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#!/usr/bin/env python3 |
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# -*- coding: utf-8 -*- |
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""" |
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Created on Mon May 7 15:49:04 2018 |
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@author: Paolo Cozzi <[email protected]> |
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Functions adapted from Jun Fan misc.py and use_zooma.py python scripts |
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""" |
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import logging |
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from image_validation.use_ontology import use_zooma |
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from common.constants import CONFIDENCES |
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# Get an instance of a logger |
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logger = logging.getLogger(__name__) |
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def call_zooma(label, zooma_type): |
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""" |
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Wrapper around use_zooma: call zooma or catch exception |
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Parameters |
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---------- |
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label : str |
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Zooma query temr. |
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zooma_type : str |
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Zooma query type (species, breed, ...). |
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Returns |
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------- |
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result : dict |
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The results of use_zooma or None |
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""" |
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result = None |
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try: |
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result = use_zooma(label, zooma_type) |
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except Exception as exc: |
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logger.error("Error in calling zooma: %s" % str(exc)) |
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return result |
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def annotate_generic(model, zooma_type): |
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"""Annotate missing terms from a generic DictTable |
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Args: |
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model (:py:class:`uid.models.DictBase`): A DictBase istance |
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zooma_type (str): the type of zooma annotation (country, species, ...) |
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""" |
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logger.debug("Processing %s" % (model)) |
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result = call_zooma(model.label, zooma_type) |
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# update object (if possible) |
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if result: |
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url = result['ontologyTerms'] |
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# https://stackoverflow.com/a/7253830 |
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term = url.rsplit('/', 1)[-1] |
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# The ontology seems correct. Annotate! |
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logger.info("Updating %s with %s" % (model, result)) |
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url = result['ontologyTerms'] |
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model.term = term |
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# get an int object for such confidence |
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confidence = CONFIDENCES.get_value( |
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result["confidence"].lower()) |
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model.confidence = confidence |
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model.save() |
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def annotate_country(country_obj): |
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"""Annotate country objects using Zooma""" |
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annotate_generic(country_obj, "country") |
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def annotate_breed(breed_obj): |
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"""Annotate breed objects using Zooma""" |
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logger.debug("Processing %s" % (breed_obj)) |
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result = call_zooma(breed_obj.supplied_breed, "breed") |
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# update object (if possible) |
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if result: |
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url = result['ontologyTerms'] |
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# https://stackoverflow.com/a/7253830 |
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term = url.rsplit('/', 1)[-1] |
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# The ontology seems correct. Annotate! |
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logger.info("Updating %s with %s" % (breed_obj, result)) |
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url = result['ontologyTerms'] |
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# this is slight different from annotate_generic |
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breed_obj.mapped_breed_term = term |
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breed_obj.mapped_breed = result['text'] |
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# get an int object for such confidence |
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confidence = CONFIDENCES.get_value( |
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result["confidence"].lower()) |
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breed_obj.confidence = confidence |
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breed_obj.save() |
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def annotate_specie(specie_obj): |
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"""Annotate specie objects using Zooma""" |
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annotate_generic(specie_obj, "species") |
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def annotate_organismpart(uberon_obj): |
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"""Annotate organism part objects using Zooma""" |
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annotate_generic(uberon_obj, "organism part") |
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def annotate_develstage(dictdevelstage_obj): |
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"""Annotate developmental stage objects using Zooma""" |
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annotate_generic(dictdevelstage_obj, "developmental stage") |
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def annotate_physiostage(dictphysiostage_obj): |
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"""Annotate physiological stage objects using Zooma""" |
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annotate_generic(dictphysiostage_obj, "physiological stage") |
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cnr-ibba /
IMAGE-InjectTool
