runParsePathway throws various exceptions on some pathways

[DWgit]

This code demonstrates exceptions thrown by runParsePathway.

import traceback
import sys

bad_pathways = ['WP1919', 'WP1978', 'WP2369', 'WP2485', 'WP3900', 'WP3923', 'WP4102', 'WP4129',
                'WP4419', 'WP5033', 'WP5105', 'WP5134', 'WP5214', 'WP5276', 'WP5279', 'WP5282']

s = WikiPathways()

for pathwayID in bad_pathways:
    print("Processing ", pathwayID, file=sys.stderr)
    try:
        g = runParsePathway(s, pathwayID)
        print("  Nodes:", len(g.nodes()), file=sys.stderr)
        print("  Edges:", len(g.edges()), file=sys.stderr)

    except BaseException as e:
        print(f"*** EXCEPTION runParsePathway raised {e=}, {type(e)=}", file=sys.stderr)
        traceback.print_exc()

The attached log shows the exceptions with stack traces. Note that there are several distinct exceptions, so this bug report may need to be split up.
minReproducible_all_bugreport.log

The issue occurs with WikiNetworks Version: 1.1.2, running on conda Python 3.9.12

[muktapalshikar]

Thank you for leaving this detailed report, and for the nice stack trace. This seems to be a little more complicated than your other bug reports and might take a while to fix. I see that the error is in mapping unlabeled groups to their closest named entities in the gpml version of the WikiPathway. I looked at a few examples and for some reason I can't find the groups (and their named interaction partners) in the visual representation of the pathway. I'm not sure why this inconsistency occurs. I will credit you in the fix.

--
Mukta