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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- All files
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- <div class='clearfix'>
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- <span class="strong">75.78% </span>
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- <span class="strong">84.62% </span>
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- <span class='fraction'>231/273</span>
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- <table class="coverage-summary">
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- <tr>
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- <th data-col="file" data-fmt="html" data-html="true" class="file">File</th>
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56
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65
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66
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67
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68
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69
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72
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90
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- <span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">// Parses "optimization_paramters," expression data sheets, and 2-column sheets
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- // from GRNmap input or output workbook
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- &nbsp;
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- var TWO_COL_SHEET_NAMES = [
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- "production_rates",
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- "degradation_rates",
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- "threshold_b",
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- "optimized_production_rates",
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- "optimized_threshold_b"];
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- &nbsp;
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- var EXPRESSION_SHEET_SUFFIXES = ["_expression", "_optimized_expression", "_sigmas"];
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- &nbsp;
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- var isExpressionSheet = function (sheetName) {
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- return EXPRESSION_SHEET_SUFFIXES.some(function (suffix) {
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- return sheetName.includes(suffix);
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- });
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- };
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- &nbsp;
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- var fillArray = function (value, array, length) { // mutator
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- while (array.length &lt; length) {
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- array.push(value);
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- }
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- return array;
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- };
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- &nbsp;
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- var parseMetaDataSheet = function (sheet) {
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- var meta = {};
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- sheet.data.forEach(function (element, index) {
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- if (index !== 0) {
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- var value = element.slice(1);
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- // Extract element from array if array contains only 1 value
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- meta[element[0]] = value.length &gt; 1 ? value : value[0];
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- }
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- });
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- return meta;
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- };
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- &nbsp;
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- var parseTwoColumnSheet = function (sheet) {
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- var data = {};
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- sheet.data.forEach(function (element, index) {
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- if (index !== 0) {
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- data[element[0]] = element[1];
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- }
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- });
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- return data;
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- };
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- &nbsp;
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- var parseExpressionSheet = function (sheet) {
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- var expressionData = {};
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- var geneData = {};
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- expressionData["time_points"] = sheet.data[0].slice(1);
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- var numberOfDataPoints = expressionData["time_points"].length;
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- sheet.data.forEach(function (sheet) {
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- var geneName = sheet[0];
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- if (geneName) {
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- var rowData = sheet.slice(1);
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- // Sometimes, missing data is at the end of the row. In this case, pad the
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- // array with nulls
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- if (rowData.length &lt; numberOfDataPoints) {
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- fillArray(null, rowData, numberOfDataPoints);
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- }
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- geneData[geneName] = rowData;
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- }
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- });
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- expressionData["data"] = geneData;
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- return expressionData;
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- };
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- &nbsp;
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- module.exports = function (workbook) {
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- var output = {
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- expression: {}, // expression data
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- meta: {},
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- test: {} // 2-column data
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- };
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- workbook.forEach(function (sheet) {
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- if (sheet.name === "optimization_parameters") {
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- output["meta"] = parseMetaDataSheet(sheet);
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- // Parse 2-column sheets
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- } else if (TWO_COL_SHEET_NAMES.includes(sheet.name)) {
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- output["test"][sheet.name] = parseTwoColumnSheet(sheet);
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- // Parse expression sheets
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- } else if (isExpressionSheet(sheet.name)) {
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- output["expression"][sheet.name] = parseExpressionSheet(sheet);
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- }
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- });
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- return output;
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- };
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- &nbsp;</pre></td></tr>
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- </table></pre>
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