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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- VERSION: "2.10",
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- &nbsp;
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- NOT_FOUND: -1,
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- WEIGHTED: "weighted",
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- UNWEIGHTED: "unweighted",
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- &nbsp;
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- GRNSIGHT_FILENAME_HEADER: "X-GRNsight-Filename",
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- &nbsp;
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- warnings: {
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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 color and" +
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- " thickness of the edges requires numerical weight values, your graph will display as an unweighted graph" +
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- " with black edges and pointed arrowheads. If you want to display the network as a weighted graph, please" +
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- " modify your input file to include weight values for all edges."
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- },
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- &nbsp;
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- EDGE_DEFAULT_NOT_DIRECTED: {
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- warningCode: "EDGE_DEFAULT_NOT_DIRECTED",
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- errorDescription: "GRNsight interprets the graph as directed unconditionally."
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- },
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- &nbsp;
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- SIF_FORMAT_WARNING: {
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- warningCode: "SIF_FORMAT_WARNING",
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- errorDescription: " GRNsight has detected that there are no tabs in your file. The GRNsight specification" +
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- " for SIF files states that data must be delimited by tabs. Please review your data. This warning may" +
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- " suggest that your SIF file has comma separated data or contains no data at all. Additionally, valid" +
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- " networks which consist of single source nodes may also trigger this warning."
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- }
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- },
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- &nbsp;
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- errors: {
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- SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR: {
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- errorCode: "SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR",
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- possibleCause: "The SIF importer detects an unweighted network with an unsupported relationship type.",
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- suggestedFix: "SIF files accepted by GRNsight must use 'pd' as the text string for the relationship type" +
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- " in unweighted networks. Please review the SIF input documentation. Additionally, this error may be have" +
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- " been caused by missing data in your file, which caused the importer to incorrectly interpret a source" +
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- " or target as the relationship."
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- },
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- &nbsp;
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- SIF_MISSING_DATA_ERROR: {
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- errorCode: "SIF_MISSING_DATA_ERROR",
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- possibleCause: "GRNsight has detected that your SIF file contains missing data. ",
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- suggestedFix: "Please review the data. In a SIF file, each entry must have a source node, relationship" +
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- " type, and at least one target node, separated by tabs. An entry with a single source node is also" +
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- " allowed."
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- },
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- &nbsp;
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- SIF_STRAY_DATA_ERROR: {
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- errorCode: "SIF_STRAY_DATA_ERROR",
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- possibleCause: "GRNsight has detected stray data and/or extraneous blank rows in your SIF file. ",
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- suggestedFix: "Please review the data and delete extraneous data from the file."
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- }
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- }
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- };
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- &nbsp;</pre></td></tr>
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- <span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">var helpers = require(__dirname + "/helpers");
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- &nbsp;
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- var grnsightToSif = require(__dirname + "/exporters/sif");
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- var grnsightToGraphMl = require(__dirname + "/exporters/graphml");
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- &nbsp;
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- var convertResponse = <span class="fstat-no" title="function not covered" >fu</span>nction (app, req, res, converter) {
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- <span class="cstat-no" title="statement not covered" > helpers.attachCorsHeader(res, app);</span>
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- <span class="cstat-no" title="statement not covered" > return res.status(200).send(converter(req.body));</span>
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- };
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- &nbsp;
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- var exportResponse = <span class="fstat-no" title="function not covered" >fu</span>nction (app, req, res, converter) {
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- <span class="cstat-no" title="statement not covered" > helpers.attachCorsHeader(res, app);</span>
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- <span class="cstat-no" title="statement not covered" > res.header("Content-Disposition", "attachment;filename=\"" + req.body.filename + "\"");</span>
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- <span class="cstat-no" title="statement not covered" > return res.status(200).send(converter(JSON.parse(req.body.network)));</span>
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- };
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- &nbsp;
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- var generalExportError = <span class="fstat-no" title="function not covered" >fu</span>nction (res, error) {
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- <span class="cstat-no" title="statement not covered" > return res.json(400, {</span>
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- message: "Invalid GRNsight format.",
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- details: {
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- name: error.name,
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- message: error.message
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- }
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- });
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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 (app) {
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- // The /convert-* routes represent pure data exchange;
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- // the /export-* ones wrap this around a file download.
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- <span class="cstat-no" title="statement not covered" > app.post("/convert-to-sif", <span class="fstat-no" title="function not covered" >fu</span>nction (req, res) {</span>
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- <span class="cstat-no" title="statement not covered" > try {</span>
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- <span class="cstat-no" title="statement not covered" > res.header("Content-Type", "text/plain");</span>
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- <span class="cstat-no" title="statement not covered" > return convertResponse(app, req, res, grnsightToSif);</span>
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- &nbsp;
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- <span class="cstat-no" title="statement not covered" > app.post("/export-to-sif", <span class="fstat-no" title="function not covered" >fu</span>nction (req, res) {</span>
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- <span class="cstat-no" title="statement not covered" > return generalExportError(res, error);</span>
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- }
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- });
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- &nbsp;
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- <span class="cstat-no" title="statement not covered" > app.post("/convert-to-graphml", <span class="fstat-no" title="function not covered" >fu</span>nction (req, res) {</span>
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- <span class="cstat-no" title="statement not covered" > res.header("Content-Type", "text/xml");</span>
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- <span class="cstat-no" title="statement not covered" > return convertResponse(app, req, res, grnsightToGraphMl);</span>
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- } catch (error) {
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- <span class="cstat-no" title="statement not covered" > return generalExportError(res, error);</span>
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- }
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- });
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- &nbsp;
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- <span class="cstat-no" title="statement not covered" > res.header("Content-Type", "text/xml");</span>
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- <span class="cstat-no" title="statement not covered" > return exportResponse(app, req, res, grnsightToGraphMl);</span>
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- } catch (error) {
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- <span class="cstat-no" title="statement not covered" > return generalExportError(res, error);</span>
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- }
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- });
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- }
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- &nbsp;
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- return {
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- grnsightToSif: grnsightToSif,
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- grnsightToGraphMl: grnsightToGraphMl
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- };
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- };
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- &nbsp;</pre></td></tr>
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