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intermine / intermine-ws-python-docs

Tutorials for the InterMine Python web client
GNU Lesser General Public License v2.1
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Tutorial 4 final steps cause an error #24

Open yochannah opened 6 years ago

yochannah commented 6 years ago

This might actually be an issue with the python package, but I'll leave that up to you to decide and open in the python client repo if needed.

The issue is in the final couple of lines of tutorial 4 - I thought I'd add a printline statement to see the output for these two lines...

query.add_path_description("ontologyAnnotations.ontologyTerm","Ontology Term")
query.add_path_description("publications","Pub.")

But when I try to print we get a badly formed query error.

You can try it out yourself in this binder instance

Error:

WebserviceError: ('There was a problem with our request', 400, 'Bad Request', u"Query does not pass XML validation. cvc-complex-type.3.2.2: Attribute 'path' is not allowed to appear in element 'pathDescription'.\ncvc-complex-type.4: Attribute 'pathString' must appear on element 'pathDescription'.\ncvc-complex-type.3.2.2: Attribute 'path' is not allowed to appear in element 'pathDescription'.\ncvc-complex-type.4: Attribute 'pathString' must appear on element 'pathDescription'.\n")
nupurgunwant commented 6 years ago

True, printing these is unsuccessful.

There seems to be a problem in the function itself, I implied this because the query that given in tutorial 4 using add_path_description, is not a valid one to post on any service(I tried flymine) using its xml which looks like this: <query longDescription="" model="genomic" name="" sortOrder="Gene.primaryIdentifier asc" view="Gene.primaryIdentifier Gene.symbol Gene.publications.year Gene.publications.firstAuthor Gene.publications.title Gene.ontologyAnnotations.ontologyTerm.name">**<pathDescription description="Ontology Term" path="Gene.ontologyAnnotations.ontologyTerm.name"/>**<constraint code="A" op="=" path="Gene.ontologyAnnotations.ontologyTerm.name" value="*biosynthetic process*"/></query>

However if I remove the bold part, its perfect. So, there is something wrong with the path Description

yochannah commented 6 years ago

@julie-sullivan any idea if pathdescription is supported by mines or not? (e.g. is this a syntax fix or should we we remove it from the tutorial and client?)