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POvisualizing edge data for networkx-generated graphviz .dot or GML files
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I have generated a graph with networkx, and exported it as a .dot file for vizualization. The .dot file looks ok, there are the nodes and the node attributes I've created, as well as the edge data (<code>via</code> below), everything in place. My problem is how to vizualize this data on linux? I've tried with gephi, it looks like the most capable among them, but it doesn't detect the edge attributes (<code>via</code>). I need to be able to explore the data interactively. Here is a simplified dot file which shows the same behavior <pre><code>strict digraph G { "README.md"; "src/modules/books/email_bk_title.php" [created="[466]"]; "functions/mysql/tmp" [created="[23, 43]"]; "src/modules/login/login_check.php" [created="[198]"]; "src/post_process_loader.php" [created="[178]"]; "src/style.css"; "src/templates/default/js/bootstrap-tooltip.js" [created="[8]"]; "src/webroot/templates/default/js/bootstrap-modal.js" [created="[23]"]; "src/webroot/templates/default/js/bootstrap-transition.js" [created="[23]"]; "src/templates/default/js/bootstrap-collapse.js" [created="[8]"]; "src/modules/books/tmp"; "src/templates/default/css/bootstrap.css" [created="[8]"]; "LICENSE.txt" [created="[6]"]; "src/templates/default/js/bootstrap.js" [created="[8]"]; "docs/app_skel_design.md" [created="[39]"]; "src/webroot/templates/default/js/bootstrap-button.js" [created="[23]"]; "src/templates/default/js/google-code-prettify/prettify.css" [created="[8]"]; "src/templates/default/js/bootstrap-tab.js" [created="[8]"]; "src/modules/logout/logout_bl.php" [created="[280]"]; "functions/books/tmp" [created="[23, 43]"]; "src/modules/admin/tmp"; "src/modules/register/tmp" [created="[73, 94]"]; "docs/database/db_constraints_behavior.md" [created="[38]"]; "src/webroot/templates/default/js/bootstrap-scrollspy.js" [created="[23]"]; "uploads/tmp" [created="[237]"]; "src/modules/login/login.php" [created="[127]"]; "src/resources/books/books.php" [created="[306, 366, 518]"]; "src/resource_holder.php" [created="[221, 250, 304, 428]"]; "src/modules/session/session_start.php" [created="[177]"]; "src/webroot/templates/default/index.html" [created="[23]"]; ".gitignore" [created="[170, 289]"]; "src/functions/mysql/tmp" [created="[44]"]; "src/webroot/templates/default/js/bootstrap.js" [created="[23]"]; "src/modules/user/user_bl.php" [created="[142, 169, 439]"]; "src/modules/logout/logout.php" [created="[156, 270]"]; "src/webroot/templates/default/js/bootstrap-tooltip.js" [created="[23]"]; "src/modules/base/functions.php" [created="[64, 158, 232, 233, 254]"]; "src/resources/base/functions.php"; "docs/roadmap/v0.2.0-v0.4.0.txt" [created="[209]"]; "src/templates/default/js/bootstrap-typeahead.js" [created="[8]"]; "docs/database/mylibrary.sql" [created="[29]"]; "src/resource_holder.php.php" [created="[216]"]; "src/webroot/templates/default/js/bootstrap-popover.js" [created="[23]"]; "src/modules/register/register.php" [created="[93, 110, 455, 457]"]; "src/webroot/style.css" [created="[41, 46, 63, 126]"]; "src/webroot/templates/default/js/jquery.js" [created="[23]"]; "docs/install on windows.md" [created="[500, 501, 502, 503]"]; "src/webroot/templates/default/js/google-code-prettify/prettify.css" [created="[23]"]; "src/templates/default/js/bootstrap-alert.js" [created="[8]"]; "src/modules/books/books_bl.php" [created="[125, 514]"]; "src/webroot/module_holder.php" [created="[51, 89]"]; "src/webroot/templates/default/js/bootstrap-dropdown.js" [created="[23]"]; "src/templates/default/js/README.md" [created="[8]"]; "src/webroot/templates/default/js/bootstrap-typeahead.js" [created="[23]"]; "src/resources/register/register_BL.php" [created="[243]"]; "src/webroot/index.php" [created="[41, 52, 113, 136, 181]"]; "docs/wireframe/my-library.ep" [created="[7]"]; "webroot/uploads/tmp"; "src/functions/base/functions.php" [created="[48]"]; "src/webroot/templates/default/js/bootstrap.min.js" [created="[23]"]; "src/functions/admin/tmp" [created="[44]"]; "src/templates/default/js/bootstrap-carousel.js" [created="[8]"]; "src/modules/recover/tmp" [created="[72, 535]"]; "src/modules/register/content.php" [created="[92, 111]"]; "docs/roadmap/roadmap.md"; "src/resources/authentication/authentication.php" [created="[255, 277, 382, 449, 460, 462]"]; "src/webroot/templates/default/css/bootstrap-responsive.css" [created="[23]"]; "src/resources/admin/admin.php" [created="[403, 414, 419, 484, 487]"]; "src/webroot/templates/default/js/bootstrap-carousel.js" [created="[23]"]; "src/webroot/templates/default/js/bootstrap-collapse.js" [created="[23]"]; "src/modules/books/books.php" [created="[117, 440]"]; "src/functions/user/tmp" [created="[44]"]; "functions/user/tmp" [created="[23, 43]"]; "src/templates/default/js/bootstrap-scrollspy.js" [created="[8]"]; "webroot/style.css"; "src/modules/admin/admin.php" [created="[296, 303, 383, 397, 412, 421, 473, 491]"]; "functions/admin/tmp" [created="[23, 43]"]; "src/webroot/templates/default/js/bootstrap-alert.js" [created="[23]"]; "src/webroot/templates/default/js/google-code-prettify/prettify.js" [created="[23]"]; "src/functions/books/tmp" [created="[44]"]; "src/templates/default/js/bootstrap.min.js" [created="[8]"]; "src/webroot/layout.php" [created="[41, 45, 84]"]; "src/modules/admin/admin_bl.php" [created="[297, 369, 398, 438, 493]"]; "src/webroot/templates/default/css/docs.css" [created="[23]"]; "src/modules/user/tmp"; "src/modules/mysql/tmp"; "src/modules/mysql/connect.php" [created="[91]"]; "src/resources/upload/upload.php" [created="[290, 389]"]; "src/dependency_loader.php" [created="[95]"]; "docs/structure.md" [created="[16, 49]"]; "src/templates/default/js/bootstrap-button.js" [created="[8]"]; "config/mysql_credentials.php-dist" [created="[170]"]; "src/webroot/templates/default/js/README.md" [created="[23]"]; "src/templates/default/js/bootstrap-modal.js" [created="[8]"]; "src/templates/default/index.html" [created="[8]"]; "src/templates/default/js/bootstrap-popover.js" [created="[8]"]; "docs/roadmap/roadmap_gantt.gan" [created="[18]"]; "src/resources/autologin/autologin.php" [created="[241]"]; "src/templates/default/js/bootstrap-transition.js" [created="[8]"]; "src/resources/mysql/mysql.php"; "src/modules/mysql/mysql.php" [created="[82]"]; "src/resources_loader.php" [created="[214]"]; "src/modules/home/home.php" [created="[64]"]; "webroot/index.php"; "src/modules/user/user.php" [created="[141, 164]"]; "README.MD" [created="[0, 1]"]; "src/templates/default/css/docs.css" [created="[8]"]; "docs/features.md" [created="[4]"]; "src/modules/upload/upload_bl.php" [created="[236]"]; "src/templates/default/css/bootstrap-responsive.css" [created="[8]"]; "src/webroot/templates/default/js/application.js" [created="[23]"]; "src/layout.php"; "src/templates/default/js/google-code-prettify/prettify.js" [created="[8]"]; "src/modules/login/login_BL.php" [created="[146]"]; "src/empty" [created="[5, 8]"]; "src/resources/user/user.php" [created="[426, 434, 522]"]; "src/resources/session/session_start.php"; "src/modules/register/validation_mail_content.php" [created="[480]"]; "src/resources/login/login_bl.php" [created="[242]"]; "src/modules/login/login_bl.php"; "src/modules/session/session_destroy.php" [created="[177, 186]"]; "src/pre_process_loader.php" [created="[179]"]; "src/router.php" [created="[78]"]; "src/resources/session/session_destroy.php"; "src/modules/login/tmp" [created="[71, 124]"]; "src/moduleBL_loader.php" [created="[112]"]; "src/webroot/templates/default/js/bootstrap-tab.js" [created="[23]"]; "src/modules/register/register_BL.php" [created="[121, 448]"]; "src/templates/default/js/bootstrap-dropdown.js" [created="[8]"]; "src/module_holder.php"; "src/webroot/templates/default/css/bootstrap.css" [created="[23]"]; "src/modules/upload/upload.php" [created="[235]"]; "src/templates/default/js/jquery.js" [created="[8]"]; "src/templates/default/js/application.js" [created="[8]"]; "todo.txt" [created="[31]"]; "src/style.css" -> "src/webroot/style.css" [via=99]; "uploads/tmp" -> "webroot/uploads/tmp" [via=394]; "src/modules/session/session_start.php" -> "src/resources/session/session_start.php" [via=212]; "src/functions/mysql/tmp" -> "src/modules/mysql/tmp" [via=64]; "src/modules/base/functions.php" -> "src/resources/base/functions.php" [via=257]; "docs/roadmap/v0.2.0-v0.4.0.txt" -> "docs/roadmap/roadmap.md" [via=227]; "src/webroot/style.css" -> "src/style.css" [via=86]; "src/webroot/style.css" -> "webroot/style.css" [via=172]; "src/webroot/module_holder.php" -> "src/module_holder.php" [via=86]; "src/resources/register/register_BL.php" -> "src/modules/register/register_BL.php" [via=256]; "src/webroot/index.php" -> "webroot/index.php" [via=172]; "src/functions/admin/tmp" -> "src/modules/admin/tmp" [via=64]; "src/functions/user/tmp" -> "src/modules/user/tmp" [via=64]; "src/functions/books/tmp" -> "src/modules/books/tmp" [via=64]; "src/webroot/layout.php" -> "src/layout.php" [via=86]; "src/modules/mysql/mysql.php" -> "src/resources/mysql/mysql.php" [via=211]; "README.MD" -> "README.md" [via=3]; "src/modules/login/login_BL.php" -> "src/modules/login/login_bl.php" [via=173]; "src/resources/login/login_bl.php" -> "src/modules/login/login_bl.php" [via=256]; "src/modules/session/session_destroy.php" -> "src/resources/session/session_destroy.php" [via=212]; } </code></pre> In networkx, I create it like this <pre><code>filegraph = nx.DiGraph() for cid, commit in enumerate(raw.commits): raw_creations = [info['path'] for info in raw.commits[cid]['info'] if info['type'] & RawRepo.TYPE_NEW] for path in raw_creations: if path in filegraph: attrs = filegraph.node[path] if 'created' in attrs: attrs['created'].append(cid) else: print("not in created") else: print("created", path) attrs = {'created': [cid]} filegraph.add_node(path, attr_dict=attrs) raw_renames = {info['from']:info['to'] for info in raw.commits[cid]['info'] if info['type'] & RawRepo.TYPE_RENAME} for fr, to in raw_renames.items(): print("rename",fr,"->",to) filegraph.add_edge(fr, to) filegraph.edge[fr][to]['via'] = cid #filegraph.add_edge(fr, to, attr_dict={'via':cid}) nx.drawing.nx_pydot.write_dot(filegraph, 'filenames.dot') </code></pre> The other viewer I've tried, ZGRViewer, doesn't show that data either. <h1>Update</h1> With cytoscape 3.0.0-beta1 it gives this error, and a similar error with cytoscape 2.8.3, when importing a GML file exported with networkx as <pre><code>nx.readwrite.gml.write_gml(filegraph, 'filenames.gml') </code></pre> The error is <pre><code>java.text.ParseException: Bad value associated with key modified at org.cytoscape.io.internal.read.gml.GMLParser.parseList(GMLParser.java:192) at org.cytoscape.io.internal.read.gml.GMLParser.parseValue(GMLParser.java:293) at org.cytoscape.io.internal.read.gml.GMLParser.parseList(GMLParser.java:189) at org.cytoscape.io.internal.read.gml.GMLParser.parseValue(GMLParser.java:293) at org.cytoscape.io.internal.read.gml.GMLParser.parseList(GMLParser.java:189) at org.cytoscape.io.internal.read.gml.GMLNetworkReader.run(GMLNetworkReader.java:190) at org.cytoscape.work.internal.task.JDialogTaskManager$TaskThread.run(JDialogTaskManager.java:241) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:679) pool-11-thread-1 WARN [org.cytoscape.work.internal.task.JDialogTaskManager] - Caught exception executing task. java.lang.RuntimeException: Bad value associated with key modified at org.cytoscape.io.internal.read.gml.GMLNetworkReader.run(GMLNetworkReader.java:193) at org.cytoscape.work.internal.task.JDialogTaskManager$TaskThread.run(JDialogTaskManager.java:241) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:679) </code></pre> The Error in cytoscape 2.8.3 looks like this: <img src="https://i.stack.imgur.com/7g2hA.png" alt="enter image description here">
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visualizing edge data for networkx-generated graphviz .dot or GML files
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