grnsight 6.0.4 → 6.0.7

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 (1197) hide show
  1. package/database/README.md +40 -16
  2. package/database/expression-database/README.md +2 -2
  3. package/database/expression-database/schema.sql +14 -14
  4. package/database/expression-database/scripts/loader.py +6 -6
  5. package/database/network-database/README.md +36 -4
  6. package/database/network-database/schema.sql +7 -7
  7. package/database/network-database/scripts/filter_genes.py +1 -1
  8. package/database/network-database/scripts/generate_network.py +1 -1
  9. package/database/network-database/scripts/generate_new_network_version.py +223 -0
  10. package/database/network-database/scripts/loader.py +3 -3
  11. package/database/network-database/scripts/loader_updates.py +99 -0
  12. package/package.json +2 -2
  13. package/server/controllers/custom-workbook-controller.js +4 -3
  14. package/server/dals/expression-dal.js +8 -7
  15. package/server/dals/network-dal.js +3 -3
  16. package/web-client/public/js/api/grnsight-api.js +56 -55
  17. package/web-client/public/js/generateNetwork.js +15 -7
  18. package/web-client/public/js/setup-load-and-import-handlers.js +171 -170
  19. package/web-client/public/js/upload.js +74 -95
  20. package/.bundle/config +0 -3
  21. package/GRNsight - Beta.html +0 -194
  22. package/Gemfile.lock +0 -259
  23. package/_gh_pages/about.html +0 -807
  24. package/_gh_pages/assets/css/bootstrap.min.css +0 -10
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- <span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">var graphmlWarnings = {
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- EDGES_WITHOUT_WEIGHTS: {
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- warningCode: "EDGES_WITHOUT_WEIGHTS",
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- errorDescription: "GRNsight has detected that one or more edges in your network are missing numerical" +
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- " weight values. Because the algorithm GRNsight uses for determining the arrowhead type and the" +
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- " color and thickness of the edges requires numerical weight values, your graph will" +
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- " display as an unweighted graph with black edges and pointed arrowheads. If you want to" +
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- " display the network as a weighted graph, please modify your input file to include weight" +
401
- " values for all edges."
402
- },
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- EDGE_DEFAULT_NOT_DIRECTED: {
404
- warningCode: "EDGE_DEFAULT_NOT_DIRECTED",
405
- errorDescription: "GRNsight interprets the graph as directed unconditionally."
406
- },
407
- };
408
- &nbsp;
409
- var graphmlErrors = {
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- GRAPHML_GENERAL_SYNTAX_ERROR: <span class="fstat-no" title="function not covered" >function (</span>error) {
411
- <span class="cstat-no" title="statement not covered" > return {</span>
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- errorCode: "GRAPHML_GENERAL_SYNTAX_ERROR",
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- possibleCause: "There are a number of things that could've triggered this error, but the general gist" +
414
- " is that there is something syntactically wrong with your file. The parcer we are using" +
415
- " has associated your syntax error with this message: &lt;b&gt;\"" + error.error + "\"&lt;/b&gt;.&lt;br&gt;&lt;br&gt;",
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- suggestedFix: "Please check the format of your file and make sure that it is in line with our" +
417
- " Documentation page. Some common errors to check for are &lt;em&gt;missing start/end tags, missing" +
418
- " quotation marks, and proper spelling of all attribute names&lt;/em&gt;."
419
- };
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- },
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- GRAPHML_INVALID_ATTRIBUTE_NAME: function (error) {
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- return {
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- errorCode: "GRAPHML_INVALID_ATTRIBUTE_NAME",
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- possibleCause: "With the help of &lt;em&gt;XML2JS&lt;/em&gt;, GRNsight has detected that one or more of your " +
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- "attribute names is either missing or has an unexpected symbol.&lt;br&gt;&lt;br&gt;",
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- suggestedFix: "Check on &lt;b&gt;line " + error.line + "&lt;/b&gt; at &lt;b&gt;column " + error.column + "&lt;/b&gt;. " +
427
- "It is possible this error was caused by the following character: \"&lt;b&gt;" + error.char + "&lt;/b&gt;\". " +
428
- "If there doesn't seem to be any syntactic errors here, be sure to check the few surrounding lines " +
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- "to make sure that everything is in line with our " +
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- "&lt;a href=\"http:\/\/dondi.github.io/GRNsight/documentation.html\" target=\"_blank\"&gt;documentation page&lt;/a&gt;."
431
- };
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- },
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- GRAPHML_UNMATCHED_CLOSE_TAG: function (error) {
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- return {
435
- errorCode: "GRAPHML_UNMATCHED_CLOSE_TAG",
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- possibleCause: "With the help of &lt;em&gt;XML2JS&lt;/em&gt;, GRNsight has detected that either one or more of your " +
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- "opening tags are missing, or you have too many close tags at the end of one of your lines.&lt;br&gt;&lt;br&gt;",
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- suggestedFix: "Check on &lt;b&gt;line " + error.line + "&lt;/b&gt; at &lt;b&gt;column " + error.column + "&lt;/b&gt;. " +
439
- "It is possible this error was caused by the following character: \"&lt;b&gt;" + error.char + "&lt;/b&gt;\". " +
440
- "If there doesn't seem to be any syntactic errors here, first be sure to check the corresponding opening " +
441
- "tag for this close tag and then make sure to check the few surrounding lines to make sure that " +
442
- "everything is in line with our " +
443
- "&lt;a href=\"http:\/\/dondi.github.io/GRNsight/documentation.html\" target=\"_blank\"&gt;documentation page&lt;/a&gt;."
444
- };
445
- },
446
- GRAPHML_MISSING_CLOSE_TAG_AFTER_FORWARD_SLASH: function (error) {
447
- return {
448
- errorCode: "GRAPHML_MISSING_CLOSE_TAG_AFTER_FORWARD_SLASH",
449
- possibleCause: "With the help of &lt;em&gt;XML2JS&lt;/em&gt;, GRNsight has detected that one or more of your closing " +
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- "tags are missing after a forward slash, it is likely that this is corresponding with a node tag.&lt;br&gt;&lt;br&gt;",
451
- suggestedFix: "Check on &lt;b&gt;line " + error.line + "&lt;/b&gt; at &lt;b&gt;column " + error.column + "&lt;/b&gt;. " +
452
- "If there doesn't seem to be any syntactic errors here, check the few surrounding lines to make sure " +
453
- "that everything is in line with our " +
454
- "&lt;a href=\"http:\/\/dondi.github.io/GRNsight/documentation.html\" target=\"_blank\"&gt;documentation page&lt;/a&gt;."
455
- };
456
- },
457
- GRAPHML_UNFINISHED_CLOSING_TAG: function (error) {
458
- return {
459
- errorCode: "GRAPHML_UNFINISHED_CLOSING_TAG",
460
- possibleCause: "With the help of &lt;em&gt;XML2JS&lt;/em&gt;, GRNsight has detected that your graph closing " +
461
- "tag is either misspelled or missing.&lt;br&gt;&lt;br&gt;",
462
- suggestedFix: "Check on &lt;b&gt;line " + error.line + "&lt;/b&gt; at &lt;b&gt;column " + error.column + "&lt;/b&gt;. " +
463
- "It is possible this error was caused by the following character: \"&lt;b&gt;" + error.char + "&lt;/b&gt;\". " +
464
- "The location of this error seems to be sporadic, if there doesn't seem to be any syntactic errors " +
465
- "here, be sure to check the few surrounding lines to make sure that everything is in line with our " +
466
- "&lt;a href=\"http:\/\/dondi.github.io/GRNsight/documentation.html\" target=\"_blank\"&gt;documentation page&lt;/a&gt;."
467
- };
468
- },
469
- GRAPHML_MISSING_GRAPHML_CLOSE_TAG: function (error) {
470
- return {
471
- errorCode: "GRAPHML_MISSING_GRAPHML_CLOSE_TAG",
472
- possibleCause: "With the help of &lt;em&gt;XML2JS&lt;/em&gt;, GRNsight has detected that your graphml closing " +
473
- "tag is either misspelled or missing.&lt;br&gt;&lt;br&gt;",
474
- suggestedFix: "Check on &lt;b&gt;line " + error.line + "&lt;/b&gt; at &lt;b&gt;column " + error.column + "&lt;/b&gt;. "
475
- };
476
- },
477
- GRAPHML_UNPAIRED_QUOTE: function (error) {
478
- return {
479
- errorCode: "GRAPHML_UNPAIRED_QUOTE",
480
- possibleCause: "With the help of &lt;em&gt;XML2JS&lt;/em&gt;, GRNsight has detected that one or more of your " +
481
- "attribute values are missing a closing quote.&lt;br&gt;&lt;br&gt;",
482
- suggestedFix: "Check on &lt;b&gt;line " + error.line + "&lt;/b&gt; at &lt;b&gt;column " + error.column + "&lt;/b&gt;. " +
483
- "It is possible this error was caused by the following character: \"&lt;b&gt;" + error.char + "&lt;/b&gt;\". " +
484
- "If there doesn't seem to be any syntactic errors here, be sure to check the few surrounding lines " +
485
- "to make sure that everything is in line with our " +
486
- "&lt;a href=\"http:\/\/dondi.github.io/GRNsight/documentation.html\" target=\"_blank\"&gt;documentation page&lt;/a&gt;."
487
- };
488
- },
489
- GRAPHML_INVALID_CHARACTER_IN_NAME: function (error) {
490
- return {
491
- errorCode: "GRAPHML_INVALID_CHARACTER_IN_NAME",
492
- possibleCause: "With the help of &lt;em&gt;XML2JS&lt;/em&gt;, GRNsight has detected that one or more of your " +
493
- "tags have an invalid symbol in the name value.&lt;br&gt;&lt;br&gt;",
494
- suggestedFix: "Check on &lt;b&gt;line " + error.line + "&lt;/b&gt; at &lt;b&gt;column " + error.column + "&lt;/b&gt;. " +
495
- "It is possible this error was caused by the following character: \"&lt;b&gt;" + error.char + "&lt;/b&gt;\". " +
496
- "If there doesn't seem to be any syntactic errors here, be sure to check the few surrounding lines " +
497
- "to make sure that everything is in line with our " +
498
- "&lt;a href=\"http:\/\/dondi.github.io/GRNsight/documentation.html\" target=\"_blank\"&gt;documentation page&lt;/a&gt;."
499
- };
500
- },
501
- GRAPHML_UNENCODED_TAG: function (error) {
502
- return {
503
- errorCode: "GRAPHML_UNENCODED_TAG",
504
- possibleCause: "With the help of &lt;em&gt;XML2JS&lt;/em&gt;, GRNsight has detected that there are one or more " +
505
- "extra tags floating somewhere in your file.&lt;br&gt;&lt;br&gt;",
506
- suggestedFix: "Check on &lt;b&gt;line " + error.line + "&lt;/b&gt; at &lt;b&gt;column " + error.column + "&lt;/b&gt;. " +
507
- "It is possible this error was caused by the following character: \"&lt;b&gt;" + error.char + "&lt;/b&gt;\". " +
508
- "If there doesn't seem to be any syntactic errors here, be sure to check the few surrounding lines " +
509
- "to make sure that everything is in line with our " +
510
- "&lt;a href=\"http:\/\/dondi.github.io/GRNsight/documentation.html\" target=\"_blank\"&gt;documentation page&lt;/a&gt;."
511
- };
512
- },
513
- GRAPHML_INCOMPLETE_CLOSING_TAG: function (error) {
514
- return {
515
- errorCode: "GRAPHML_INCOMPLETE_CLOSING_TAG",
516
- possibleCause: "With the help of &lt;em&gt;XML2JS&lt;/em&gt;, GRNsight has detected that one or more " +
517
- "of the closing tags in your file are incomplete. More specifically, it is most likely an " +
518
- "error with a closing tag formatted as such: " + "\"&amp;#60;/edge&gt;\".&lt;br&gt;&lt;br&gt;",
519
- suggestedFix: "Check on &lt;b&gt;line " + error.line + "&lt;/b&gt; at &lt;b&gt;column " + error.column + "&lt;/b&gt;. " +
520
- "It is possible this error was caused by the following character: \"&lt;b&gt;" + error.char + "&lt;/b&gt;\". " +
521
- "If there doesn't seem to be any syntactic errors here, be sure to check the few surrounding lines " +
522
- "to make sure that everything is in line with our " +
523
- "&lt;a href=\"http:\/\/dondi.github.io/GRNsight/documentation.html\" target=\"_blank\"&gt;documentation page&lt;/a&gt;."
524
- };
525
- },
526
- GRAPHML_MISSING_OPEN_QUOTE: function (error) {
527
- return {
528
- errorCode: "GRAPHML_MISSING_OPEN_QUOTE",
529
- possibleCause: "With the help of &lt;em&gt;XML2JS&lt;/em&gt;, GRNsight has detected that one or more " +
530
- "of the opening quotes in your file are missing.&lt;br&gt;&lt;br&gt;",
531
- suggestedFix: "Check on &lt;b&gt;line " + error.line + "&lt;/b&gt; at &lt;b&gt;column " + error.column + "&lt;/b&gt;. " +
532
- "It is possible this error was caused by the following character: \"&lt;b&gt;" + error.char + "&lt;/b&gt;\". " +
533
- "If there doesn't seem to be any syntactic errors here, be sure to check the few surrounding lines " +
534
- "to make sure that everything is in line with our " +
535
- "&lt;a href=\"http:\/\/dondi.github.io/GRNsight/documentation.html\" target=\"_blank\"&gt;documentation page&lt;/a&gt;."
536
- };
537
- },
538
- };
539
- &nbsp;
540
- var errorMessageToGraphmlError = {
541
- "Invalid attribute name": graphmlErrors.GRAPHML_INVALID_ATTRIBUTE_NAME,
542
- "Unexpected close tag": graphmlErrors.GRAPHML_UNMATCHED_CLOSE_TAG,
543
- "Forward-slash in opening tag not followed by &gt;": graphmlErrors.GRAPHML_MISSING_CLOSE_TAG_AFTER_FORWARD_SLASH,
544
- "Invalid tagname in closing tag.": graphmlErrors.GRAPHML_UNFINISHED_CLOSING_TAG,
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- "Unclosed root tag": graphmlErrors.GRAPHML_MISSING_GRAPHML_CLOSE_TAG,
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- "No whitespace between attributes": graphmlErrors.GRAPHML_UNPAIRED_QUOTE,
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- "Invalid character in entity name": graphmlErrors.GRAPHML_INVALID_CHARACTER_IN_NAME,
548
- "Unencoded &lt;": graphmlErrors.GRAPHML_UNENCODED_TAG,
549
- "Invalid characters in closing tag": graphmlErrors.GRAPHML_INCOMPLETE_CLOSING_TAG,
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- "Unquoted attribute value": graphmlErrors.GRAPHML_MISSING_OPEN_QUOTE,
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- };
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- &nbsp;
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- var pairError = function (error) {
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- return errorMessageToGraphmlError.hasOwnProperty(error.error) ?
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- errorMessageToGraphmlError[error.error](error) :
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- <span class="branch-1 cbranch-no" title="branch not covered" > graphmlErrors.GRAPHML_GENERAL_SYNTAX_ERROR(error);</span>
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- };
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- &nbsp;
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- module.exports = {
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- graphmlErrors: graphmlErrors,
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- graphmlWarnings: graphmlWarnings,
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- errorMessageToGraphmlError: errorMessageToGraphmlError,
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- pairError: pairError,
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- };
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- &nbsp;</pre></td></tr>
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