class ReferenceDocument(DocType):
pk = fields.IntegerField(attr='pk')
sid = fields.IntegerField(attr='sid')
pmid = string_field(attr='pmid')
study = ObjectField(properties={
"pk": fields.IntegerField(),
"name": string_field('name'),
})
name = string_field("name")
doi = string_field("doi")
title = string_field("title")
abstract = text_field("abstract")
journal = text_field("journal")
date = fields.DateField()
pdf = fields.FileField(fielddata=True)
authors = ObjectField(properties={
'first_name': string_field("first_name"),
'last_name': string_field("last_name"),
'pk': fields.IntegerField(),
})
class Meta(object):
model = Reference
# Ignore auto updating of Elasticsearch when a model is saved
# or deleted:
ignore_signals = True
# Don't perform an index refresh after every update (overrides global setting):
auto_refresh = False
def common_setfields(model, attr=None):
if attr is None:
attr = model
return ObjectField(
properties={
"descriptions":
ObjectField(properties={
'text': text_field("text"),
'pk': fields.IntegerField()
},
multi=True),
model:
ObjectField(attr=attr, properties={
"pk": fields.FloatField(),
}),
"comments":
fields.ObjectField(properties={
'text':
text_field("text"),
'user':
fields.ObjectField(
properties={
'first_name': string_field("first_name"),
'last_name': string_field("last_name"),
'pk': string_field("last_name"),
'username': string_field("username"),
})
},
multi=True)
})
class DescriptionDocument(DocType):
pk = fields.IntegerField(attr='pk')
text = text_field('text')
class Meta(object):
model = Description
# Ignore auto updating of Elasticsearch when a model is saved
# or deleted:
ignore_signals = True
# Don't perform an index refresh after every update (overrides global setting):
auto_refresh = False
class DescriptionDocument(Document):
pk = fields.IntegerField(attr='pk')
text = text_field('text')
class Django:
model = Description
# Ignore auto updating of Elasticsearch when a model is saved/deleted
ignore_signals = True
# Don't perform an index refresh after every update
auto_refresh = False
class Index:
name = 'descriptions'
settings = elastic_settings
class CommentDocument(DocType):
pk = fields.IntegerField(attr='pk')
user = ObjectField(
properties={
'first_name': string_field('first_name'),
'last_name': string_field('last_name'),
})
text = text_field('text')
date_time = fields.DateField()
class Meta(object):
model = Comment
# Ignore auto updating of Elasticsearch when a model is saved
# or deleted:
ignore_signals = True
# Don't perform an index refresh after every update (overrides global setting):
auto_refresh = False
class CommentDocument(Document):
pk = fields.IntegerField(attr='pk')
user = ObjectField(
properties={
'first_name': string_field('first_name'),
'last_name': string_field('last_name'),
})
text = text_field('text')
date_time = fields.DateField()
class Django:
model = Comment
# Ignore auto updating of Elasticsearch when a model is saved/deleted
ignore_signals = True
# Don't perform an index refresh after every update
auto_refresh = False
class Index:
name = 'comments'
settings = elastic_settings
class ReferenceDocument(Document):
pk = fields.IntegerField(attr='pk')
sid = string_field(attr='sid')
pmid = string_field(attr='pmid')
study = ObjectField(
properties={
"pk":
fields.IntegerField(),
"sid":
string_field('sid'),
"name":
string_field('name'),
"licence":
string_field("licence"),
"creator":
fields.ObjectField(
properties={
'first_name': string_field("first_name"),
'last_name': string_field("last_name"),
'pk': string_field("pk"),
'username': string_field("username"),
}),
"curators":
fields.ObjectField(attr="ratings",
properties={
'first_name': string_field(
"user.first_name"),
'last_name': string_field("user.last_name"),
'pk': string_field("user.pk"),
'username': string_field("user.username"),
'rating': fields.FloatField(attr='rating')
},
multi=True),
"collaborators":
fields.ObjectField(attr="collaborators",
properties={
'first_name': string_field("first_name"),
'last_name': string_field("last_name"),
'pk': string_field("pk"),
'username': string_field("username")
},
multi=True)
})
name = string_field("name")
doi = string_field("doi")
title = string_field("title")
abstract = text_field("abstract")
journal = text_field("journal")
date = fields.DateField()
pdf = fields.FileField(fielddata=True)
authors = ObjectField(
properties={
'first_name': string_field("first_name"),
'last_name': string_field("last_name"),
'pk': fields.IntegerField(),
})
class Django:
model = Reference
# Ignore auto updating of Elasticsearch when a model is saved/deleted
ignore_signals = True
# Don't perform an index refresh after every update (overrides global setting):
auto_refresh = False
class Index:
name = 'references'
settings = elastic_settings
class StudyDocument(Document):
id = fields.StringField(attr='sid')
pk = fields.StringField(attr='sid')
sid = string_field(attr='sid')
pkdb_version = fields.IntegerField(attr='pkdb_version')
descriptions = ObjectField(properties={
'text': text_field("text"),
'pk': fields.IntegerField()
},
multi=True)
comments = fields.ObjectField(properties={
'text':
text_field("text"),
'user':
fields.ObjectField(
properties={
'first_name': string_field("first_name"),
'last_name': string_field("last_name"),
'pk': string_field("last_name"),
'username': string_field("username"),
})
},
multi=True)
creator = fields.ObjectField(
properties={
'first_name': string_field("first_name"),
'last_name': string_field("last_name"),
'pk': string_field("pk"),
'username': string_field("username"),
})
name = string_field("name")
licence = string_field("licence")
access = string_field("access")
reference = ObjectField(
properties={
'sid': string_field(attr='sid'),
'pk': fields.IntegerField(attr='pk'),
'name': string_field(attr="name")
})
curators = fields.ObjectField(attr="ratings",
properties={
'first_name':
string_field("user.first_name"),
'last_name':
string_field("user.last_name"),
'pk': string_field("user.pk"),
'username':
string_field("user.username"),
'rating':
fields.FloatField(attr='rating')
},
multi=True)
collaborators = fields.ObjectField(attr="collaborators",
properties={
'first_name':
string_field("first_name"),
'last_name':
string_field("last_name"),
'pk': string_field("pk"),
'username': string_field("username")
},
multi=True)
substances = string_field(attr="get_substances", multi=True)
files = ObjectField(
attr="files_ordered",
properties={
'pk':
fields.IntegerField(),
'file':
fields.StringField(attr="file.url",
fielddata=True,
analyzer=autocomplete,
search_analyzer=autocomplete_search,
fields={
'raw': fields.KeywordField(),
}),
'name':
fields.StringField(fielddata=True,
analyzer=autocomplete,
search_analyzer=autocomplete_search,
fields={
'raw': fields.KeywordField(),
}),
'timecourses':
ObjectField(properties={
'pk': fields.IntegerField(multi=True),
},
multi=True)
},
multi=True)
groupset = common_setfields("groups")
individualset = common_setfields("individuals")
interventionset = common_setfields("interventions", "interventions_normed")
outputset = ObjectField(
properties={
"descriptions":
ObjectField(properties={
'text': text_field("text"),
'pk': fields.IntegerField()
},
multi=True),
# "count_outputs" : fields.FloatField(),
"outputs":
ObjectField(attr="outputs_normed",
properties={
"pk": fields.FloatField(),
}),
# "count_timecourses": fields.FloatField(),
"timecourses":
ObjectField(attr="timecourses_normed",
properties={
"pk": fields.FloatField(),
}),
"comments":
fields.ObjectField(properties={
'text':
text_field("text"),
'user':
fields.ObjectField(
properties={
'first_name': string_field("first_name"),
'last_name': string_field("last_name"),
'pk': string_field("last_name"),
'username': string_field("username"),
})
},
multi=True)
})
group_count = fields.IntegerField()
individual_count = fields.IntegerField()
intervention_count = fields.IntegerField()
output_count = fields.IntegerField()
output_calculated_count = fields.IntegerField()
timecourse_count = fields.IntegerField()
class Django:
model = Study
# Ignore auto updating of Elasticsearch when a model is saved/deleted
ignore_signals = True
# Don't perform an index refresh after every update (overrides global setting):
auto_refresh = False
class Index:
name = 'studies'
settings = elastic_settings
class StudyDocument(DocType):
id = fields.StringField(attr='sid')
pk = fields.StringField(attr='sid')
sid = string_field(attr='sid')
pkdb_version = fields.IntegerField(attr='pkdb_version')
descriptions = ObjectField(
properties={
'text': text_field("text"),
'pk': fields.IntegerField()
},
multi=True)
comments = fields.ObjectField(
properties={
'text': text_field("text"),
'user': fields.ObjectField(
properties={
'first_name': string_field("first_name"),
'last_name': string_field("last_name"),
'pk': string_field("last_name"),
'username': string_field("username"),
}
)
},
multi=True)
creator = fields.ObjectField(
properties={
'first_name': string_field("first_name"),
'last_name': string_field("last_name"),
'pk': string_field("pk"),
'username': string_field("username"),
}
)
name = string_field("name")
licence = string_field("licence")
access = string_field("access")
reference = ObjectField(properties={
'sid': fields.IntegerField(attr='sid'),
'pk': fields.IntegerField(attr='pk'),
'name': string_field("name")
})
curators = fields.ObjectField(
attr="ratings",
properties={
'first_name': string_field("user.first_name"),
'last_name': string_field("user.last_name"),
'pk': string_field("user.pk"),
'username': string_field("user.username"),
'rating': fields.FloatField(attr='rating')
},
multi=True
)
collaborators = fields.ObjectField(
attr="collaborators",
properties={
'first_name': string_field("first_name"),
'last_name': string_field("last_name"),
'pk': string_field("pk"),
'username': string_field("username")
},
multi=True
)
substances = string_field(attr="substances_name", multi=True)
keywords = string_field(attr="keywords_name", multi=True)
files = ObjectField(
properties={
'pk': fields.IntegerField(),
'file': fields.StringField(
attr="file.url",
fielddata=True,
analyzer=autocomplete,
search_analyzer=autocomplete_search,
fields={'raw': fields.KeywordField(), }
),
'name': fields.StringField(
fielddata=True,
analyzer=autocomplete,
search_analyzer=autocomplete_search,
fields={'raw': fields.KeywordField(), }
),
'timecourses': ObjectField(
properties={
'pk': fields.IntegerField(multi=True),
}, multi=True)
},
multi=True
)
groupset = common_setfields("groups")
individualset = common_setfields("individuals")
interventionset = common_setfields("interventions", "interventions_normed")
outputset = ObjectField(
properties={
"descriptions": ObjectField(
properties={
'text': text_field("text"),
'pk': fields.IntegerField()
},
multi=True),
# "count_outputs" : fields.FloatField(),
"outputs": ObjectField(
attr="outputs_normed",
properties={
"pk": fields.FloatField(),
}
),
# "count_timecourses": fields.FloatField(),
"timecourses": ObjectField(
attr="timecourses_normed",
properties={
"pk": fields.FloatField(),
}
),
"comments": fields.ObjectField(
properties={
'text': text_field("text"),
'user': fields.ObjectField(
properties={
'first_name': string_field("first_name"),
'last_name': string_field("last_name"),
'pk': string_field("last_name"),
'username': string_field("username"),
}
)
},
multi=True)
}
)
group_count = fields.IntegerField()
individual_count = fields.IntegerField()
intervention_count = fields.IntegerField()
output_count = fields.IntegerField()
output_calculated_count = fields.IntegerField()
timecourse_count = fields.IntegerField()
class Meta(object):
model = Study
related_models = [Substance, Reference, Keyword, Individual, Group, Intervention, Timecourse, Output]
# Ignore auto updating of Elasticsearch when a model is saved
# or deleted:
ignore_signals = True
# Don't perform an index refresh after every update (overrides global setting):
auto_refresh = False
def get_instances_from_related(self, related_instance):
"""If related_models is set, define how to retrieve the instance(s) from the related model.
The related_models option should be used with caution because it can lead in the index
to the updating of a lot of items.
"""
if isinstance(related_instance, Substance):
return related_instance.studies.all()
elif isinstance(related_instance, Reference):
return related_instance.study.all()
elif isinstance(related_instance, Keyword):
return related_instance.studies.all()
elif isinstance(related_instance, Individual):
return related_instance.study