GPMLs that break json-svg conversion

[AlexanderPico]

Just to keep track of the remaining "problem children" from the recent sync of all approved pathways, here's a list pathways that can't be converted to pvjson, svg and png using our main script. I debugged quite a few, but these remain error-prone and I have no idea what to do about them. So, I'm ignore them for now :)

WP435 WP466 WP983 WP2371 WP3197 WP5287 WP590

[Chris-Evelo]

I quickly checked WP91 and the only special thing I saw is the "^" character in some of the compound names. Could that reason? For WP435 Tyms seems to have two anchors. I don't expect that to be the problem, but it is probably wrong anyway.

[AlexanderPico]

Manually uploaded old PNG and SVG to wp-assets and wp.gh.io/assets/img for these cases:

WP435 WP466 WP983 WP2371 WP3197 WP5287

[AlexanderPico]

Error for a new problematic GPML WP5271

generating JSON and SVG files for WP5271
WP5271
/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/pathways/WP5271/WP5271.gpml
/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-assets/pathways/WP5271/WP5271.svg
WP5271
/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/pathways/WP5271/WP5271.gpml
/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-assets/pathways/WP5271/WP5271.json

/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/scripts/generate-svgs/node_modules/bridgedb/src/spinoffs/TSVGetter.ts:96
        throw new VError(err, callString);
              ^
VError: in TSVGetter.get(
    url=https://webservice.bridgedb.org/Caulobacter vibrioides/xrefsBatch,
    method=POST,
    body=LMSP01020002   LIPID MAPS
A0A0H3C6D9  Uniprot-TrEMBL
LMFA01010001    LIPID MAPS
LMFA07050000    LIPID MAPS
LMSP02020000    LIPID MAPS
17115   ChEBI
LMSP02080000    LIPID MAPS
LMFA07050360    LIPID MAPS
A0A0H3C7E9  Uniprot-TrEMBL
A0A0H3C8X0  Uniprot-TrEMBL
A0A0H3C8X7  Uniprot-TrEMBL
15346   ChEBI
29863195    PubMed
34969973    PubMed
70360   Rhea
14762   Rhea
70528   Rhea
) with httpOptions={
  "timeout": 4000,
  "retryLimit": 2,
  "retryDelay": 3000
}
       tsvOptions={
  "headers": false,
  "objectMode": true,
  "delimiter": "\t",
  "comment": "#"
}: ajax error 500 in Rx.Observable.prototype.throughNodeStream
    at CatchSubscriber.selector (/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/scripts/generate-svgs/node_modules/bridgedb/src/spinoffs/TSVGetter.ts:96:15)
    at CatchSubscriber.error (/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/scripts/generate-svgs/node_modules/src/operators/catchError.ts:106:23)
    at MapSubscriber.Subscriber._error (/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/scripts/generate-svgs/node_modules/src/Subscriber.ts:143:22)
    at MapSubscriber.Subscriber.error (/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/scripts/generate-svgs/node_modules/src/Subscriber.ts:113:12)
    at AjaxSubscriber.Subscriber._error (/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/scripts/generate-svgs/node_modules/src/Subscriber.ts:143:22)
    at AjaxSubscriber.Subscriber.error (/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/scripts/generate-svgs/node_modules/src/Subscriber.ts:113:12)
    at XMLHttpRequest.xhrReadyStateChange [as onreadystatechange] (/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/scripts/generate-svgs/node_modules/src/observable/dom/AjaxObservable.ts:378:22)
    at XMLHttpRequest.dispatchEvent (/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/scripts/generate-svgs/node_modules/xhr2/lib/xhr2.js:76:20)
    at XMLHttpRequest._setReadyState (/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/scripts/generate-svgs/node_modules/xhr2/lib/xhr2.js:422:14)
    at XMLHttpRequest._onHttpResponseEnd (/home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/scripts/generate-svgs/node_modules/xhr2/lib/xhr2.js:616:14)
gpmlconverter: Unknown Error
An error occurred in line 208 of file /home/runner/work/wikipathways-database/wikipathways-database/wikipathways-database/scripts/generate-svgs/gpmlconverter:
    bridgedb xrefs -f json \
gpmlconverter: Unknown Error
An error occurred in line 240 of file ./gpmlconverter:
  "$SCRIPT_DIR/gpmlconverter" --id "$ID" --pathway-version "$PATHWAY_VERSION" -i "$path_in" -o "$json_f"
Error: Process completed with exit code 1.

[AlexanderPico]

@hasanbalci This ticket has a short list of GPMLs that break the json-svg step. While you're looking into fixes to include in the next release of pvjson, you might want to run each of these and see if you have any ideas.

[hasanbalci]

I had a chance to check what the problems are with these pathway files and here are my initial observations:

WP435: I think this enters into an infinite loop somewhere during the generation of svg (in pvjs repo), because it gives memory error after some time.

WP466, WP983 and WP3197: It seems there are some arcs and/or nodes in these pathways that pvjs repo doesn't like while trying to generate the corresponding svg images. I identified some of them and if I remove those graph elements temporarily, svgs are generated but this time svg-to-png conversion gives error and cannot generate png images.

WP2371 and WP5287: It seems that svgs are generated but svg-to-png conversion gives error and cannot generate png images.

[hasanbalci]

WP590 also enters into infinite loop like WP435 while generating svg.