchr reviewed Oct 27, 2022

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Change to citation key filter to the existing FileNameCleaner

4cc19c1

Siedlerchr added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Oct 27, 2022

Siedlerchr approved these changes Oct 27, 2022

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ThiloteE added the external files label Oct 27, 2022

ThiloteE removed the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Oct 28, 2022

Add tests for "exact" and "startsWith" matches of auto-linking files

492d150

xianghao-wang mentioned this pull request Oct 29, 2022

Replace "start-with" auto-linking with "fuzzy-search" auto-linking #9322

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calixtus approved these changes Oct 30, 2022

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Siedlerchr added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Oct 30, 2022

Siedlerchr approved these changes Oct 30, 2022

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Siedlerchr merged commit 46b7339 into JabRef:main Oct 30, 2022

ThiloteE mentioned this pull request Jan 13, 2023

Main file directory is used if not empty, even if deactivated #9556

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Fix issue: Auto-linking files with safe character replacements #9267 #9316

Fix issue: Auto-linking files with safe character replacements #9267 #9316

Rita-Zhou commented Oct 27, 2022 •

edited by Siedlerchr

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Siedlerchr commented Oct 30, 2022

Fix issue: Auto-linking files with safe character replacements #9267 #9316

Fix issue: Auto-linking files with safe character replacements #9267 #9316

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Rita-Zhou commented Oct 27, 2022 • edited by Siedlerchr Loading

Short Description

UI changes

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