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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78
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81
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- generated by <a href="http://istanbul-js.org/" target="_blank">istanbul</a> at Fri Sep 29 2017 00:22:47 GMT-0700 (PDT)
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- <span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">var constants = require(__dirname + "/../constants");
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- var semanticChecker = require(__dirname + "/../semantic-checker");
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- &nbsp;
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- var GENE_NAME = 0;
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- var RELATIONSHIP = 1;
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- var TARGET = 2;
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- &nbsp;
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- &nbsp;
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- module.exports = function (sif) {
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- &nbsp;
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- var warnings = [];
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- var errors = [];
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- &nbsp;
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- // Workaround for empty SIF file handling
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- var emptySifFile = sif === "";
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- sif = sif || " ";
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- &nbsp;
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- // Replace any carriage return characters with new lines.
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- sif = sif.replace(/\r\n/g, "\n");
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- &nbsp;
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- // Stray data detected when there are 2 or more consecutive tabs NOT followed by a newline in the SIF file.
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- // OR Stray data detected when there are 2 or more consecutive new lines
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- if (sif.match(/(?=.*[\t]{2,}?[^\n\t]).*/g) || sif.match(/[\n]{2,}/g)) {
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- errors.push(constants.errors.SIF_STRAY_DATA_ERROR);
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- }
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- &nbsp;
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- // Detects comma separated SIF files
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- if (!sif.match(/[\t]+/g) &amp;&amp; sif.match(/[,]+/g)) {
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- errors.push(constants.warnings.SIF_FORMAT_WARNING);
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- }
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- &nbsp;
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- var isNumber = function (relationship) {
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- return !isNaN(+relationship);
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- };
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- &nbsp;
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- var sifNetworkType = function (sifEntries) {
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- var errors = [];
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- var relationships = [];
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- var numRowsWithTwoColumns = 0;
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- var unweightedRelationshipTypeErrorDetected = false;
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- &nbsp;
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- sifEntries.forEach(function (entry) {
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- if (entry.length &gt; TARGET) {
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- if (!isNumber(entry[RELATIONSHIP])) {
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- if (entry[RELATIONSHIP] !== "pd") {
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- unweightedRelationshipTypeErrorDetected = true;
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- }
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- }
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- relationships.push(entry[RELATIONSHIP]);
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- } else if (entry.length === 2) {
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- numRowsWithTwoColumns++;
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- }
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- });
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- &nbsp;
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- if (unweightedRelationshipTypeErrorDetected) {
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- errors.push(constants.errors.SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR);
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- }
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- &nbsp;
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- if (numRowsWithTwoColumns &gt; 0) {
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- errors.push(constants.errors.SIF_MISSING_DATA_ERROR);
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- }
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- &nbsp;
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- var hasNumbers = relationships.some(isNumber);
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- var allNumbers = relationships.every(isNumber);
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- return {
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- sheetType: allNumbers ? constants.WEIGHTED : constants.UNWEIGHTED,
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- warnings: hasNumbers &amp;&amp; !allNumbers ? constants.warnings.EDGES_WITHOUT_WEIGHTS : null,
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- errors: errors
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- };
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- };
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- &nbsp;
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- var entries = sif.match(/[^\r\n]+/g).map(function (line) {
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- return line.match(/[^\t]+/g);
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- });
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- &nbsp;
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- var genes = [];
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- var links = [];
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- var networkType = "unweighted";
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- &nbsp;
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- var nullEntries = entries.filter(function (entry) {
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- return entry === null;
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- });
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- &nbsp;
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- <span class="missing-if-branch" title="if path not taken" >I</span>if (nullEntries.length &gt; 0) {
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- <span class="cstat-no" title="statement not covered" > errors.push(constants.errors.SIF_STRAY_DATA_ERROR);</span>
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- } else {
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- entries.forEach(function (entry) {
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- if (entry.length &amp;&amp; entry[GENE_NAME] &amp;&amp; genes.indexOf(entry[GENE_NAME]) === constants.NOT_FOUND) {
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- genes.push(entry[GENE_NAME]);
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- }
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- });
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- &nbsp;
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- networkType = sifNetworkType(entries);
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- if (networkType.warnings) {
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- warnings.push(networkType.warnings);
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- }
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- &nbsp;
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- <span class="missing-if-branch" title="else path not taken" >E</span>if (networkType.errors) {
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- networkType.errors.forEach(function (error) {
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- errors.push(error);
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- });
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- }
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- &nbsp;
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- entries.forEach(function (entry) {
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- if (entry.length &gt; TARGET) {
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- var sourceIndex = genes.indexOf(entry[GENE_NAME]);
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- var targets = entry.slice(TARGET);
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- targets.forEach(function (target) {
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- var targetIndex = genes.indexOf(target);
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- if (targetIndex === constants.NOT_FOUND) {
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- genes.push(target);
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- targetIndex = genes.indexOf(target);
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- }
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- var link = {
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- source: sourceIndex,
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- target: targetIndex
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- };
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- if (networkType.sheetType === constants.WEIGHTED) {
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- link.value = +entry[RELATIONSHIP];
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- }
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- links.push(link);
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- });
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- }
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- });
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- }
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- &nbsp;
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- var network = {
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- genes: emptySifFile ? [] : genes.map(function (geneName) {
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- return { name: geneName };
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- }),
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- links: links,
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- errors: errors,
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- warnings: warnings,
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- sheetType: networkType.sheetType,
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- positiveWeights: [],
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- negativeWeights: []
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- };
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- &nbsp;
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- return (network.errors.length === 0) ? semanticChecker(network) : network;
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- &nbsp;
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- };
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- &nbsp;</pre></td></tr>
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- </table></pre>
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