Add "Look up DOIs" to Quality menu #2442

koppor · 2016-12-31T17:47:40Z

This adds "Lookup DOIs" to the quality menu. Additionally: Rename lookup to look up (see http://notaverb.com/lookup)

With an updating status bar:

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Check documentation status (Issue created for outdated help page at help.jabref.org?)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?

Additionally: Rename lookup to look up (see http://notaverb.com/lookup)

Siedlerchr · 2016-12-31T23:15:43Z

src/main/java/net/sf/jabref/gui/worker/LookupDOIsWorker.java

+ NamedCompound namedCompound = new NamedCompound(Localization.lang("Look up DOIs"));
+ int count = 0;
+ int foundCount = 0;
+ for (BibEntry bibEntry : bibEntries) {


Wouldn't it make sense to directly filter out the bibtex fields which have a DOI here with a stream?
e.g bibentries.stream().filter(x->hasField(FielName.DOI).....

I have no idea how to create a progress bar there.

I found http://stackoverflow.com/a/26814087/873282, but that code looks much more complicated than the current code. Should I change it?

Na then go for it now.,

Siedlerchr · 2016-12-31T23:19:27Z

src/main/java/net/sf/jabref/gui/worker/LookupDOIsWorker.java

+ frame.output(Localization.lang("Looking up DOIs... - entry %0 out of %1 - found %2", Integer.toString(count), totalCount, Integer.toString(foundCount)));
+ if (!bibEntry.hasField(FieldName.DOI)) {
+ Optional<DOI> doi = DOI.fromBibEntry(bibEntry);
+ if (doi.isPresent()) {


You could chain the optionals with flatmap, avoid the ifPresent cascading...

http://www.nurkiewicz.com/2013/08/optional-in-java-8-cheat-sheet.html

No clue how I can do that with progress...

Okay, was just an idea. If it does not make it easier forget about it

Siedlerchr

Some minor changes and its okay from my side

tobiasdiez · 2017-01-01T11:18:41Z

src/main/java/net/sf/jabref/gui/worker/LookupDOIsWorker.java

+
+ private static final Log LOGGER = LogFactory.getLog(LookupDOIsWorker.class);
+
+ public LookupDOIsWorker(JabRefFrame frame) {


For maximal reusability, could you please make this class independent on DOI. There are many other identifier for which such an automatic look-up makes sense.

Language: Either ID or let the caller set the DOI name

lines 43 to 46 somehow extract. Interface: CanCompleteEntry

@koppor can you please rebase and I will implement then the rest. Deal?

# Conflicts: # CHANGELOG.md # src/main/java/org/jabref/gui/BasePanel.java # src/main/java/org/jabref/gui/JabRefFrame.java

tobiasdiez · 2017-03-17T15:13:06Z

@koppor thanks for rebased. I generalized it now to also work for other identifiers so this PR is now ready for review.

koppor · 2017-03-17T17:11:07Z

src/main/java/org/jabref/model/entry/identifier/Identifier.java

@@ -0,0 +1,8 @@
+package org.jabref.model.entry.identifier;
+
+public interface Identifier {


Should we call this class HasIdentifier?

koppor · 2017-03-17T17:21:00Z

LGTM 😇

I get multiple errors when using it. I don't get the information which entry is affected. But this is not an issue of this PR. Just wanted to note it down somewhere.

2017-03-17 18:14:36,528 Spin-0 ERROR Recursive call to appender GuiLogger

Caused by: org.jabref.logic.importer.ParseException: CrossRef API JSON format has changed
        at org.jabref.logic.importer.fetcher.CrossRef.jsonItemToBibEntry(CrossRef.java:131) ~[main/:?]
        at org.jabref.logic.importer.fetcher.CrossRef.lambda$getParser$3(CrossRef.java:88) ~[main/:?]
        at org.jabref.logic.importer.IdParserFetcher.findIdentifier(IdParserFetcher.java:75) ~[main/:?]
        ... 8 more
Caused by: org.json.JSONException: JSONObject["given"] not found.
        at org.json.JSONObject.get(JSONObject.java:471) ~[json-20160212.jar:?]
        at org.json.JSONObject.getString(JSONObject.java:717) ~[json-20160212.jar:?]
        at org.jabref.logic.importer.fetcher.CrossRef.toAuthors(CrossRef.java:144) ~[main/:?]
        at org.jabref.logic.importer.fetcher.CrossRef.jsonItemToBibEntry(CrossRef.java:117) ~[main/:?]
        at org.jabref.logic.importer.fetcher.CrossRef.lambda$getParser$3(CrossRef.java:88) ~[main/:?]
        at org.jabref.logic.importer.IdParserFetcher.findIdentifier(IdParserFetcher.java:75) ~[main/:?]

Caused by: java.io.IOException: Server returned HTTP response code: 500 for URL: http://api.crossref.org/works?query.title=A+%28sub%29graph+isomorphism+algorithm+for+matching+large+graphs&query.author=L.P.+Cordella+and+P.+Foggia+and+C.+Sansone+and+M.+Vento&filter=from-pub-date%3A2004&rows=20&offset=0

* upstream/master: Localization: General: French: Translation of new entries Localization: Menu: French: Translation of an entry (#2685) Fix #2680 and fix #2667: Swing errors are catched properly and without freezing (#2681) Do not log AND throw Replace misleading error message for fetcher connection error Document CrossRef test Fix subtitle detection for CrossRef fetcher Revert "Invoke LogMessages.add in JavaFX thread" Use global user agent Update mockito from 2.7.17 to 2.7.18 Move GuiAppender to GUI package Invoke LogMessages.add in JavaFX thread [WIP] Put the PDFAnnotationImporter under Test, enhance FileAnnotationTab (#2640) Fix for "Paying off technical debt: almost all utility classes have a private constructor now." (#2672) Revert "Paying off technical debt: almost all utility classes have a private constructor now. (#2649)" (#2670) Paying off technical debt: almost all utility classes have a private constructor now. (#2649) Changed codeformatting for better fxml annotation (#2668) Disalbe Google Scholar tests on all CI environments (#2654) Fix JSONException in Crossref fetcher as mentioned in #2442

Add "Look up DOIs" to Quality menu

bf77a68

Additionally: Rename lookup to look up (see http://notaverb.com/lookup)

koppor added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Dec 31, 2016

Siedlerchr reviewed Dec 31, 2016

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Siedlerchr approved these changes Dec 31, 2016

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tobiasdiez reviewed Jan 1, 2017

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tobiasdiez removed the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Jan 9, 2017

koppor added on-hold and removed on-hold labels Jan 20, 2017

koppor and others added 3 commits March 17, 2017 09:08

Merge branch 'master' into lookupdoi

ecbdd11

# Conflicts: # CHANGELOG.md # src/main/java/org/jabref/gui/BasePanel.java # src/main/java/org/jabref/gui/JabRefFrame.java

Adapt to new WebFetchers.getIdFetcherForIdentifier(DOI.class) thing

fd5b71b

Generalize look up to other identifiers

b11cecc

tobiasdiez added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Mar 17, 2017

koppor commented Mar 17, 2017

View reviewed changes

Fix Codacy

e29be92

Siedlerchr approved these changes Mar 17, 2017

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koppor merged commit 63620ff into master Mar 18, 2017

koppor deleted the lookupdoi branch March 18, 2017 08:44

tobiasdiez added a commit that referenced this pull request Mar 19, 2017

Fix JSONException in Crossref fetcher as mentioned in #2442

51653c1

stefan-kolb mentioned this pull request Mar 23, 2017

Lookup DOI (sometimes) freezes JabRef #2680

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Add "Look up DOIs" to Quality menu #2442

Add "Look up DOIs" to Quality menu #2442

koppor commented Dec 31, 2016

Siedlerchr Dec 31, 2016

koppor Jan 29, 2017

Siedlerchr Jan 29, 2017

Siedlerchr Dec 31, 2016

koppor Jan 29, 2017

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koppor Jan 20, 2017 •

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koppor Mar 17, 2017

koppor commented Mar 17, 2017


		private static final Log LOGGER = LogFactory.getLog(LookupDOIsWorker.class);

		public LookupDOIsWorker(JabRefFrame frame) {

		@@ -0,0 +1,8 @@
		package org.jabref.model.entry.identifier;

		public interface Identifier {

Add "Look up DOIs" to Quality menu #2442

Add "Look up DOIs" to Quality menu #2442

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