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-no">&nbsp;</span>
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- <span class="cline-any cline-no">&nbsp;</span>
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- <span class="cline-any cline-no">&nbsp;</span>
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- <span class="cline-any cline-neutral">&nbsp;</span>
543
- <span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">// var multiparty = require("multiparty");
544
- // var xlsx = require("node-xlsx");
545
- // var util = require("util");
546
- // var path = require("path");
547
- // var cytoscape = require("cytoscape");
548
- //
549
- // var helpers = require(__dirname + "/helpers");
550
- &nbsp;
551
- var numbersToLetters = {
552
- 0:"A", 1:"B", 2:"C", 3:"D", 4:"E", 5:"F", 6:"G", 7:"H", 8: "I", 9:"J", 10:"K", 11:"L", 12:"M", 13:"N",
553
- 14:"O", 15:"P", 16:"Q", 17:"R", 18:"S", 19:"T", 20:"U", 21:"V", 22:"W", 23:"X", 24:"Y", 25:"Z", 26:"AA",
554
- 27:"AB", 28:"AC", 29:"AD", 30:"AE", 31:"AF", 32:"AG", 33:"AH", 34:"AI", 35:"AJ", 36:"AK", 37:"AL", 38:"AM",
555
- 39:"AN", 40:"AO", 41:"AP", 42:"AQ", 43:"AR", 44:"AS", 45:"AT", 46:"AU", 47:"AV", 48:"AW", 49:"AX", 50:"AY",
556
- 51:"AZ", 52:"BA", 53:"BB", 54:"BC", 55:"BD", 56:"BE", 57:"BF", 58:"BG", 59:"BH", 60:"BI", 61:"BJ", 62:"BK",
557
- 63:"BL", 64:"BM", 65:"BN", 66:"BO", 67:"BP", 68:"BQ", 69:"BR", 70:"BS", 71:"BT", 72:"BU", 73:"BV", 74:"BW",
558
- 75:"BX", 76:"BY"
559
- };
560
- &nbsp;
561
- var warningsList = {
562
- missingSourceGeneWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
563
- var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
564
- var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
565
- <span class="cstat-no" title="statement not covered" > return {</span>
566
- warningCode: "MISSING_SOURCE",
567
- errorDescription: "A source gene name is missing in cell " + colLetter + rowNum + "."
568
- };
569
- },
570
- &nbsp;
571
- missingTargetGeneWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
572
- var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
573
- var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
574
- <span class="cstat-no" title="statement not covered" > return {</span>
575
- warningCode: "MISSING_TARGET",
576
- errorDescription: "A target gene name is missing in cell " + colLetter + rowNum + "."
577
- };
578
- },
579
- &nbsp;
580
- invalidMatrixDataWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
581
- var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
582
- var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
583
- <span class="cstat-no" title="statement not covered" > return {</span>
584
- warningCode: "INVALID_DATA",
585
- errorDescription: "The value in cell " + colLetter + rowNum + ", is undefined."
586
- };
587
- },
588
- &nbsp;
589
- randomDataWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (type, row, column) {
590
- var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
591
- var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
592
- <span class="cstat-no" title="statement not covered" > return {</span>
593
- warningCode: "RANDOM_DATA",
594
- errorDescription: "The value in cell " + colLetter + rowNum + ", has a corresponding source" +
595
- " and/or target gene that is detected as " + type + "."
596
- };
597
- },
598
- &nbsp;
599
- emptyRowWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (row) {
600
- var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
601
- <span class="cstat-no" title="statement not covered" > return {</span>
602
- warningCode: "EMPTY_ROW",
603
- errorDescription: "Row " + rowNum + " was found to contain no data."
604
- };
605
- },
606
- &nbsp;
607
- networkSizeWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (genesLength, edgesLength) {
608
- <span class="cstat-no" title="statement not covered" > return {</span>
609
- warningCode: "INVALID_NETWORK_SIZE",
610
- errorDescription: "Your network has " + genesLength + " genes, and " + edgesLength +
611
- " edges. Please note that networks are recommended to have less than 50 genes and 100 edges."
612
- };
613
- },
614
- };
615
- &nbsp;
616
- var errorList = {
617
- &nbsp;
618
- emptyNetworkError: <span class="fstat-no" title="function not covered" >fu</span>nction () {
619
- <span class="cstat-no" title="statement not covered" > return {</span>
620
- errorCode: "EMPTY_NETWORK_ERROR",
621
- possibleCause: "GRNsight detects that the file you uploaded is empty and \
622
- does not contain any network information.",
623
- suggestedFix: "Please review the file and ensure that it specifies a network."
624
- };
625
- },
626
- &nbsp;
627
- semanticDuplicateGeneError: <span class="fstat-no" title="function not covered" >fu</span>nction (geneName) {
628
- <span class="cstat-no" title="statement not covered" > return {</span>
629
- errorCode: "SEMANTIC_DUPLICATE_GENE",
630
- possibleCause: "There exists a duplicate for " + geneName + ".",
631
- suggestedFix: "Please remove the duplicate gene and submit again."
632
- };
633
- },
634
- &nbsp;
635
- geneLengthError: <span class="fstat-no" title="function not covered" >fu</span>nction (geneName) {
636
- <span class="cstat-no" title="statement not covered" > return {</span>
637
- errorCode: "INVALID_GENE_LENGTH",
638
- possibleCause: "Gene " + geneName + " is more than 12 characters in length.",
639
- suggestedFix: "Genes may only be between 1 and 12 characters in length. Please" +
640
- " shorten the name and submit again."
641
- };
642
- },
643
- &nbsp;
644
- networkSizeError: <span class="fstat-no" title="function not covered" >fu</span>nction (genesLength, edgesLength) {
645
- <span class="cstat-no" title="statement not covered" > return {</span>
646
- errorCode: "INVALID_NETWORK_SIZE",
647
- possibleCause: "This network has " + genesLength + " genes, and " + edgesLength + " edges.",
648
- suggestedFix: "Networks may not have more than 75 genes or 150 edges. Please reduce the size" +
649
- " of your network and try again."
650
- };
651
- },
652
- &nbsp;
653
- specialCharacterError: <span class="fstat-no" title="function not covered" >fu</span>nction (geneName) {
654
- <span class="cstat-no" title="statement not covered" > return {</span>
655
- errorCode: "INVALID_CHARACTER",
656
- possibleCause: "The value under gene name " + geneName + " contains invalid character.",
657
- suggestedFix: "Please ensure all values in the data does not contain special characters" +
658
- " except for '-' and '_'."
659
- };
660
- },
661
- &nbsp;
662
- errorsCountError: {
663
- errorCode: "ERRORS_OVERLOAD",
664
- possibleCause: "This network has over 20 errors.",
665
- suggestedFix: "Please check the format of your spreadsheet with the guidlines outlined on the" +
666
- "Documentation page and try again. If you fix these errors and try to upload again, there may be " +
667
- "further errors detected. As a general approach for fixing the errors, consider copying and " +
668
- "pasting just your adjacency matrix into a fresh Excel Workbook and saving it."
669
- },
670
- &nbsp;
671
- warningsCountError: {
672
- errorCode: "WARNINGS_OVERLOAD",
673
- possibleCause: "This network has over 75 warnings.",
674
- suggestedFix: "Please check the format of your spreadsheet with the guidlines outlined on the" +
675
- "Documentation page and try again. If you fix these errors and try to upload again, there may be " +
676
- "further errors detected. As a general approach for fixing the errors, consider copying and " +
677
- "pasting just your adjacency matrix into a fresh Excel Workbook and saving it."
678
- },
679
- &nbsp;
680
- unknownError: {
681
- errorCode: "UNKNOWN_ERROR",
682
- possibleCause: "An unexpected error occurred.",
683
- suggestedFix: "Please contact the GRNsight team at kdahlquist@lmu.edu, and attach the spreadsheet you" +
684
- " attempted to upload."
685
- }
686
- &nbsp;
687
- };
688
- &nbsp;
689
- /*
690
- var addMessageToArray = function (messageArray, message) {
691
- messageArray.push(message);
692
- };
693
- var addError = function (network, message) {
694
- var errorsCount = network.errors.length;
695
- var MAX_ERRORS = 20;
696
- if (errorsCount &lt; MAX_ERRORS) {
697
- addMessageToArray(network.errors, message);
698
- } else {
699
- addMessageToArray(network.errors, errorList.errorsCountError);
700
- return false;
701
- }
702
- };
703
- var addWarning = function (network, message) {
704
- var warningsCount = network.warnings.length;
705
- var MAX_WARNINGS = 75;
706
- if (warningsCount &lt; MAX_WARNINGS) {
707
- addMessageToArray(network.warnings, message);
708
- } else {
709
- addMessageToArray(network.errors, errorList.warningsCountError);
710
- return false;
711
- }
712
- };
713
- */
714
- &nbsp;
715
- var checkNetworkSize = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray, warningArray, genesList, positiveWeights, negativeWeights) {
716
- var genesLength = <span class="cstat-no" title="statement not covered" >genesList.length;</span>
717
- var edgesLength = <span class="cstat-no" title="statement not covered" >positiveWeights.length + negativeWeights.length;</span>
718
- var GENE_MAX_WARNING = <span class="cstat-no" title="statement not covered" >50;</span>
719
- var EDGE_MAX_WARNING = <span class="cstat-no" title="statement not covered" >100;</span>
720
- var GENE_MAX_ERROR = <span class="cstat-no" title="statement not covered" >75;</span>
721
- var EDGE_MAX_ERROR = <span class="cstat-no" title="statement not covered" >150;</span>
722
- &nbsp;
723
- <span class="cstat-no" title="statement not covered" > if ((genesLength &gt;= GENE_MAX_WARNING &amp;&amp; genesLength &lt; GENE_MAX_ERROR) ||</span>
724
- (edgesLength &gt;= EDGE_MAX_WARNING &amp;&amp; edgesLength &lt; EDGE_MAX_ERROR)) {
725
- <span class="cstat-no" title="statement not covered" > warningArray.push(warningsList.networkSizeWarning(genesLength, edgesLength));</span>
726
- } else <span class="cstat-no" title="statement not covered" >if (genesLength &gt;= GENE_MAX_ERROR || edgesLength &gt;= EDGE_MAX_ERROR) {</span>
727
- <span class="cstat-no" title="statement not covered" > errorArray.push(errorList.networkSizeError(genesLength, edgesLength));</span>
728
- }
729
- };
730
- &nbsp;
731
- var checkDuplicateErrors = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray) {
732
- <span class="cstat-no" title="statement not covered" > for (var i = 0; i &lt; errorArray.length; i++) {</span>
733
- <span class="cstat-no" title="statement not covered" > if (errorArray[i].errorCode === "DUPLICATE_GENE") {</span>
734
- <span class="cstat-no" title="statement not covered" > return true;</span>
735
- }
736
- }
737
- };
738
- &nbsp;
739
- var checkDuplicates = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray, genesList) {
740
- <span class="cstat-no" title="statement not covered" > if (!checkDuplicateErrors(errorArray)) {</span>
741
- var genesName = <span class="cstat-no" title="statement not covered" >[];</span>
742
- <span class="cstat-no" title="statement not covered" > for (var i = 0; i &lt; genesList.length; i++) {</span>
743
- <span class="cstat-no" title="statement not covered" > genesName.push(genesList[i].name);</span>
744
- }
745
- &nbsp;
746
- <span class="cstat-no" title="statement not covered" > genesName.sort();</span>
747
- <span class="cstat-no" title="statement not covered" > for (var j = 0; j &lt; genesName.length - 1; j++) {</span>
748
- <span class="cstat-no" title="statement not covered" > if (genesName[j] === genesName[j + 1]) {</span>
749
- <span class="cstat-no" title="statement not covered" > errorArray.push(errorList.semanticDuplicateGeneError(genesName[j]));</span>
750
- }
751
- }
752
- }
753
- };
754
- &nbsp;
755
- var checkGeneLength = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray, genesList) {
756
- // Check if any genes are over the gene length (currently 12)
757
- var maxGeneLength = <span class="cstat-no" title="statement not covered" >12;</span>
758
- <span class="cstat-no" title="statement not covered" > for (var i = 0; i &lt; genesList.length; i++) {</span>
759
- <span class="cstat-no" title="statement not covered" > if (genesList[i].name.length &gt; maxGeneLength) {</span>
760
- <span class="cstat-no" title="statement not covered" > errorArray.push(errorList.geneLengthError(genesList[i].name));</span>
761
- }
762
- }
763
- };
764
- &nbsp;
765
- var checkSpecialCharacter = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray, genesList) {
766
- var regex = <span class="cstat-no" title="statement not covered" >/[^a-z0-9\_\-]/gi;</span>
767
- <span class="cstat-no" title="statement not covered" > for (var i = 0; i &lt; genesList.length; i++) {</span>
768
- <span class="cstat-no" title="statement not covered" > if (genesList[i].name.match(regex) !== null) {</span>
769
- <span class="cstat-no" title="statement not covered" > errorArray.push(errorList.specialCharacterError(genesList[i].name));</span>
770
- }
771
- }
772
- };
773
- &nbsp;
774
- var checkIfEmptyNetwork = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray, genesList) {
775
- <span class="cstat-no" title="statement not covered" > if (genesList.length === 0) {</span>
776
- <span class="cstat-no" title="statement not covered" > errorArray.push(errorList.emptyNetworkError());</span>
777
- }
778
- };
779
- &nbsp;
780
- // TODO Entry-point semantic checker function goes here.
781
- module.exports = <span class="fstat-no" title="function not covered" >fu</span>nction (network) {
782
- <span class="cstat-no" title="statement not covered" > checkSpecialCharacter(network.errors, network.genes);</span>
783
- <span class="cstat-no" title="statement not covered" > checkDuplicates(network.errors, network.genes);</span>
784
- <span class="cstat-no" title="statement not covered" > checkGeneLength(network.errors, network.genes);</span>
785
- <span class="cstat-no" title="statement not covered" > checkNetworkSize(network.errors, network.warnings, network.genes, network.positiveWeights, network.negativeWeights);</span>
786
- <span class="cstat-no" title="statement not covered" > checkIfEmptyNetwork(network.errors, network.genes);</span>
787
- // We're done. Return the network.
788
- <span class="cstat-no" title="statement not covered" > return network;</span>
789
- };
790
- &nbsp;</pre></td></tr>
791
- </table></pre>
792
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799
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801
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802
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804
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