Issue 764 etc #778
Issue 764 etc #778
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…client) npm module; not finished yet (fails)
…m/PathwayCommons/app-ui into issue_764_etc # Conflicts: # src/client/features/interactions/index.js
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Fixes #764 |
| const params = { | ||
| source : sources, | ||
| pattern : ['controls-phosphorylation-of','in-complex-with','controls-expression-of', 'interacts-with'], | ||
| kind : sources.length>1 ? 'pathsbetween' : 'neighborhood', |
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Is it the case that 'pathsbetween' will not return 'interacts-with'?
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My changes (using one universal new method ServerAPI.pcQuery instead of ServerAPI.getNeighborhood): bc43b13#diff-48d6e306661f0412cd8851fd566e8bba
ServerAPI.getNeighborhood (removed by bc43b13#diff-0e447967aaeb299d989022e921439ad2) used the same graph query parameters.
No, these changes have nothing to do with the other issue about and pathsbetween, which never finds interacts-with due its implementation in java (Paxtools/pattern).
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Ah, let me fix a bug in pc queries to download pathway data in different formats (SIF, BioPAX, etc.) from the right panel... Please wait, don't merge this PR. |
| ServerAPI.datasources() | ||
| .then(result => { | ||
| this.setState({ | ||
| dataSources: Object.values(result).filter(ds => ds.hasPathways==true) |
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No, it was always returned for each datasource in the array - by /pc2/metadata/datasources query.
I just added this filed to the server-side pc code (https://github.com/PathwayCommons/app-ui/blob/issue_764_etc/src/server/pathway-commons/index.js#L107) and can filter as shown above.
PS:
note that internal pc client module is now just one file: src/server/pathway-commons/index.js, and there is no 'pathway-commons' import from npm.
| .then(id=> _.words(id.traverseEntry[0].value[0]).length===1 ? id.traverseEntry[0].value[0].split('_')[0] : ''): | ||
| source.replace(/\//g,' ') | ||
| //get ids from uris | ||
| const geneIds = sources.map(source => |
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What case was this traverse trying to handle?
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It says "get ids from uris" in the comment line above that code (if, e.g., an uri is standard PR's uri, I bet); @logmosier can comment on exact purpose of this. I did not change the purpose of this code. It would be great to have more comments in the code, in many places.
PS(other): - (interactions) queries like /pc-client/graph?source=9241 should use gene symbol instead id; - there are many errors on the sbgn views and sif like "Edge `Complex_9fb32941a08115fc12311985e436d989--to--Transport_feac0a7c834893e7b53f8f0bcfcfde40_LEFT_TO_RIGHT` has invalid endpoints and so it is impossible to draw...", which I guess are not related to changes in this branch (cytoscape.js model, dependencies?... might I am wrong.)
…into issue_764_etc
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I am curious, who named a branch 'garbage-pc-search'? So untrue and hurts for some reason :/ |
Implemented PC_URL environment option made other improvements, such as simplified PC web service queries - pathway-commons-client (npm) module is not required anymore, and the pc client code is now simpler and reused better.
Also implemented one solution for #761 (see my comments there).