Export OO/LO citations to new database #1630

oscargus · 2016-07-26T14:44:26Z

Based on a forum discussion, http://discourse.jabref.org/t/export-a-bibtex-file-with-all-papers-cited-in-a-doc-via-ooplugin/87 . 40 minutes later.

Change in CHANGELOG.md described
Manually tested changed features in running JabRef

Siedlerchr · 2016-07-26T15:19:41Z

src/main/java/net/sf/jabref/gui/openoffice/OOBibBase.java

+                        if (!resultDatabase.getEntryByKey(crossref).isPresent()) {
+                            Optional<BibEntry> refEntry = loopDatabase.getEntryByKey(crossref);
+                            if (refEntry.isPresent()) {
+                                resultDatabase.insertEntry(refEntry.get());


Here I would use ifPresent(resultDatabase.insertEntry)

Makes sense. Copied the code from the AUX parser where more things were done in the corresponding place and didn't reflect on it.

oscargus · 2016-07-26T15:22:45Z

OK, this is not flawless. Generating the database a second time in the same JabRef session leads to duplicate entries. Third time, tripled entries and so on...

Siedlerchr · 2016-07-26T15:27:20Z

src/main/java/net/sf/jabref/gui/openoffice/OOBibBase.java

+                    BibEntry clonedEntry = (BibEntry) entry.get().clone();
+                    clonedEntry.setId(IdGenerator.next());
+                    resultDatabase.insertEntry(clonedEntry);
+                    entry.get().getFieldOptional(FieldName.CROSSREF).ifPresent(crossref -> {


'Avoid checking every optional for isPresent, use a flatMap for chained optionals:
(Optional FlatMap example)
http://codingjunkie.net/working-with-java8-optionals/

I had some plans to break the loop once the key was found. In that case one is stuck with isPresent as far as I know.

The break solved the problem with the multiple entries. I was really confused for a while, but since the function looks through all tabs, it found the first generated database and included those entries once more and so on... :-)

Okay. This whole loop with all the presents looked very complex and confusing at the first moment. 😕

I added some comments. Most of the time I like Optional (even though I'm at the best is using ifPresent), but the lack of if ... else ... and the fact that the lambda becomes its own function (which is very natural, but still prohibits writing some things, like return or break) is a bit annoying.

oscargus · 2016-07-26T19:38:16Z

src/main/java/net/sf/jabref/gui/openoffice/OOBibBase.java

+
+        // For each cited key
+        for (String key : cited) {
+            // Loop through the avialables databases


Bad spelling. Fixed it, but will not push just for that.

lenhard · 2016-07-28T09:13:09Z

Apart from the things mentioned above, LGTM code-wise. But since I do not use open office, I have not tested the feature itself.

@comment

* master: Unified some equals (JabRef#1640) Export OO/LO citations to new database (JabRef#1630) Fixed JabRef#1639 (JabRef#1641) Replaced some getField and fixed some bugs (JabRef#1631) Keep @comment text in a bib file (JabRef#1638) # Conflicts: # src/main/java/net/sf/jabref/importer/AppendDatabaseAction.java

@comment

Move event (JabRef#1601) * Move event package to model Update dependencies: postgres 9.4.1208 -> 9.4.1209 and wiremock from 2.1.6 to 2.1.7 Added ISBN integrity checker (JabRef#1586) Added ISBN integrity checker * Extracted ISBN class Reenable errorprone (see http://errorprone.info/) Extend the OpenConsoleFeature (JabRef#1582) * Extend the OpenConsoleFeature by selection of custom terminal emulator. - Add radio selection to the AdvancedTab - Add new JabRefPreferences - Add file check and execution commands - Add localization keys * Fix localization key. * Move console selection to ExternalTab.java * Change localization entry. * Add command executor. * Fix placeholder replacement. * Fix codacy. * Update localization key. * Remove "Specify terminal emulator" option. Add GUI outputs. * Set default command for Windows. Fix localization entries. * Remove empty lines in language files. * Use lambda expressions insead of ActionListeners * Refactoring. * Update CHANGELOG.md. * Small refactorings. Move preferences (JabRef#1604) * Move preferences-related classes into separate package * Rename JabRefPreferencesFilterDialog -> PreferencesFilterDialog and move it to gui * Fix checkstyle warning Set user agent to fix 403 status error Replace getField with getFieldOptional in all of the tests and in som… (JabRef#1591) * Replace getField with getFieldOptional in all of the tests and in some more code * Some more conversions Added filter to not show selected integrity checks (JabRef#1588) * Added filter to not show selected integrity checks * Removed unused variable Some Globals.prefs injection in logic and model (JabRef#1593) * Some Globals.prefs injection in logic and model * Some more conversions and some fixes * More injections * Even more injections * Yes, even more injections * Indeed, even more injections * Probably the last injections for now * Removed unrequired dependency and fixed issue * Dropped support for selecting sub/super to equations * Added preference classes for LatexFieldFormatter and FieldContentParser * Removed some left over code * Added JournalAbbreviationPreferences * Encapsulated LatexFieldFormatterPreferences in SavePreferences * Changed getShortDescription to accept boolean argument * Removed Globals.prefs from tests and removed unused imports * Unused import * Unused import Rewrite MedlineImporter with JAXB and add nbib fields (JabRef#1479) Add test in BibEntryWriterTest for type change When clicking on a tab, the first field now has the focus (JabRef#988) * the first Field does now have focus when clicking on a tab in the entry editor * Make first field focused when selecting a tab in entry editor The field list gets the focus as soon as it is focused (JabRef#1541) Test CustomImporter (JabRef#1501) * Test CustomImporter Fixes imports Added model.entry.FieldName that contains field name constants (JabRef#1602) * Added model.entry.FieldName that contains field name constants * More constants * Renamed and added more constants * Some more fields and cleanups * Removed MedlineHandler left from merge conflicts More fields added to FieldName (JabRef#1614) * More fields added to FieldName * Some Medline fixes [WIP] Create new fetcher infrastructure (JabRef#1594) * Introduce new Fetcher interfaces * Refactor arXiv fulltext fetcher * Add query based arXiv fetcher * Reformat code * Add a few tests for the arxiv parser * Make new arXiv fetcher available * Fix small problems related to files * Fix tests * Rename interface methods * Add changelog entry * Mark old EntryFetcher interface as deprecated * Move fetcher to importer \ fetcher * Move HelpFile from gui.help to logic.help * Rename fetchers * Rename FulltextFinder * Optimize imports * Fix failing test * Ignore failing test Added LayoutFormatterPreferences (and related files) (JabRef#1608) * Added LayoutFormatterPreferences (and related files) * Rebased * Included JournalAbbreviationLoader in LayoutPreferences Added more fields and fixed some issues (JabRef#1617) Resolves JabRef#1613 Use Jabref default icon for uninstaller for now (JabRef#1616) Always use https for help files (JabRef#1615) Implemented JabRef#1345 - cleanup ISSN (JabRef#1590) * Implemented JabRef#1345 - cleanup ISSN * Fixed comments * Extracted ISSN class * Added tests for ISSN and ISBN Added DateFormatter to LayoutEntry so that it actually works... (JabRef#1619) Converted a few getField to getFieldOptional (JabRef#1625) * Converted a few getField to getFieldOptional Fixed JabRef#636 by using DOICheck and DOIStrip in export filters (JabRef#1624) Improved LaTeX to Unicode/HTML formatters to output more sensible values for unknown commands (JabRef#1622) Updated preview entries (JabRef#1606) * Updated preview entries, which return new entry Moved, removed, and used String constants (JabRef#1618) * Moved, removed, and used String constants * Some more fixes * Moved NEWLINE, made FILE_SEPARATOR public and used it * Moved NEWLINE and FILE_SEPARATOR to OS * Moved ENCODING_PREFIX and SIGNATURE * Corrected Globals in a few comments... * Apparently the localization tests find commented out text... More field names and a method (JabRef#1627) * Introduced FieldName in ArXiV * Some more field names * More field names Cleanup FindFile and asssociated tests (JabRef#1596) * Cleanup FindFile and rework it using Streams and nio methods- * Unignore test for trying on CI * Use explicit List and Set in findFiles and caller methods * Use Lazy Stream to find files changes should be tested manually Some enhancements and cleanups related to dates (JabRef#1575) * Some enhancements and cleanups related to dates * Fixed some time zone issues * Replaced SimpleDateFormat in ZipFileChooser and replaced arrays with Lists * Changed EasyDateFormat constructors * Fixed stupid mistake * Added CHANGELOG entry * Maybe tests are passing now? * Some server side print debugging... * As it should be * Tryng LocalDateTime * No time zone * Added test for Cookie * Fixed imports... * Added a third possible date format as it turns out that the server changed while developing this PR Builds are now stored via build-upload.jabref.org Consistent file name casing (and other localization improvements) (JabRef#1629) * AUX files * ZIP files * BIB files * JAR files * didn't * Couldn't what's * Consistent casing * AUX apparently is commonly used in French words... * Fixed the flawed quick-and-dirty find-and-replace failures define xjc input/ouput dir (subsequent builds will be faster) (JabRef#1628) Execute task only when input/output dir changed. Fixed a minor issue and refactored MergeEntries (JabRef#1634) * Fixed a minor issue and refactored MergeEntries * Fixed import * Added CHANGELOG entry Added LabelPatternPreferences (JabRef#1607) * Added LabelPatternPreferences * Removed static initializer More tests (JabRef#1635) * Added more tests for Cookie * Enabled some layout tests and added test for StringUtil.intValueOfWithNull * Updated a test * Split tests Updated Errorprone to 2.0.11 (JabRef#1636) * Updated Errorprone to 2.0.11 * Corrected test Keep @comment text in a bib file (JabRef#1638) * Kep @comment text in a bib file * Add test for @comment that contains regular entries Replaced some getField and fixed some bugs (JabRef#1631) * Replaced some getField and fixed some bugs * Fixed a few things * Added CHANGELOG entries * Improved equals implementation * Text book equals and hashCode Fixed JabRef#1639 (JabRef#1641) * Fixed JabRef#1639 * Removed old code Export OO/LO citations to new database (JabRef#1630) * Export OO/LO citations to new database * Fixed problem with duplicates * Added some comments * Fixed spelling in comment * Removed general Exception Unified some equals (JabRef#1640) * Unified some equals * Imported correct Objects... Fixed one more NPE which should have been fixed in JabRef#1631 (JabRef#1649) Finished method to hide visible fields and show hidden fields - Hide method done - Show method done - ToDo repaint hidden field - ToDo test class finished field repaint remove sysouts

Export OO/LO citations to new database

7754ee8

oscargus added type: enhancement status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers openoffice/libreoffice labels Jul 26, 2016

Siedlerchr reviewed Jul 26, 2016
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oscargus mentioned this pull request Jul 26, 2016

Copy "complete" BibEntry to a new database JabRef/jabref-koppor#144

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oscargus added 3 commits July 26, 2016 21:22

Fixed problem with duplicates

e30fa1c

Added some comments

8b607c8

Fixed spelling in comment

a4201f3

oscargus reviewed Jul 26, 2016
View reviewed changes

Removed general Exception

fba22d9

lenhard merged commit f30bcd5 into master Jul 29, 2016

lenhard deleted the extractoobibdatabase branch July 29, 2016 12:32

oscargus mentioned this pull request Jul 31, 2016

Made possible to make the OO/LO panel a bit more narrow #1652

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Export OO/LO citations to new database #1630

Export OO/LO citations to new database #1630

oscargus commented Jul 26, 2016 •

edited

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Siedlerchr Jul 26, 2016

oscargus Jul 26, 2016

oscargus commented Jul 26, 2016

Siedlerchr Jul 26, 2016

oscargus Jul 26, 2016

oscargus Jul 26, 2016

Siedlerchr Jul 26, 2016

oscargus Jul 26, 2016

oscargus Jul 26, 2016

lenhard commented Jul 28, 2016

Export OO/LO citations to new database #1630

Export OO/LO citations to new database #1630

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lenhard commented Jul 28, 2016

oscargus commented Jul 26, 2016 •

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