SMART common issue and indivo dev branch

[wc...@njit.edu]

Hi,

I'm hoping someone can help me with this isse.  I upgraded my indivo from 2.0 to develop branch in order to take advantage of smart v0.5 schemas and now I have this problem relating to smart-commons:

Any help would be appreciated.

No handlers could be found for logger "rdflib.term"

Traceback (most recent call last):

  File "/usr/lib/python2.7/wsgiref/handlers.py", line 85, in run

    self.result = application(self.environ, self.start_response)

  File "/usr/local/lib/python2.7/dist-packages/django/contrib/staticfiles/handlers.py", line 67, in __call__

    return self.application(environ, start_response)

  File "/usr/local/lib/python2.7/dist-packages/django/core/handlers/wsgi.py", line 219, in __call__

    self.load_middleware()

  File "/usr/local/lib/python2.7/dist-packages/django/core/handlers/base.py", line 45, in load_middleware

    mod = import_module(mw_module)

  File "/usr/local/lib/python2.7/dist-packages/django/utils/importlib.py", line 35, in import_module

    __import__(name)

  File "/opt/data/indivo_server/indivo/middlewares/authentication.py", line 8, in <module>

    from indivo.accesscontrol import security

  File "/opt/data/indivo_server/indivo/accesscontrol/__init__.py", line 6, in <module>

    from access_rule import AccessRule

  File "/opt/data/indivo_server/indivo/accesscontrol/access_rule.py", line 4, in <module>

    from indivo.views import *

  File "/opt/data/indivo_server/indivo/views/__init__.py", line 24, in <module>

    from documents  import *

  File "/opt/data/indivo_server/indivo/views/documents/__init__.py", line 10, in <module>

    from document           import *

  File "/opt/data/indivo_server/indivo/views/documents/document.py", line 16, in <module>

    from indivo.document_processing.document_utils import DocumentUtils

  File "/opt/data/indivo_server/indivo/document_processing/__init__.py", line 193, in <module>

    loader.import_schemas()

  File "/opt/data/indivo_server/indivo/document_processing/__init__.py", line 65, in import_schemas

    for schema_name, schema_etree, transform_func in self.discover_schema_dirs():

  File "/opt/data/indivo_server/indivo/document_processing/__init__.py", line 125, in discover_schema_dirs

    transformation_func = transform_handler(schema_dir)

  File "/opt/data/indivo_server/indivo/document_processing/__init__.py", line 163, in _get_transform_from_py

    reload(module)

  File "/opt/data/indivo_server/indivo/../indivo/schemas/data/core/rdf/transform.py", line 3, in <module>

    from indivo.rdf import parser

  File "/opt/data/indivo_server/indivo/rdf/parser.py", line 5, in <module>

    from .transforms import *

  File "/opt/data/indivo_server/indivo/rdf/transforms/__init__.py", line 1, in <module>

    from .medication import MedicationTransform

  File "/opt/data/indivo_server/indivo/rdf/transforms/medication.py", line 5, in <module>

    from .base import BaseRDFTransform

  File "/opt/data/indivo_server/indivo/rdf/transforms/base.py", line 4, in <module>

    from smart_common.rdf_tools.rdf_ontology import api_types

  File "/opt/data/indivo_server/smart_common/rdf_tools/rdf_ontology.py", line 513, in <module>

    parse_ontology(f)

  File "/opt/data/indivo_server/smart_common/rdf_tools/rdf_ontology.py", line 480, in parse_ontology

    m = parse_rdf(f)

  File "/opt/data/indivo_server/smart_common/rdf_tools/util.py", line 44, in parse_rdf

    model.default_context.parse(data=string, format="n3")

  File "build/bdist.linux-x86_64/egg/rdflib/graph.py", line 1035, in parse

    parser.parse(source, self, **args)

  File "build/bdist.linux-x86_64/egg/rdflib/plugins/parsers/notation3.py", line 1887, in parse

    TurtleParser.parse(self, source, conj_graph, encoding, turtle=False)

  File "build/bdist.linux-x86_64/egg/rdflib/plugins/parsers/notation3.py", line 1858, in parse

    p.loadStream(source.getByteStream())

  File "build/bdist.linux-x86_64/egg/rdflib/plugins/parsers/notation3.py", line 422, in loadStream

    return self.loadBuf(stream.read())    # Not ideal

  File "build/bdist.linux-x86_64/egg/rdflib/plugins/parsers/notation3.py", line 428, in loadBuf

    self.feed(buf)

  File "build/bdist.linux-x86_64/egg/rdflib/plugins/parsers/notation3.py", line 454, in feed

    i = self.directiveOrStatement(s, j)

  File "build/bdist.linux-x86_64/egg/rdflib/plugins/parsers/notation3.py", line 477, in directiveOrStatement

    return self.checkDot(argstr, j)

  File "build/bdist.linux-x86_64/egg/rdflib/plugins/parsers/notation3.py", line 1147, in checkDot

    "expected '.' or '}' or ']' at end of statement")

  File "build/bdist.linux-x86_64/egg/rdflib/plugins/parsers/notation3.py", line 1603, in BadSyntax

    raise BadSyntax(self._thisDoc, self.lines, argstr, i, msg)

BadSyntax: at line 6 of <>:

Bad syntax (expected '.' or '}' or ']' at end of statement) at ^ in:

"...ms/" >

    <!ENTITY foaf "http://xmlns.com/foaf/0.1/" >

    ^<!ENTITY owl "http://www.w3.org/2002/07/owl#" >

    <!ENTITY..."

[18/Sep/2014 14:35:45] "POST /oauth/internal/session_create HTTP/1.1" 500 59

[Nikolai Schwertner]

Hmm... It does sound like you may be facing a configuration issue with RDFLIB's logging functionality (see http://stackoverflow.com/questions/17393664/no-handlers-could-be-found-for-logger-rdflib-term). Unfortunately, Indivo is not my area of expertise. My colleague, Pascal, who may be able to answer this is currently on vacation, but I am CC-ing him anyway.

-Nikolai

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[Pascal Pfiffner]

I wish I was on vacation. ;)

It complains about a syntax error in the RDF+XML shown at the bottom, however since I haven't worked on Indivo's SMART implementation and the person who has is no longer with us I'm afraid there is little I can do.

[Nikolai Schwertner]

Another 2 cents... there may be a mismatch in the rdflib version and the code. Just a wild guess. ;)

Sorry that we can't be of more help.

[wc...@njit.edu]

Thank you both!

Once I fixed the logger I did get something about the contents being wrong:

INFO 2014-09-18 15:43:30,797 rdflib RDFLib Version: 4.1.2

WARNING 2014-09-18 15:44:56,754 rdflib.term file:///opt/data/?xml version="1.0"? does not look like a valid URI, trying to serialize this will break.

WARNING 2014-09-18 15:44:56,754 rdflib.term !DOCTYPE rdf:RDF [

    <!ENTITY dcterms "http://purl.org/dc/terms/"  does not look like a valid URI, trying to serialize this will break.

WARNING 2014-09-18 15:44:56,754 rdflib.term !ENTITY foaf "http://xmlns.com/foaf/0.1/"  does not look like a valid URI, trying to serialize this will break.

WARNING 2014-09-18 15:45:17,282 rdflib.term file:///opt/data/?xml version="1.0"? does not look like a valid URI, trying to serialize this will break.

WARNING 2014-09-18 15:45:17,283 rdflib.term !DOCTYPE rdf:RDF [

    <!ENTITY dcterms "http://purl.org/dc/terms/"  does not look like a valid URI, trying to serialize this will break.

WARNING 2014-09-18 15:45:17,283 rdflib.term !ENTITY foaf "http://xmlns.com/foaf/0.1/"  does not look like a valid URI, trying to serialize this will break.

I will try to figure out what the problem is with these lines

[wc...@njit.edu]

Anyone else have any idea what the issue could be with this document? Or how to get in touch with Travers.

Error:

Bad syntax (expected '.' or '}' or ']' at end of statement) at ^ in:

"...ms/" >

    <!ENTITY foaf "http://xmlns.com/foaf/0.1/" >

    ^<!ENTITY owl "http://www.w3.org/2002/07/owl#" >

    <!ENTITY...". Skipping...

Doc goes like this:

<?xml version="1.0"?>

<!DOCTYPE rdf:RDF [

<!ENTITY dcterms 'http://purl.org/dc/terms/'>

<!ENTITY foaf 'http://xmlns.com/foaf/0.1/'>

<!ENTITY owl 'http://www.w3.org/2002/07/owl#'>

<!ENTITY mime 'http://purl.org/NET/mediatypes/'>

<!ENTITY sp 'http://smartplatforms.org/terms#'>

<!ENTITY dc 'http://purl.org/dc/elements/1.1/'>

<!ENTITY v 'http://www.w3.org/2006/vcard/ns#'>

<!ENTITY xsd 'http://www.w3.org/2001/XMLSchema#'>

<!ENTITY examples 'http://smartplatforms.org/examples#'>

<!ENTITY cemterms 'http://smartplatforms.org/cemterms#'>

<!ENTITY api 'http://smartplatforms.org/terms/api#'>

<!ENTITY rdfs 'http://www.w3.org/2000/01/rdf-schema#'>

<!ENTITY spcode 'http://smartplatforms.org/terms/codes/'>

<!ENTITY calls 'http://smartplatforms.org/terms/api/calls#'>

<!ENTITY rdf 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'>

<!ENTITY fidelity 'http://smartplatforms.org/terms/code/fidelity#'>

<!ENTITY LabStatus 'http://smartplatforms.org/terms/codes/LabStatus#'>

<!ENTITY EncounterType 'http://smartplatforms.org/terms/codes/EncounterType#'>

<!ENTITY BloodPressureMethod 'http://smartplatforms.org/terms/codes/BloodPressureMethod#'>

<!ENTITY TranslationFidelity 'http://smartplatforms.org/terms/codes/TranslationFidelity#'>

<!ENTITY LabResultInterpretation 'http://smartplatforms.org/terms/codes/LabResultInterpretation#'>

<!ENTITY ImmunizationRefusalReason 'http://smartplatforms.org/terms/codes/ImmunizationRefusalReason#'>

<!ENTITY ImmunizationAdministrationStatus 'http://smartplatforms.org/terms/codes/ImmunizationAdministrationStatus#'>

]>

<rdf:RDF xmlns="http://smartplatforms.org/terms#"

     xml:base="http://smartplatforms.org/terms"

     xmlns:dc="http://purl.org/dc/elements/1.1/"

     xmlns:BloodPressureMethod="&spcode;BloodPressureMethod#"

     xmlns:EncounterType="&spcode;EncounterType#"

     xmlns:sp="http://smartplatforms.org/terms#"

     xmlns:LabStatus="&spcode;LabStatus#"

     xmlns:foaf="http://xmlns.com/foaf/0.1/"

     xmlns:spcode="http://smartplatforms.org/terms/codes/"

     xmlns:LabResultInterpretation="&spcode;LabResultInterpretation#"

     xmlns:TranslationFidelity="&spcode;TranslationFidelity#"

     xmlns:calls="http://smartplatforms.org/terms/api/calls#"

     xmlns:cemterms="http://smartplatforms.org/cemterms#"

     xmlns:ImmunizationRefusalReason="&spcode;ImmunizationRefusalReason#"

     xmlns:dcterms="http://purl.org/dc/terms/"

     xmlns:v="http://www.w3.org/2006/vcard/ns#"

     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"

     xmlns:fidelity="http://smartplatforms.org/terms/code/fidelity#"

     xmlns:ImmunizationAdministrationStatus="&spcode;ImmunizationAdministrationStatus#"

     xmlns:owl="http://www.w3.org/2002/07/owl#"

     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"

     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"

     xmlns:api="http://smartplatforms.org/terms/api#"

     xmlns:mime="http://purl.org/NET/mediatypes/"

     xmlns:examples="http://smartplatforms.org/examples#">

    <owl:Ontology rdf:about="http://smartplatforms.org/terms#"/>

rest is mostly irrelevant the issue seems to be with the entity declarations.  I looked but they appear to follow the proper format for declaring entities in the doctype. Am I missing something?

[Natalie Hodge]

how do I get off this list? 

[Josh Mandel]

Hi Natalie,

I've removed you from the email list. (You're still subscribed to the google group, but you won't receive emails.) You can manage your own subscription further at https://groups.google.com/forum/#!forum/smart-app-developers

Best,

  Josh