Open AlexanderPico opened 1 year ago
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.
Manually uploaded old PNG and SVG to wp-assets and wp.gh.io/assets/img for these cases:
WP435 WP466 WP983 WP2371 WP3197 WP5287
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.
@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.
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.
WP590 also enters into infinite loop like WP435 while generating svg.
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