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crash when editing a workflow #39

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hmenager opened this issue Jul 26, 2019 · 2 comments
Closed

crash when editing a workflow #39

hmenager opened this issue Jul 26, 2019 · 2 comments
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bug Something isn't working

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@hmenager
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when trying to edit https://github.com/EBI-Metagenomics/workflow-is-cwl/blob/master/workflows/TranscriptomeAssembly-wf.paired-end.cwl the editor will crash with the following tb:

INFO:benten.langserver.server:Client query: textDocument/didOpen
ERROR:benten.langserver.server:Unexpected error: unhashable type: 'CommentedSeq'
Traceback (most recent call last):
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 63, in run
    self.handle(request)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 93, in handle
    response = to_dict(self._dispatch(client_query))
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 142, in _dispatch
    return f(client_query)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/fileoperation.py", line 60, in serve_textDocument_didOpen
    language_models=self.config.lang_models)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/models/document.py", line 87, in __init__
    self.update(text)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/models/document.py", line 96, in update
    parse_document(cwl, self.doc_uri, self.text, self.language_models, problems)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/models/languagemodel.py", line 221, in parse_document
    requirements=None)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/models/languagemodel.py", line 824, in parse
    completer.wf_completer.analyze_workflow(node, doc_uri, problems)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/models/languagemodel.py", line 927, in analyze_workflow
    self.validate_step_connections(step, step_id, problems)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/models/languagemodel.py", line 976, in validate_step_connections
    if conn_id not in self.all_connections:
TypeError: unhashable type: 'CommentedSeq'
INFO:benten.langserver.server:Client query: textDocument/documentSymbol
ERROR:benten.langserver.server:Unexpected error: 'file:///home/hmenager/galaxycwl/workflow-is-cwl/workflows/TranscriptomeAssembly-wf.paired-end.cwl'
Traceback (most recent call last):
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 63, in run
    self.handle(request)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 93, in handle
    response = to_dict(self._dispatch(client_query))
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 142, in _dispatch
    return f(client_query)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/documentsymbol.py", line 22, in serve_textDocument_documentSymbol
    doc = self.open_documents[doc_uri]
KeyError: 'file:///home/hmenager/galaxycwl/workflow-is-cwl/workflows/TranscriptomeAssembly-wf.paired-end.cwl'
@hmenager
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also happens with:
https://github.com/EBI-Metagenomics/workflow-is-cwl/blob/master/workflows/TranscriptomeAssembly-wf.single-end.cwl

INFO:benten.langserver.server:Client query: textDocument/didOpen
DEBUG:benten.models.document:Took 0.0814s to load document
DEBUG:benten.models.document:Took 0.047s to parse document
INFO:benten.langserver.server:Client query: textDocument/documentSymbol
INFO:benten.langserver.server:Client query: textDocument/didOpen
DEBUG:benten.models.document:Took 0.154s to load document
DEBUG:benten.models.document:Took 0.0471s to parse document
INFO:benten.langserver.server:Client query: textDocument/documentSymbol
INFO:benten.langserver.server:Client query: textDocument/didOpen
DEBUG:benten.models.document:Took 0.019s to load document
DEBUG:benten.models.document:Took 0.0113s to parse document
INFO:benten.langserver.server:Client query: textDocument/documentSymbol
INFO:benten.langserver.server:Client query: textDocument/didClose
INFO:benten.langserver.server:Client query: textDocument/didClose
INFO:benten.langserver.server:Client query: textDocument/didClose
INFO:benten.langserver.server:Client query: textDocument/didOpen
ERROR:benten.langserver.server:Unexpected error: unhashable type: 'CommentedSeq'
Traceback (most recent call last):
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 63, in run
    self.handle(request)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 93, in handle
    response = to_dict(self._dispatch(client_query))
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 142, in _dispatch
    return f(client_query)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/fileoperation.py", line 60, in serve_textDocument_didOpen
    language_models=self.config.lang_models)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/models/document.py", line 87, in __init__
    self.update(text)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/models/document.py", line 96, in update
    parse_document(cwl, self.doc_uri, self.text, self.language_models, problems)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/models/languagemodel.py", line 221, in parse_document
    requirements=None)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/models/languagemodel.py", line 824, in parse
    completer.wf_completer.analyze_workflow(node, doc_uri, problems)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/models/languagemodel.py", line 927, in analyze_workflow
    self.validate_step_connections(step, step_id, problems)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/models/languagemodel.py", line 976, in validate_step_connections
    if conn_id not in self.all_connections:
TypeError: unhashable type: 'CommentedSeq'
INFO:benten.langserver.server:Client query: textDocument/documentSymbol
ERROR:benten.langserver.server:Unexpected error: 'file:///home/hmenager/galaxycwl/workflow-is-cwl/workflows/TranscriptomeAssembly-wf.single-end.cwl'
Traceback (most recent call last):
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 63, in run
    self.handle(request)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 93, in handle
    response = to_dict(self._dispatch(client_query))
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 142, in _dispatch
    return f(client_query)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/documentsymbol.py", line 22, in serve_textDocument_documentSymbol
    doc = self.open_documents[doc_uri]
KeyError: 'file:///home/hmenager/galaxycwl/workflow-is-cwl/workflows/TranscriptomeAssembly-wf.single-end.cwl'
INFO:benten.langserver.server:Client query: textDocument/hover
ERROR:benten.langserver.server:Unexpected error: 'file:///home/hmenager/galaxycwl/workflow-is-cwl/workflows/TranscriptomeAssembly-wf.single-end.cwl'
Traceback (most recent call last):
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 63, in run
    self.handle(request)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 93, in handle
    response = to_dict(self._dispatch(client_query))
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/server.py", line 142, in _dispatch
    return f(client_query)
  File "/home/hmenager/.local/pipx/venvs/benten/lib/python3.7/site-packages/benten/langserver/hover.py", line 22, in serve_textDocument_hover
    doc = self.open_documents[doc_uri]
KeyError: 'file:///home/hmenager/galaxycwl/workflow-is-cwl/workflows/TranscriptomeAssembly-wf.single-end.cwl'
INFO:benten.langserver.server:Client query: $/cancelRequest
ERROR:benten.langserver.server:Unknown method: $/cancelRequest

@ghost ghost self-assigned this Jul 26, 2019
@ghost ghost added the bug Something isn't working label Jul 26, 2019
@ghost ghost mentioned this issue Jul 26, 2019
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@ghost
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ghost commented Jul 28, 2019

Thanks for reporting this @hmenager ! This issue is fixed by 20720e8 . This will be merged into master in a short time - I want to finish up some work related to workflow structure analysis.

@ghost ghost closed this as completed Jul 28, 2019
This issue was closed.
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