grnsight 6.0.4 → 7.1.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1245) hide show
  1. package/.eslintrc.yml +4 -4
  2. package/database/README.md +224 -79
  3. package/database/constants.py +42 -0
  4. package/database/expression-database/README.md +2 -2
  5. package/database/expression-database/schema.sql +14 -14
  6. package/database/expression-database/scripts/loader.py +6 -6
  7. package/database/filter_update.py +168 -0
  8. package/database/grnsettings-database/README.md +52 -0
  9. package/database/grnsettings-database/schema.sql +4 -0
  10. package/database/loader.py +30 -0
  11. package/database/loader_update.py +36 -0
  12. package/database/network-database/README.md +36 -4
  13. package/database/network-database/schema.sql +7 -7
  14. package/database/network-database/scripts/generate_network.py +16 -24
  15. package/database/network-database/scripts/generate_new_network_version.py +216 -0
  16. package/database/protein-protein-database/README.md +71 -0
  17. package/database/protein-protein-database/schema.sql +37 -0
  18. package/database/protein-protein-database/scripts/generate_protein_network.py +227 -0
  19. package/database/protein-protein-database/scripts/remove_duplicates.sh +4 -0
  20. package/database/utils.py +418 -0
  21. package/package.json +2 -2
  22. package/server/app.js +2 -0
  23. package/server/config/config.js +4 -4
  24. package/server/controllers/additional-sheet-parser.js +2 -1
  25. package/server/controllers/constants.js +5 -0
  26. package/server/controllers/custom-workbook-controller.js +8 -6
  27. package/server/controllers/demo-workbooks.js +1460 -4
  28. package/server/controllers/export-constants.js +3 -2
  29. package/server/controllers/exporters/sif.js +6 -1
  30. package/server/controllers/exporters/xlsx.js +8 -3
  31. package/server/controllers/expression-sheet-parser.js +0 -6
  32. package/server/controllers/grnsettings-database-controller.js +17 -0
  33. package/server/controllers/importers/sif.js +29 -11
  34. package/server/controllers/network-database-controller.js +2 -2
  35. package/server/controllers/network-sheet-parser.js +54 -12
  36. package/server/controllers/protein-database-controller.js +18 -0
  37. package/server/controllers/sif-constants.js +4 -4
  38. package/server/controllers/spreadsheet-controller.js +44 -1
  39. package/server/controllers/workbook-constants.js +21 -4
  40. package/server/dals/expression-dal.js +8 -7
  41. package/server/dals/grnsetting-dal.js +49 -0
  42. package/server/dals/network-dal.js +13 -12
  43. package/server/dals/protein-dal.js +106 -0
  44. package/test/export-tests.js +136 -9
  45. package/test/import-sif-tests.js +54 -13
  46. package/test/test.js +1 -1
  47. package/test-files/additional-sheet-test-files/optimization-parameters-default.xlsx +0 -0
  48. package/test-files/demo-files/18_proteins_81_edges_PPI.xlsx +0 -0
  49. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx +0 -0
  50. package/web-client/config/config.js +4 -4
  51. package/web-client/public/js/api/grnsight-api.js +72 -56
  52. package/web-client/public/js/constants.js +26 -12
  53. package/web-client/public/js/generateNetwork.js +173 -67
  54. package/web-client/public/js/graph.js +420 -150
  55. package/web-client/public/js/grnsight.js +25 -4
  56. package/web-client/public/js/grnstate.js +3 -1
  57. package/web-client/public/js/iframe-coordination.js +3 -3
  58. package/web-client/public/js/setup-handlers.js +28 -32
  59. package/web-client/public/js/setup-load-and-import-handlers.js +196 -170
  60. package/web-client/public/js/update-app.js +84 -17
  61. package/web-client/public/js/upload.js +193 -157
  62. package/web-client/public/lib/bootstrap.file-input/bootstrap.file-input.js +0 -1
  63. package/web-client/public/stylesheets/grnsight.styl +40 -16
  64. package/web-client/views/components/demo.pug +7 -5
  65. package/web-client/views/upload.pug +63 -49
  66. package/.bundle/config +0 -3
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  68. package/Gemfile.lock +0 -259
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- <span class="cline-any cline-neutral">&nbsp;</span>
480
- <span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">var constants = require(__dirname + "/../constants");
481
- var parseString = require("xml2js").parseString;
482
- var semanticChecker = require(__dirname + "/../semantic-checker");
483
- &nbsp;
484
- /*
485
- var graphmlWarnings = {
486
- EDGES_WITHOUT_WEIGHTS: {
487
- warningCode: "EDGES_WITHOUT_WEIGHTS",
488
- errorDescription: "GRNsight has detected that one or more edges in your network are missing numerical weight" +
489
- " values. Because the algorithm GRNsight uses for determining the arrowhead type and the" +
490
- " color and thickness of the edges requires numerical weight values, your graph will" +
491
- " display as an unweighted graph with black edges and pointed arrowheads. If you want to" +
492
- " display the network as a weighted graph, please modify your input file to include weight" +
493
- " values for all edges."
494
- },
495
- &nbsp;
496
- EDGE_DEFAULT_NOT_DIRECTED: {
497
- warningCode: "EDGE_DEFAULT_NOT_DIRECTED",
498
- errorDescription: "GRNsight interprets the graph as directed unconditionally."
499
- }
500
- };
501
- &nbsp;
502
- */
503
- &nbsp;
504
- var graphmlErrors = {
505
- GRAPHML_GENERAL_SYNTAX_ERROR: function (error) {
506
- return {
507
- errorCode: "GRAPHML_GENERAL_SYNTAX_ERROR",
508
- possibleCause: "There are a number of things that could've triggered this error, but the general gist" +
509
- " is that there is something syntactically wrong with your file. The parcer we are using" +
510
- " has associated your syntax error with this message: " + error + ".",
511
- suggestedFix: "Please check the format of your file and make sure that it is in line with our" +
512
- " Documentation page. Some common errors to check for are missing start/end tags, missing" +
513
- " quotation marks, and proper spelling of all attribute names."
514
- };
515
- }
516
- };
517
- &nbsp;
518
- module.exports = function (graphml) {
519
- var graph;
520
- var key;
521
- &nbsp;
522
- var network = {
523
- genes: [],
524
- links: [],
525
- errors: [],
526
- warnings: [],
527
- positiveWeights: [],
528
- negativeWeights: [],
529
- sheetType: constants.UNWEIGHTED
530
- };
531
- &nbsp;
532
- var readErrorFromErr = function (err) {
533
- var isolatedError = (err + "").split(": ")[1];
534
- isolatedError = isolatedError.substring(0, isolatedError.length - 5);
535
- return isolatedError;
536
- };
537
- &nbsp;
538
- var pushRelevantError = function (err) {
539
- var parseError = readErrorFromErr(err);
540
- network.errors.push(graphmlErrors.GRAPHML_GENERAL_SYNTAX_ERROR(parseError));
541
- &nbsp;
542
- // TODO Ask Dondi about how to do this in a more data-driven manner.
543
- &nbsp;
544
- // switch(parseError) {
545
- // case "Invalid attribute name":
546
- // network.errors.push(graphmlErrors.UNKNOWN_ERROR);
547
- // break;
548
- // default:
549
- // network.errors.push(graphmlErrors.GRAPHML_GENERAL_SYNTAX_ERROR);
550
- // }
551
- };
552
- &nbsp;
553
- // Note this relies on sync execution being the default, *not* async.
554
- //
555
- // Limitation is due to the way the import function is expected to return its result.
556
- // To address this later on, import functions should accept a callback instead.
557
- parseString(graphml, function (err, result) {
558
- if (err) {
559
- pushRelevantError(err);
560
- } else {
561
- // Quick fix to handle completely empty GraphML file. #428
562
- <span class="missing-if-branch" title="if path not taken" >I</span>if (!result) {
563
- <span class="cstat-no" title="statement not covered" > return semanticChecker(network);</span>
564
- }
565
- key = result.graphml &amp;&amp; result.graphml.key;
566
- graph = result.graphml &amp;&amp; result.graphml.graph &amp;&amp; result.graphml.graph[0];
567
- }
568
- });
569
- &nbsp;
570
- if (network.errors.length &gt; 0) {
571
- return network;
572
- }
573
- &nbsp;
574
- var findKeyId = function (attrName, attrFor) {
575
- return key &amp;&amp; key.reduce(function (keyId, keyElement) {
576
- return keyId || (keyElement.$["attr.name"] === attrName &amp;&amp;
577
- (attrFor ? keyElement.$.for === attrFor : true) ? keyElement.$.id : null);
578
- }, "");
579
- };
580
- &nbsp;
581
- var findYFilesKeyId = function (yFilesType, attrFor) {
582
- return key &amp;&amp; key.reduce(function (keyId, keyElement) {
583
- return keyId || (keyElement.$["yfiles.type"] === yFilesType &amp;&amp;
584
- (attrFor ? keyElement.$.for === attrFor : <span class="branch-1 cbranch-no" title="branch not covered" >true)</span> ? keyElement.$.id : null);
585
- }, "");
586
- };
587
- &nbsp;
588
- var findKey = function (element, keyId) {
589
- <span class="missing-if-branch" title="if path not taken" >I</span>if (!element.data) {
590
- <span class="cstat-no" title="statement not covered" > return null;</span>
591
- }
592
- &nbsp;
593
- var keyMatch = element.data.filter(function (data) {
594
- return data.$.key === keyId;
595
- });
596
- &nbsp;
597
- return keyMatch.length ? keyMatch[0]._ : <span class="branch-1 cbranch-no" title="branch not covered" >null;</span>
598
- };
599
- &nbsp;
600
- var findYFilesKey = function (element, keyId) {
601
- if (!element.data) {
602
- return null;
603
- }
604
- &nbsp;
605
- var keyMatch = element.data.filter(function (data) {
606
- return data.$.key === keyId;
607
- });
608
- &nbsp;
609
- return keyMatch.length ? keyMatch[0] : <span class="branch-1 cbranch-no" title="branch not covered" >null;</span>
610
- };
611
- &nbsp;
612
- &nbsp;
613
- // We will only consider GraphML data to be weighted if:
614
- // (a) A key for the weight attribute is present, AND
615
- // (b) Every edge in the file has a data element with that key
616
- var weightId = findKeyId("weight"/*, "edge"*/);
617
- // Edge condition temporarily commented out pending Cytoscape GraphML export bug fix.
618
- &nbsp;
619
- if (weightId &amp;&amp; graph.edge &amp;&amp; graph.edge.every(function (edge) { // What
620
- return edge.data &amp;&amp; edge.data.some(function (data) {
621
- return data.$.key === weightId &amp;&amp; !isNaN(+data._);
622
- });
623
- })) {
624
- network.sheetType = constants.WEIGHTED;
625
- } else if (weightId) {
626
- network.warnings.push(constants.warnings.EDGES_WITHOUT_WEIGHTS);
627
- }
628
- &nbsp;
629
- if (!graph.$ || graph.$.edgedefault !== "directed") {
630
- network.warnings.push(constants.warnings.EDGE_DEFAULT_NOT_DIRECTED);
631
- }
632
- &nbsp;
633
- var nameId = findKeyId("name", "node");
634
- var sharedNameId = findKeyId("shared name", "node");
635
- var yFilesNodeId = findYFilesKeyId("nodegraphics", "node");
636
- &nbsp;
637
- var geneIds = [];
638
- <span class="missing-if-branch" title="else path not taken" >E</span>if (graph.node) {
639
- network.genes = graph.node.map(function (node) {
640
- var nodeName = node.$.id;
641
- &nbsp;
642
- if (yFilesNodeId) {
643
- var yNodeGraphics = findYFilesKey(node, yFilesNodeId);
644
- if (yNodeGraphics) {
645
- var yShapeNode = yNodeGraphics["y:ShapeNode"];
646
- var yNodeLabel = yShapeNode &amp;&amp; yShapeNode[0]["y:NodeLabel"];
647
- <span class="missing-if-branch" title="else path not taken" >E</span>if (yNodeLabel) {
648
- // The yNodeLabel may either be plain text or have subelements, so...
649
- nodeName = (yNodeLabel[0]._ || yNodeLabel[0]).trim();
650
- }
651
- }
652
- }
653
- &nbsp;
654
- if (sharedNameId) {
655
- var sharedName = findKey(node, sharedNameId);
656
- <span class="missing-if-branch" title="else path not taken" >E</span>if (sharedName) {
657
- nodeName = sharedName;
658
- }
659
- }
660
- &nbsp;
661
- if (nameId) {
662
- var name = findKey(node, nameId);
663
- <span class="missing-if-branch" title="else path not taken" >E</span>if (name) {
664
- nodeName = name;
665
- }
666
- }
667
- &nbsp;
668
- geneIds.push(node.$.id);
669
- return { name: nodeName };
670
- });
671
- }
672
- &nbsp;
673
- <span class="missing-if-branch" title="else path not taken" >E</span>if (graph.edge) {
674
- graph.edge.forEach(function (edge) {
675
- var link = {
676
- source: geneIds.indexOf(edge.$.source),
677
- target: geneIds.indexOf(edge.$.target)
678
- };
679
- &nbsp;
680
- if (link.source === constants.NOT_FOUND || link.target === constants.NOT_FOUND) {
681
- return;
682
- }
683
- &nbsp;
684
- if (network.sheetType === constants.WEIGHTED) {
685
- link.value = +edge.data.filter(function (data) {
686
- return data.$.key === weightId;
687
- })[0]._;
688
- }
689
- &nbsp;
690
- network.links.push(link);
691
- });
692
- }
693
- &nbsp;
694
- return (network.errors.length === 0) ? semanticChecker(network) : <span class="branch-1 cbranch-no" title="branch not covered" >network;</span>
695
- &nbsp;
696
- };
697
- &nbsp;</pre></td></tr>
698
- </table></pre>
699
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