[WIP] Paper Reference Relationship Visualization by bruehldev · Pull Request #2041 · JabRef/jabref

bruehldev · 2016-09-22T18:08:13Z

Remark for contributors:

Add external Prefux.jar library to your project. The path is JabRef/lib/Prefux.jar.
The prefux library is a little bit modified see here

bruehldev · 2016-09-22T18:18:15Z

New Prrv (Paper Reference Relationship Visualization) Plugin using JavaFX and Prefux library (https://github.com/effrafax/Prefux).
Based on following issue: JabRef#95

tobiasdiez · 2016-09-22T19:05:21Z

Depending on how powerful and easy-to-use the Prefux library is, you also might consider d3 (which in my opinion is an amazing library). For the relationship of papers, you can use a directed graph or be a bit more creative with http://www.findtheconversation.com/concept-map/# or http://mbostock.github.io/d3/talk/20111116/bundle.html (should look good if you group by keyword). If you decide to go this way, here are a few links which might be helpful:

using javafx: https://github.com/stefaneidelloth/javafx-d3
real-live example using javafx: http://blog.mirkosertic.de/javastuff/fxdesktopsearch
github: https://github.com/d3/d3
tutorial: http://alignedleft.com/tutorials/d3/binding-data
sunburst example: https://bl.ocks.org/kerryrodden/7090426 and https://bl.ocks.org/mbostock/4063423 and http://bl.ocks.org/mbostock/5944371 and collapsing or expanding subtrees https://www.youtube.com/watch?v=ck3Mm9THtlY
treemap example: http://bl.ocks.org/mbostock/6bbb0a7ff7686b124d80
tree example: http://bl.ocks.org/mbostock/ff91c1558bc570b08539547ccc90050b
circle packing example: http://bl.ocks.org/mbostock/ca5b03a33affa4160321
word cloud example: https://github.com/jasondavies/d3-cloud and for inspiration http://blog.arungupta.me/wp-content/uploads/2015/05/javaone2015-tagcloud-devops-abstract.png surpasses [WIP] Word cloud generation #1832
gallery: https://github.com/d3/d3/wiki/gallery

bruehldev · 2016-09-28T18:12:24Z

@tobiasdiez I tried to use https://github.com/stefaneidelloth/javafx-d3 because I already coded with d3 and it sounded very tempting to display these variations. But it's not possible to simply wrap your d3.js code and put it in JavaFx. You have to use the javafxd3 library which is not completed yet. When I was at the point where I set out my nodes I discovered the whole force layout (https://github.com/stefaneidelloth/javafx-d3/blob/master/javafx-d3/main/java/org/treez/javafxd3/d3/layout/Force.java) and other listener are not implemented yet. The prefux library is not perfect, because i had to implemented arrowheads and some listener on myself, but at least I am not fully depending on the library.

koppor · 2016-09-29T01:26:43Z

@bruehldev It would be nice if you provided a link to code where one could inspect your experiments.

bruehldev · 2016-10-02T19:13:45Z

@koppor I pushed my changes on JabRef so far. The prefux plugin works and can be tested over JabRef ->View -> Paper Reference Relationship Visualization. Each bib entry needs a field for references. Inside of the highest jabref folder is a seminar.bib which can be loaded to test it.
My currently problems are:

It's not possible to safe the references in severel rows. Somehow i need to know when another reference starts, should i norm it with an semicolon?
I can't transform my outputstream into an inputstream: Error Message in PrrvDialogView: https://github.com/bruehldev/jabref/blob/PRRV/src/main/java/net/sf/jabref/gui/prrv/PrrvDialogView.java#L74)

prefux.data.io.DataIOException: java.io.IOException: Write end dead
at prefux.data.io.GraphMLReader.readGraph(GraphMLReader.java:79)
at net.sf.jabref.gui.prrv.PrrvDialogView.show(PrrvDialogView.java:74)
...
Missing arrow head in prefux, i tried to add it but I can't bind it to the correct x and y coordinates. https://github.com/bruehldev/Prefux/blob/604d494a5e77640e8b93cfdcd9dc9230437f0431/src/main/java/prefux/render/EdgeRenderer.java#L137
Error Message of the right click listener when i try to display the label.

I will move the model to the correct folder, and delete the d3 test files and library on the next commit.

koppor · 2016-10-05T18:42:31Z

OutputStream to InputStream: http://stackoverflow.com/a/16973800/873282

-Added Prefux to external-libraries.txt -Deleted D3 content -Table insertion to prefux.jar

Fixed wrong order of rendering Added color renderer Deleted defaultedgerenderer

Corrected extern to external

…graph

Ask user for root node of his document

boceckts

Looks nice but some work is still needed.

boceckts · 2016-10-18T16:15:33Z

 License: BSD 3-Clause

+
+


Why did you insert empty lines here?

boceckts · 2016-10-18T16:24:16Z

+        Optional<String> result = dialog.showAndWait();
+        String inputValue = result.get();
+
+        return inputValue;


Please return the Optional as I think this will throw an exception if the input dialog is empty. return dialog.showAndWait();

boceckts · 2016-10-18T16:31:20Z

+     * @return inputValue as String of the input field
+     */
+    public static String showTextInputDialogAndWait(String defaultText, String title, String context) {
+        TextInputDialog dialog = new TextInputDialog(defaultText);


The whole point of the FXDialogs class is that it provides methods to easily instantiate a dialog that inherits from FXAlert. This is important as JavaFX dialogs do not natively disable and unfocus swing windows which is why we need a class that takes care of it; the FXAlert class. So please create a custom TextInputDialog that inherits from FXAlert.

boceckts · 2016-10-18T16:32:57Z

+    /**
+     * This will create and display a new textinputdialog of the specified
+     * {@link AlertType} but with user defined buttons as optional
+     * {@link ButtonType}s.


The comment doesn't apply to this method.

boceckts · 2016-10-18T16:36:14Z

+
+/**
+ * Created by Daniel on 10/13/2016.
+ */


Please replace with a describing javadoc comment as I have no idea what this class does or if it is even needed.

boceckts · 2016-10-18T17:08:17Z

+
+            // Create edges & external nodes
+            for (int sourceID = 0; pureEntryList.size() > sourceID; sourceID++) {
+                if (pureEntryList.get(sourceID).getField("cites").isPresent()) {


This can be filtered by using the pureEntryList.stream.filter(...) method outside of the for loop.

boceckts · 2016-10-18T17:11:01Z

+            for (int sourceID = 0; pureEntryList.size() > sourceID; sourceID++) {
+                if (pureEntryList.get(sourceID).getField("cites").isPresent()) {
+                    // Split cites
+                    String[] citeLines = pureEntryList.get(sourceID).getField("cites").get().split(",");


If you convert the array to a list you can also filter the list by using a stream and calling the filter method to remove all null values. This way you need less if statement inside the for loop.

boceckts · 2016-10-18T17:13:13Z

+                            for (int targetID = 0; pureEntryList.size() > targetID; targetID++) {
+                                // Don't refer to yourself
+                                // Cite matching with bibtexkey of any bibtex entry?
+                                if (citeLine.trim().equals((pureEntryList.get(targetID).getField("bibtexkey").get().trim())) && sourceID != targetID) {


As far as I know the getField() method of an entry returns an optional which can also be null. Can it happen that at his stage an entry in the pureEntryList has no BibTeX-key?

boceckts · 2016-10-18T17:14:35Z

+     *
+     * @param sourceID start of the edge
+     * @param targetID end of the edge
+     */


Parameter missing and I think "Adds an edge to the graph" is more appropriate.

boceckts · 2016-10-18T17:16:49Z


 About_JabRef=About_JabRef

+Paper_Reference_Relationship_Visualization = Paper_Reference_Relationship_Visualization


You need to run ./gradlew localizationUpdate to include the string in the remaining property files.

Show bibtex as label instead of tooltips Boolean for externalnodes and nodes without edges

Show bibtexkey as label instead of tooltip

# Conflicts: # external-libraries.txt # seminar.bib # src/main/java/net/sf/jabref/gui/JabRefFrame.java # src/main/java/net/sf/jabref/gui/prrv/PrrvDialogView.java # src/main/java/net/sf/jabref/gui/prrv/ReferenceRelationship.java

Refine code

# Conflicts: # src/main/java/net/sf/jabref/gui/maintable/MainTableSelectionListener.java # src/main/java/net/sf/jabref/model/entry/FieldName.java

Addded missing Check_integrity in JabRef_... Added missing Paper_Reference_Relationship_Visualization in Menu_... Deleted No_references_found

New chapter in javafx changelog (feature)

lenhard · 2017-01-20T15:35:11Z

@bruehldev Any news on this? How far is the PR regarding merging?

koppor · 2017-02-15T18:37:10Z

Looks good at demonstration settings.

When used at a real-life database, it has the issue that closing and reopening does not work.
The master branch has to be merged.
The prefux updates from https://github.com/bruehldev/Prefux/ should be generalized and sent back to the main repository
Since prefux is currently integrated as a jar, we have to work on getting prefux published on maven central.

We as JabRef developers currently don't have the time to work on this as are currently trying to focus on other things. 🔥
We will come back later to this topic, therefore closing adding on-hold label and closing this PR for now.

koppor · 2017-04-18T08:03:45Z

Related question on tex.sx: Tool to visualize connections between bibtex entries

boceckts added the stupro label Sep 23, 2016

bruehldev closed this Oct 2, 2016

bruehldev deleted the PRRV branch October 2, 2016 18:28

bruehldev restored the PRRV branch October 2, 2016 18:28

bruehldev reopened this Oct 2, 2016

koppor changed the title ~~[WIP] Prrv~~ [WIP] PRRV Oct 5, 2016

koppor changed the title ~~[WIP] PRRV~~ [WIP] Paper Reference Relationship Visualization Oct 5, 2016

New PPRV init after git merge:

3fecf18

-Added Prefux to external-libraries.txt -Deleted D3 content -Table insertion to prefux.jar

bruehldev force-pushed the PRRV branch from 33806b7 to 3fecf18 Compare October 6, 2016 17:23

bruehldev added 12 commits October 11, 2016 20:07

Implemented direct input of bib entry data

b866454

Fixed wrong order of rendering Added color renderer Deleted defaultedgerenderer

Fix wrong display of extern nodes

4ed536a

Corrected extern to external

Improved comments

00b0b38

Deleted unnecessary comments

f3f7988

Better color feedback on nodes

08d1ac3

Added exception catch ending with an alert dialog

2468a0f

Added more stability with queries.

9dd8bf2

Added cite as optional cite data field

3e88eb3

PRRV is now compare bibtexkey instead of title

b7ab42b

changed cite field name to cites

90b5156

PRRV take now cites values instead of references value to create the …

3e64b9b

…graph

Added showTextInputDialogAndWait for JavaFX

ee2a098

Ask user for root node of his document

koppor mentioned this pull request Oct 14, 2016

Integrate all maintained plugins into JabRef #152

Closed

13 tasks

Checkbox to show all node keys

91a12af

boceckts added the stupro-ready-for-internal-review label Oct 18, 2016

boceckts reviewed Oct 18, 2016

View reviewed changes

boceckts removed the stupro-ready-for-internal-review label Oct 18, 2016

bruehldev added 9 commits October 25, 2016 21:24

Deleted guide dialogs

28fd818

Show bibtex as label instead of tooltips Boolean for externalnodes and nodes without edges

Implemented focus on node if bibtexkey is selected

6a5c436

Show bibtexkey as label instead of tooltip

Window can't be started twice now to prevent errors

aab146a

Applied QS

0f35432

Refine code

Merge remote-tracking branch 'upstream/javafx' into PRRV

7d42fc7

# Conflicts: # src/main/java/net/sf/jabref/gui/maintable/MainTableSelectionListener.java # src/main/java/net/sf/jabref/model/entry/FieldName.java

Fixed checkstyleMain-test

d419fa4

Fixed failing unit tests

6a6e750

Addded missing Check_integrity in JabRef_... Added missing Paper_Reference_Relationship_Visualization in Menu_... Deleted No_references_found

Deleted example bib file

783b436

New chapter in javafx changelog (feature)

koppor closed this Feb 15, 2017

lenhard added the on-hold label Feb 15, 2017


		About_JabRef=About_JabRef

		Paper_Reference_Relationship_Visualization = Paper_Reference_Relationship_Visualization

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