Check duplicate DOI #6333

koppor · 2020-04-21T21:49:11Z

Result of #latemob session with @skufer322.

Includes quick refactorings to increase code quality.
Should also speedup our integrity check and reduce memory footprint (since the checkers are created per database check run - and not per entry check run)
Tests missing. Proposal: Leave tests for students 😇 ---> Add simple Unit tests #6207

Change in CHANGELOG.md described (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 documentation: Is the information available and up to date? If not created an issue at https://github.com/JabRef/user-documentation/issues or, even better, submitted a pull request to the documentation repository.

Siedlerchr · 2020-04-22T06:21:29Z

src/main/java/org/jabref/logic/integrity/DoiDuplicationChecker.java

+    @Override
+    public List<IntegrityMessage> check(BibEntry entry) {
+        if (errors == null) {
+            errors = new HashMap<>();


Why not directly initialize that HashMap in the field declaration?

MAybe you did not see that the later code uses the BibtexDatabase from the constructor. We decided to put the code into check - and not into the constructor - to have a lean constructor and not have high CPU usage when initializing the checker, but at the first time an entry is checked.

This seems like premature optimization for me.

Why are you caching the errors anyway? Also in case you are worrying about performance, why do you choose to implement a solution that has O(n^2) (with n = entries). Why not implement a O(n) solution (e.g. https://stackoverflow.com/a/31341963/873661) which you call in checkDatabase below?

See in line 30 that the method is called once per entry. Is is by design of the Checker interface that there is method for checking each entry. There is no method for checking a complete database. There is also no interface for a complete database.

At the first call, the result map is filled. At all subsequent calls do not fill the map and reuse it.

We are O(n+m) where n is the size of the database and m is the number of entries with DOIs.

To make the code more reable, I moved the call to the error check to the constructor. See fd7621d

koppor · 2020-04-22T06:44:37Z

src/main/java/org/jabref/logic/integrity/DoiDuplicationChecker.java

+            BiMap<DOI, List<BibEntry>> duplicateMap = HashBiMap.create(bibEntries.size());
+            for (BibEntry bibEntry : bibEntries) {
+                bibEntry.getDOI().ifPresent(doi ->
+                        duplicateMap.computeIfAbsent(doi, x -> new ArrayList<>()).add(bibEntry));


It is doi, not entry. However, doi cannot be used as the variable name is already bound.

@koppor Please have a close look. The second argument of duplicateMap.computeIfAbsent refers to the value and this clearly is of type List. So then maybe name it entries

@Siedlerchr Please explain the JavaDoc to me. The Map is FROM doi TO list. https://www.geeksforgeeks.org/hashmap-computeifabsent-method-in-java-with-examples/ explains the computeIfAbsent.

To me, it reads, that the key is passed to Function<? super K, ? extends V> remappingFunction. The key is clearly (!) a DOI not a list. -- Am I wrong?

To make the code more reable, I called the variable absentDoi. See 6f9b148

koppor · 2020-04-22T06:44:37Z

src/main/java/org/jabref/logic/integrity/DoiDuplicationChecker.java

+            BiMap<DOI, List<BibEntry>> duplicateMap = HashBiMap.create(bibEntries.size());
+            for (BibEntry bibEntry : bibEntries) {
+                bibEntry.getDOI().ifPresent(doi ->
+                        duplicateMap.computeIfAbsent(doi, x -> new ArrayList<>()).add(bibEntry));


It is doi, not entry. However, doi cannot be used as the variable name is already bound.

tobiasdiez

That seems way more complicated than it need to be: https://stackoverflow.com/a/31341963/873661

tobiasdiez · 2020-04-22T12:16:14Z

src/main/java/org/jabref/logic/integrity/IntegrityCheck.java

    }

-    public List<IntegrityMessage> checkDatabase() {
+    private void initCheckers(BibDatabaseContext bibDatabaseContext, BibtexKeyPatternPreferences bibtexKeyPatternPreferences, JournalAbbreviationRepository journalAbbreviationRepository) {


To be honest, I don't see any advantage of this refactoring. Just makes the code more complex and harder to maintain in my opinion.

If you really feel like the original code needs a refactoring, then you create a list of all checkers that need to be run a) always, b) bibtex c)biblatex (still I would create these lists only in the checkdatabase method). This would get ride of the repeated check methods below. But to be honest, I don't think this yields a more readable code either.

We initialize the checkers once per database check - not once per entry check. In case of a 20k database, approx 100k less java objects in memory per quality check.

We ensured that each checker is stateless - thus, it can be reused for acroess entries.

I agree with your proposal though.

With your proposal, the code is much more reable. 🎉 03dd2a0

tobiasdiez · 2020-04-22T12:26:39Z

src/main/java/org/jabref/logic/integrity/DoiDuplicationChecker.java

+    @Override
+    public List<IntegrityMessage> check(BibEntry entry) {
+        if (errors == null) {
+            errors = new HashMap<>();


Why are you caching the errors anyway? Also in case you are worrying about performance, why do you choose to implement a solution that has O(n^2) (with n = entries). Why not implement a O(n) solution (e.g. https://stackoverflow.com/a/31341963/873661) which you call in checkDatabase below?

koppor · 2020-04-22T21:26:49Z

That seems way more complicated than it need to be: stackoverflow.com/a/31341963/873661

I dont get in the stack overlfow thing, how they check

Stream((entry1, doi1), (entry2, doi1), (enty3, doi3))

Think, I have to implement a comparator comparing two bibentries by doi only. At the DOI comparison, I need to make a DOI object. I could cache that (which is unwanted) or I can reconstruct it every time (which is slower than oru approach above -- there, we construct the DOI object once per bib entry)

We need to construct the DOI object to be able to compare two DOIs. We decided that equals is a domain function belonging to the DOI object. (This respects the antipattern AnemicDomainModel https://martinfowler.com/bliki/AnemicDomainModel.html)

Co-authored-by: Oliver Kopp <[email protected]>

tobiasdiez

Very nice refactoring! Looks good to me, just a bit of nitpicking.

tobiasdiez · 2020-04-23T10:35:21Z

src/main/java/org/jabref/logic/integrity/Checker.java

+import org.jabref.model.entry.BibEntry;
+
+@FunctionalInterface
+public interface Checker {


Rename to EntryChecker?

tobiasdiez · 2020-04-23T10:37:04Z

src/main/java/org/jabref/logic/integrity/DoiDuplicationChecker.java

+        return duplicateMap.inverse().keySet().stream()
+                           .filter(list -> list.size() > 1)
+                           .flatMap(list -> list.stream())
+                           .map(item -> new IntegrityMessage(Localization.lang("Unique DOI used in multiple entries"), item, StandardField.DOI))


I think "The same DOI is used..." is better

Just "Same DOI..." will do.

tobiasdiez · 2020-04-23T10:39:56Z

src/main/java/org/jabref/logic/integrity/IntegrityCheck.java

    }

-    public List<IntegrityMessage> checkDatabase() {
+    List<IntegrityMessage> executeAllCheckers() {


Name it simply check?

# Conflicts: # src/main/java/org/jabref/logic/integrity/IntegrityCheck.java # src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java

…into check-duplicate-doi

koppor

Thank you

* upstream/master: (50 commits) Keep group pane size when resizing window (#6180) (#6423) Changelog: Fix missing citation for biblatex-mla Update AUTHORS Check duplicate DOI (#6333) Fix missing citation for biblatex-mla Change EasyBind dependency (#6480) Add testing of latest dev version as mandatory Squashed 'src/main/resources/csl-styles/' changes from 5dad23d..586e0b8 Fix libre office connection and other progress dialogs (#6478) Fix clear year and month field when converting to biblatex (#6434) Add truncate as a BibTex key modifier (#6427) Add new authors (not all - they need more work) Remove empty line Add simple Unit Tests for #6207 (#6240) Enforce LeftCurly rule (#6452) Implement task progress indicator (and dialog) in the toolbar (#6443) Consider empty brackets Changelog update Added a test Fixed brackets in regular expressions ...

# By dependabot-preview[bot] (18) and others # Via GitHub (17) and others * upstream/master: (77 commits) Reenable caching of gradle Refactor BibtexKeyPatternPreferences (#6489) Update CHANGELOG.md Add changelog entry and remove unnecessary code EasyBind revision part two Fix Drag and Drop on empty database Truncates DOIs and URLs in the column "Linked identifiers" in main table, if too long (#6498) Bump flexmark-ext-gfm-tasklist from 0.61.26 to 0.61.30 Bump flexmark from 0.61.26 to 0.61.30 Bump xmlunit-matchers from 2.6.4 to 2.7.0 Bump java-string-similarity from 1.2.1 to 2.0.0 Bump flexmark-ext-gfm-strikethrough from 0.61.26 to 0.61.30 Bump xmlunit-core from 2.6.4 to 2.7.0 Truncates the link and/or the link description in the column "linked files" in main table, if too long (#6179) Keep group pane size when resizing window (#6180) (#6423) Changelog: Fix missing citation for biblatex-mla Update AUTHORS Check duplicate DOI (#6333) Fix missing citation for biblatex-mla Change EasyBind dependency (#6480) ... # Conflicts: # src/main/java/org/jabref/gui/actions/ActionHelper.java # src/main/java/org/jabref/gui/customentrytypes/CustomEntryTypeDialogViewModel.java # src/main/java/org/jabref/gui/customentrytypes/CustomizeEntryTypeDialogView.java # src/main/java/org/jabref/model/entry/field/FieldFactory.java

f6c778e Update emerald-harvard.csl (#6335) d6c6a16 Fix Brazilian quotes on chicago-author-date.csl (#6317) a1549b6 Update medizinische-hochschule-hannover.csl (#6330) da88073 Update journal-of-the-american-college-of-cardiology.csl (#6334) a520d8e Bump nokogiri from 1.13.9 to 1.13.10 (#6333) ba54b44 Update royal-society-of-chemistry.csl (#6328) 1378ba7 LUSEM: Remove full stop (#6332) 9e3cf89 Create interpreting.csl (#6254) bef74ed Create conservation-science-and-practice.csl (#6258) 9fb7eb7 Bug fixes triangle.csl (#6251) e6112ba Update ucl-university-college-apa.csl (#6250) 6dcba3a Update engineering-technology-and-applied-science-research.csl (#6247) 00fe4a2 Create constructivist-foundations.csl (#6243) 03ad71b Create les-mondes-du-travail.csl (#6234) a2bce86 Corrections based on author instructions (#6306) git-subtree-dir: buildres/csl/csl-styles git-subtree-split: f6c778e

84dba23 Update international-union-of-crystallography.csl (#6279) 13dd9e8 Update zeitschrift-fur-deutsche-philologie.csl (#6340) d95b652 Create cahiers-mondes-anciens.csl (#6203) ded567c Create rassegna-degli-archivi-di-stato-bibliografia-generale.csl (#6275) 124777a Create scientific-online-letters-on-the-atmosphere.csl (#6261) 3c276e7 Create american-medical-association-no-url-alphabetical.csl (#6252) 595ad95 Bump mathieudutour/github-tag-action from 6.0 to 6.1 (#6287) 7008128 Create cambridge-a (#6336) 17e930c Update norsk-apa-manual-note.csl (#6338) b360859 Update norsk-apa-manual.csl (#6337) f6c778e Update emerald-harvard.csl (#6335) d6c6a16 Fix Brazilian quotes on chicago-author-date.csl (#6317) a1549b6 Update medizinische-hochschule-hannover.csl (#6330) da88073 Update journal-of-the-american-college-of-cardiology.csl (#6334) a520d8e Bump nokogiri from 1.13.9 to 1.13.10 (#6333) ba54b44 Update royal-society-of-chemistry.csl (#6328) 1378ba7 LUSEM: Remove full stop (#6332) 9e3cf89 Create interpreting.csl (#6254) bef74ed Create conservation-science-and-practice.csl (#6258) 9fb7eb7 Bug fixes triangle.csl (#6251) e6112ba Update ucl-university-college-apa.csl (#6250) 6dcba3a Update engineering-technology-and-applied-science-research.csl (#6247) 00fe4a2 Create constructivist-foundations.csl (#6243) 03ad71b Create les-mondes-du-travail.csl (#6234) a2bce86 Corrections based on author instructions (#6306) git-subtree-dir: buildres/csl/csl-styles git-subtree-split: 84dba23

stefan-kolb and others added 9 commits April 21, 2020 21:27

ioebnfgoeoignboieg

2e07d9b

asdf

c3724a8

WIP: Add equals to DOI

1a7aa44

rbrbbrbr

a1b0fbc

Flatmap

9b46f85

Fix checkstyle

ae89990

Remove obsolete .

006c241

Add CHANGELOG.md entry

b3e703b

Fix tests by using "old school" for loop with appropriate Optional check

2c00e7d

koppor added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Apr 21, 2020

koppor changed the title ~~Check duplicate doi~~ Check duplicate DOI Apr 22, 2020

Siedlerchr requested changes Apr 22, 2020

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koppor commented Apr 22, 2020

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tobiasdiez requested changes Apr 22, 2020

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koppor removed the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Apr 22, 2020

koppor and others added 5 commits April 23, 2020 05:52

Rearrange code (to make it more readable)

fd7621d

Create List of checkers at the contructor

03dd2a0

Fix variable name

6f9b148

add new interface DatabaseChecker

2de1858

Co-authored-by: Oliver Kopp <[email protected]>

Add FunctionalInterface annotation to DatabaseChecker

4c9e687

Co-authored-by: Oliver Kopp <[email protected]>

koppor marked this pull request as draft April 23, 2020 10:38

tobiasdiez requested changes Apr 23, 2020

View reviewed changes

Move comments

97b9cbe

koppor self-assigned this Apr 26, 2020

jmoosmann added 5 commits May 15, 2020 10:22

remove unused import

eaebdf5

Merge remote-tracking branch 'upstream/master' into check-duplicate-doi

7c72d52

# Conflicts: # src/main/java/org/jabref/logic/integrity/IntegrityCheck.java # src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java

Merge branch 'check-duplicate-doi' of https://github.com/JabRef/jabref …

c8296c3

…into check-duplicate-doi

fix filename of DoiValidityCheckerTest

6597dc6

fix condition

de629d2

address comments

5a5046c

koppor marked this pull request as ready for review May 15, 2020 09:29

koppor commented May 15, 2020

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koppor merged commit 7bfbe44 into master May 15, 2020

koppor deleted the check-duplicate-doi branch May 15, 2020 09:37

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Check duplicate DOI #6333

Check duplicate DOI #6333

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