dansarie/jsnowball

Program for performing systematic literature studies through snowballing and for visualization of citation relations between academic papers.

jsnowball's Issues

Horizontal scroll bar

Add horizontal scroll bar on articles, authors, journals and tags tab.

Semantic Scholar API support

Clicking on journal in right article tab should select the same journal in the left journal list

Draw reference direction in graph

Pressing escape in the save yes/no/cancel dialog displayed when closing the window should result in the cancel option

Currently, it exits the program without saving the work.

NullPointerException in Article.getReferences

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
        at java.base/java.util.ArrayList.<init>(ArrayList.java:179)
        at se.dansarie.jsnowball.model.Article.getReferences(Article.java:352)
        at se.dansarie.jsnowball.JSnowball$1.getEdges(JSnowball.java:112)
        at se.dansarie.jsnowball.JSnowball$1.getEdges(JSnowball.java:1)
        at se.dansarie.jsnowball.gui.GraphPanel.updateEdges(GraphPanel.java:105)
        at se.dansarie.jsnowball.gui.GraphPanel.updateNodes(GraphPanel.java:137)
        at se.dansarie.jsnowball.gui.GraphPanel.contentsChanged(GraphPanel.java:144)
        at se.dansarie.jsnowball.model.SnowballListModel.fireChanged(SnowballListModel.java:51)
        at se.dansarie.jsnowball.model.SnowballState.lambda$0(SnowballState.java:115)
        at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
        at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
        at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
        at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
        at java.base/java.security.AccessController.doPrivileged(Native Method)
        at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
        at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
        at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
        at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
        at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
        at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
        at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

Highlight selected node and nodes in starting set in graph

Import tags

Make possible to save and import/export tags between projects

Undo

Include book search/add by ISBN number

Add feature for ISBN numbers, to import books and references :)

Confirm reference removal

JSONObject["family"] not found

org.json.JSONException: JSONObject["family"] not found.
org.json.JSONException: JSONObject["family"] not found.
        at org.json.JSONObject.get(JSONObject.java:572)
        at org.json.JSONObject.getString(JSONObject.java:859)
        at se.dansarie.jsnowball.model.CrossRef$Author.<init>(CrossRef.java:283)
        at se.dansarie.jsnowball.model.CrossRef.<init>(CrossRef.java:89)
        at se.dansarie.jsnowball.model.CrossRef.getDoi(CrossRef.java:214)
        at se.dansarie.jsnowball.model.CrossRef.addCrossRefReference(CrossRef.java:233)
        at se.dansarie.jsnowball.gui.ArticlePanel$2$1.doInBackground(ArticlePanel.java:124)
        at se.dansarie.jsnowball.gui.ArticlePanel$2$1.doInBackground(ArticlePanel.java:1)
        at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:304)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:343)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base/java.lang.Thread.run(Thread.java:829)
org.json.JSONException: JSONObject["family"] not found.
org.json.JSONException: JSONObject["family"] not found.
        at org.json.JSONObject.get(JSONObject.java:572)
        at org.json.JSONObject.getString(JSONObject.java:859)
        at se.dansarie.jsnowball.model.CrossRef$Author.<init>(CrossRef.java:283)
        at se.dansarie.jsnowball.model.CrossRef.<init>(CrossRef.java:89)
        at se.dansarie.jsnowball.model.CrossRef.getDoi(CrossRef.java:214)
        at se.dansarie.jsnowball.model.CrossRef.addCrossRefReference(CrossRef.java:233)
        at se.dansarie.jsnowball.gui.ArticlePanel$2$1.doInBackground(ArticlePanel.java:124)
        at se.dansarie.jsnowball.gui.ArticlePanel$2$1.doInBackground(ArticlePanel.java:1)
        at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:304)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:343)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base/java.lang.Thread.run(Thread.java:829)

Pruning of authors/journals without articles

Comparison method violates its general contract!

Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: Comparison method violates its general contract!
        at java.base/java.util.ComparableTimSort.mergeHi(ComparableTimSort.java:870)
        at java.base/java.util.ComparableTimSort.mergeAt(ComparableTimSort.java:487)
        at java.base/java.util.ComparableTimSort.mergeCollapse(ComparableTimSort.java:413)
        at java.base/java.util.ComparableTimSort.sort(ComparableTimSort.java:213)
        at java.base/java.util.Arrays.sort(Arrays.java:1249)
        at java.desktop/javax.swing.DefaultRowSorter.sort(DefaultRowSorter.java:616)
        at java.desktop/javax.swing.DefaultRowSorter.allRowsChanged(DefaultRowSorter.java:863)
        at java.desktop/javax.swing.JTable.notifySorter(JTable.java:4263)
        at java.desktop/javax.swing.JTable.sortedTableChanged(JTable.java:4123)
        at java.desktop/javax.swing.JTable.tableChanged(JTable.java:4400)
        at java.desktop/javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:297)
        at java.desktop/javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:199)
        at se.dansarie.jsnowball.JSnowball$SnowballTableModel.contentsChanged(JSnowball.java:1017)
        at se.dansarie.jsnowball.model.SnowballListModel.fireChanged(SnowballListModel.java:51)
        at se.dansarie.jsnowball.model.SnowballState.lambda$0(SnowballState.java:115)
        at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
        at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
        at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
        at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
        at java.base/java.security.AccessController.doPrivileged(Native Method)
        at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
        at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
        at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
        at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
        at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
        at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
        at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: Comparison method violates its general contract!
        at java.base/java.util.ComparableTimSort.mergeHi(ComparableTimSort.java:870)
        at java.base/java.util.ComparableTimSort.mergeAt(ComparableTimSort.java:487)
        at java.base/java.util.ComparableTimSort.mergeForceCollapse(ComparableTimSort.java:426)
        at java.base/java.util.ComparableTimSort.sort(ComparableTimSort.java:222)
        at java.base/java.util.Arrays.sort(Arrays.java:1249)
        at java.desktop/javax.swing.DefaultRowSorter.sort(DefaultRowSorter.java:616)
        at java.desktop/javax.swing.DefaultRowSorter.allRowsChanged(DefaultRowSorter.java:863)
        at java.desktop/javax.swing.JTable.notifySorter(JTable.java:4263)
        at java.desktop/javax.swing.JTable.sortedTableChanged(JTable.java:4123)
        at java.desktop/javax.swing.JTable.tableChanged(JTable.java:4400)
        at java.desktop/javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:297)
        at java.desktop/javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:199)
        at se.dansarie.jsnowball.JSnowball$SnowballTableModel.contentsChanged(JSnowball.java:1017)
        at se.dansarie.jsnowball.model.SnowballListModel.fireChanged(SnowballListModel.java:51)
        at se.dansarie.jsnowball.model.SnowballState.lambda$0(SnowballState.java:115)
        at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
        at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
        at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
        at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
        at java.base/java.security.AccessController.doPrivileged(Native Method)
        at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
        at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
        at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
        at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
        at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
        at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
        at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

Empty article is inserted if get article from DOI is run with bad DOI

Related: trim entered DOI.

Graph layout algorithm is broken

• Default constants are bad.
• Nodes vibrate too much.
• Division by zero/small number or similar reason sometimes makes nodes fly away.

Author initial matching / author alises

Tooltips over nodes in graphs

SSLHandshakeException when attempting to fetch data from HTTPS APIs

javax.net.ssl.SSLHandshakeException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target

The error occurs when the TLS root certificate is not in the JVM keystore. This can happen if the user's computer is connected to a network with a firewall that performs TLS interception.

Notify users of new releases

Pull information on the latest release from https://api.github.com/repos/dansarie/jsnowball/releases/latest when the application starts and notify the user if there is a more recent release.

Tooltips over table headers

The table headers should display descriptive tooltips when hovering over them.

ArXiv API support

Add "reference to" with right-click

Fix graph drawing

Store more window preferences

Store if maximized.
Store split pane positions.
Store graph view settings.

Sort article/author names by Levenshtein distance when merging

Text search / filter

Ability to search for and filter by text in author/article/journal names and other fields.

Link/icon for opening DOI in browser

There should be a link or icon next to the DOI field that opens that link in the system browser.

Duplicate detection (articles, authors, journals)