Fix lookup fulltext document not finding files #5216

Siedlerchr · 2019-08-24T14:17:52Z

Followup from #5118
Look up fulltext documents now searches for existing local files before attempting to download it

Change in CHANGELOG.md described
Tests created for changes
Manually tested changed features in running JabRef
Screenshots added in PR description (for bigger UI changes)
Ensured that the git commit message is a good one
Check documentation status (Issue created for outdated help page at help.jabref.org?)

…xlookupfulltext * 'master' of git://github.com/PedroPerozin/jabref: Change variable name Issue#3874 Fix import order Issue #3874 Fix checkstyle Issue #3874 Fix travis Fix issue #3874

* upstream/master: fix bug where main file directory is not set correctly (#5215) Use UTF-8 as default encoding for files (#5213) fix: missing separator for unchanged diff words fix: use UTF-8 as default encoding for files ~ resolves #5133 Minor improvements to TexParser Fix lookup entry types in enums (#5209)

tobiasdiez · 2019-08-24T22:41:48Z

Why is this the intended behavior? For me this are two completely different use cases and as a user I usually know if I have the file already on the disk or still have to download it. Probably worth to discuss a bit at jabcon...

Siedlerchr · 2019-08-24T22:51:48Z

There was a discussion in #3874 and the common sense seemed to be to check for files existed it and only download if not existing

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

* upstream/master: (27 commits) remove wrong dependencies add missing dependencies Fix exception when adding field formatter in 'Cleanup entries' dialog Disables the preview cycling Removed unused method (#5219) Switch from tika-parsers to tika-core (#5217) Fix for issue 4629 (#5150) fix l10n, again fix l10n Fix checkstyle Removed old entrypreview and corresponding actions Prototype Add minor improvements and remove unused code Update CHANGELOG.md Update to current entry types and reformat code Convert Integer type to primitive Fix localization keys fix checkstyle again fix checkstyle erros Bibtexextractor ...

extract fetchers to the top

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

# By Tobias Diez (109) and others # Via GitHub (109) and others * upstream/master: (404 commits) set jabrefHost.py executable (#5530) Add CHANGELOG entry for #5482 Fix text colour in Merge dialogue (#5521) Remove empty customization warning Fix typos in external-libraries.txt file Fix new entry serialization test Add test for alphabetic serialization of fields in BibEntry Fix XMP null error Bring back the scrollbars (#5515) Fix metadata serialization order (#5514) New ADS Fetcher (#5501) snap: Add browser proxy for confined browser integration (#5512) Fix dark theme loading Update PreviewViewer.java [WIP] Try to fix dark theme path Use Platform.runLater Fixes #5485 Bump com.github.ben-manes.versions from 0.26.0 to 0.27.0 Bump src/main/resources/csl-styles from `68a697b` to `c3fd4bd` Bump byte-buddy-parent from 1.10.1 to 1.10.2 ... # Conflicts: # src/main/resources/l10n/JabRef_en.properties

Siedlerchr · 2019-11-06T15:07:29Z

I recently refactored the issues here. This should be ready for merge now,

tobiasdiez · 2019-11-06T18:25:11Z

I'm still not really convinced that we should reimplement the old behavior. Let's discuss this in the next devcall.

koppor · 2019-11-16T14:13:12Z

Is this magic button vs. explicit functionality? Should we add a "magic wand" icon in addition? I remember that @stefan-kolb wished that functionality some years ago!

koppor · 2019-11-22T15:59:48Z

Decision:

Button for download (only) --> Rename to "Download fulltext"
Download file
If file is equal to existing linked file, do not link and do not keep
If file is not equal to already linked files (or no linked files are there), add it as another file (with second file)
Other existing files (which are currently not linked - even if they match the filename pattern), are ignored.

Reasons:

auto-lookup exists per entry: Look up fulltext documents does not link existing PDFs #3874
clear separation of functionality

Possible follow up issues:

Remember choice that it should not be linked (at auto link at entry editor)
At startup: find unlinked files matching the file pattern
- in the side bar; not as dialog
- DO NOT link other files --> Refs Find unlinked files should ignore Thumbs.db etc. jabref-koppor#373
Make "File Magic Wizard" --> Create "File Magic Wizard" jabref-koppor#380
- Auto-link all files
- Download all missing files

Closes #3874 and surpasses #5216.

koppor · 2019-11-24T21:49:40Z

We have a follow-up PR at #5667. For the open issues, I created follow-up issues at https://github.com/koppor/jabref/issues

30fb68e Create BJEDIS-ABNT-Number (#5255) aafb868 Update geochimica-et-cosmochimica-acta.csl (#5321) 60ba25f british-journal-of-anaesthesia.csl: add comma delimiter between non-sequential citations eg. 1 4 7-9 -> 1, 4, 7-9 (#5313) 67e6564 Reindent/reorder (#5318) c0d2a39 Ruby 3.0.0 (#5309) 76d60ff Update harvard-anglia-ruskin-university.csl (#5310) bc18ac9 Create journal-for-the-study-of-the-new-testament.csl (#5312) aff602c Update journal-of-food-protection.csl (#5315) 4503826 Update muscle-and-nerve.csl (#5317) 3bed58e constant redefinition 4d718a0 update documentaiton link fa99e2f add comma delimiter between succesive numbers d396f8b Allow privileged testing of PRs (#5307) 43b22c7 Update masarykova-univerzita-pravnicka-fakulta.csl, pravnik.csl, iso690-full-note-cs.csl (#5308) 8a31c1e Update copernicus-publications.csl (#5303) 96760bb Update anabases.csl (#5304) 744de6d removed locale (#5300) 7eb0d60 Update aviation-space-and-environmental-medicine.csl (#5297) 2769970 Update ruhr-universitat-bochum-lehrstuhl-fur-industrial-sales-and-ser… (#5298) 51e3f4c Update harvard-university-of-bath.csl (#5299) 5fce84f Create cns-spectrums.csl (#5290) bb8082c Create journal-of-surgical-oncology.csl (#5259) 90c13ae Update ruhr-universitat-bochum-lehrstuhl-fur-industrial-sales-and-ser… (#5288) 4bab1ad Update early-christianity.csl (#5289) 636ba78 Update tatup-zeitschrift-fur-technikfolgenabschatzung-in-theorie-und-… (#5291) b7cc511 Create biotechnologia.csl (#5292) 5bab881 Update journal-of-orthopaedic-trauma.csl (#5287) 5943413 Fix locales (#5285) 302bd65 Update universite-du-quebec-a-montreal-departement-dhistoire.csl (#5286) 860ae48 Add Haaga-Helia University of Applied Sciences Harvard style (#5282) c1c27de Localize Metropolia style title (#5283) 508da89 Fix presentation for Methods of Information in Medicine (#5284) 53e1d0b Create geschichte-und-gesellschaft.csl (#5216) d7ed0cb Create universite-de-geneve-departement-de-francais-moderne.csl (#5212) 80c404b Update journal-of-orthopaedic-trauma.csl (#5281) 20c143a Adding publishers' names (#5280) 6e5cd59 Update sodertorns-hogskola-oxford.csl (#5279) 52f2621 dollar-brace a260294 Create journal-of-microbiology-and-biotechnology.csl (#5277) 1fc979e Create qeios.csl (#5261) 86347b7 GH does this for us -- again, sorry guys b649589 Create experimental-biology-and-medicine.csl (#5276) 12ae0b1 Revert "tell sheldon about the job state" bdcae89 tell sheldon about the job state 1240067 Add Vegetation classification and Survey (#5271) 6f398f0 Major update to Gallia.csl (#5269) 2a74b2c Update filters.yaml (#5273) 20046d2 Update spec_helper.rb (#5272) 2ee0dd8 Create the-sociological-review.csl (#5260) 5b8d09c move filters to inert file to pacify Sheldon (#5268) e5f3315 Localize more language descriptors in style titles (#5270) bfd2942 Localize more language descriptors in style titles (#5267) 35e276f Fix variable used for the label after indication of number of pages (#5240) 60f6371 Create Universidade-do-Estado-do-Rio-de-Janeiro.csl (#5247) d8cc2ae Create the-journal-of-the-acoustical-society-of-america-numeric.csl (#5256) 92259c1 Create journal-of-financial-and-quantitative-analysis.csl (#5264) 6ba8aab Create journal-of-vestibular-research.csl (#5258) 0c88f41 Update european-journal-of-international-law.csl (#5265) cff5abc Put language descriptor within parentheses 4a62709 Update monash-university-harvard.csl (#5253) 64fd1aa Localize more language descriptors in style titles (#5262) f6519cb Localize more language descriptors in style titles (#5257) 170ccae tiny fixes for universitat-basel-iberoromanistik.csl (#5254) b7284c9 Localize more language descriptors in style titles (#5252) f4ef858 Add "Baishideng Publishing Group" dependents (#5251) 266e7c3 Make world-journal-of-hepatology.csl to bpg.csl parent (#5243) 9129098 fix small formatting issues for mclc.csl (#5229) 5d9560b Create crispr-journal.csl (#5249) a217299 Change "Czech" to "Čeština" in titles (#5248) 4fef39a Create journal-of-open-research-software.csl (#5245) 2bff1a6 Change "Dutch" to "Nederlands" in titles (#5242) f28da34 Update spec_helper.rb (#5246) e0e977c Move content from wiki pages to markdown files (#5194) 018304c Update universite-de-montreal-apa.csl (#5239) 3b83e5c Create sodertorns-hogskola-oxford.csl (#5234) 1335378 Stop notifying 8827 port on Zotero servers (#5237) f079b2a Update author-year disambiguation (#5238) 60bb0c9 Update technische-universitat-dresden-medizin.csl (#5236) e374657 Create Leidraad voor juridische auteurs 2019 (Dutch) (#5223) 0450d89 Add new style for U of Mannheim, Germanistische Linguistik (#5228) 81f0689 Create health-sports-rehabilitation-medicine.csl (#5233) c152a44 Update Gemfile.lock (#5235) 748e1eb Update geochimica-et-cosmochimica-acta.csl (#5231) 06b9ce8 Update zeitschrift-fur-theologie-und-philosophie.csl (#5230) e747cb1 haute-ecole-de-gestion-de-geneve: Make polyglot & et al changes 4cfedb7 Create universite-de-sherbrooke-histoire.csl (#5210) a96a61e Update journal-of-glaciology.csl (#5222) c6a94c9 Add Journal of Human Rights (#5227) c5c9c5f Update ruhr-universitat-bochum-lehrstuhl-fur-industrial-sales-and-ser… (#5214) ffb7aa6 Create comparativ.csl (#5215) e07329a Update lancaster-university-harvard.csl (#5220) c075d41 Update mimesis-edizioni.csl (#5219) 502970a Removed space in year only citation (#5218) 13e8c6b Update acta-scientiae-veterinariae.csl (#5209) 0699da6 Remake mammallia.csl for Oct/2020 guidelines. (#5207) b2dd3fd Update journal-of-international-business-studies.csl (#5217) dd52bfe Update quaternaire.csl (#5199) ccb1b0d rebuild webpage and article-journal citations in journal-of-forensic-sciences.csl (#5203) f02f4fb Create pedosphere.csl (#5196) 70dd87a Create open-gender-journal.csl (#5198) d272998 Create the-quarterly-journal-of-economics.csl (#5197) d27cab3 fix locale issues, add cite-locator (#5206) git-subtree-dir: buildres/csl/csl-styles git-subtree-split: 30fb68e

PedroPerozin and others added 8 commits July 11, 2019 16:25

Fix issue #3874

2731f8f

Fix travis

47656e7

Fix checkstyle Issue #3874

2fc1c49

Fix import order Issue #3874

ec3ad69

Change variable name Issue#3874

88118f4

Merge branch 'master' of git://github.com/PedroPerozin/jabref into fi…

33fb6c5

…xlookupfulltext * 'master' of git://github.com/PedroPerozin/jabref: Change variable name Issue#3874 Fix import order Issue #3874 Fix checkstyle Issue #3874 Fix travis Fix issue #3874

Fulltext lookup now searches for local files before

d2c4724

Siedlerchr mentioned this pull request Aug 24, 2019

Fix lookup fulltext document not finding files# #5118

Closed

6 tasks

Siedlerchr added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Aug 24, 2019

koppor requested changes Aug 25, 2019

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Siedlerchr added 4 commits August 25, 2019 10:50

fix formatting

f81fa9e

extract fetchers to the top

Fixes l10n

5559f9c

fix indendation, add comment

4f079a3

koppor removed the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Aug 25, 2019

tobiasdiez reviewed Aug 25, 2019

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

koppor changed the title ~~Fix lookup fulltext document not finding files~~ [WIP] Fix lookup fulltext document not finding files Aug 25, 2019

koppor added the status: waiting-for-feedback The submitter or other users need to provide more information about the issue label Aug 25, 2019

Siedlerchr added 2 commits October 27, 2019 21:14

separate find fulltext and download methods

14ade56

Siedlerchr added status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers and removed status: waiting-for-feedback The submitter or other users need to provide more information about the issue labels Oct 27, 2019

Siedlerchr changed the title ~~[WIP] Fix lookup fulltext document not finding files~~ Fix lookup fulltext document not finding files Oct 27, 2019

fix indent to make the intellij people happy...

eed70a5

tobiasdiez added status: devcall and removed status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers labels Oct 27, 2019

koppor removed the status: devcall label Nov 22, 2019

tobiasdiez added a commit that referenced this pull request Nov 23, 2019

Rename "lookup fulltext" to "download fulltext"

690566f

Closes #3874 and surpasses #5216.

tobiasdiez mentioned this pull request Nov 23, 2019

Rename "lookup fulltext" to "download fulltext" #5667

Merged

5 tasks

koppor pushed a commit that referenced this pull request Nov 24, 2019

Rename "lookup fulltext" to "download fulltext" (#5667)

d0d3d0b

Closes #3874 and surpasses #5216.

This was referenced Nov 24, 2019

When a new file link is proposed and the user declines: Remember choice JabRef/jabref-koppor#378

Open

Create "File Magic Wizard" JabRef/jabref-koppor#380

Closed

At startup: find unlinked files matching the file pattern JabRef/jabref-koppor#379

Open

koppor closed this Nov 24, 2019

koppor deleted the fixlookupfulltext branch November 24, 2019 21:49

koppor added the external files label Nov 24, 2019

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Fix lookup fulltext document not finding files #5216

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Fix lookup fulltext document not finding files #5216

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