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scigraph_client.py
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scigraph_client.py
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#!/usr/bin/env python3
"""WARNING: DO NOT MODIFY THIS FILE
IT IS AUTOMATICALLY GENERATED BY scigraph.py
AND WILL BE OVERWRITTEN
Swagger Version: 2.0, API Version: 1.0.1
generated for http://localhost:9000/scigraph/swagger.json
by scigraph.py
"""
import re
import copy
import inspect
import builtins
from urllib.parse import parse_qs
import requests
from ast import literal_eval
from json import dumps
from urllib import parse
BASEPATH = 'https://scicrunch.org/api/1/sparc-scigraph'
exten_mapping = {'application/graphml+xml': 'graphml+xml', 'application/graphson': 'graphson', 'application/javascript': 'javascript', 'application/json': 'json', 'application/xgmml': 'xgmml', 'application/xml': 'xml', 'image/jpeg': 'jpeg', 'image/png': 'png', 'text/csv': 'csv', 'text/gml': 'gml', 'text/html': 'html', 'text/plain': 'plain', 'text/plain; charset=utf-8': 'plain; charset=utf-8', 'text/tab-separated-values': 'tab-separated-values'}
class restService:
""" Base class for SciGraph rest services. """
_api_key = None
_hrx = re.compile('^https?://')
def __init__(self, cache=False, safe_cache=False, key=None, do_error=False):
self._session = requests.Session()
adapter = requests.adapters.HTTPAdapter(pool_connections=1000, pool_maxsize=1000)
self._session.mount('http://', adapter)
self._do_error = do_error
if cache:
#print('WARNING: cache enabled, if you mutate the contents of return values you will mutate the cache!')
self._cache = dict()
if safe_cache:
self._get = self._safe_cache_get
else:
self._get = self._cache_get
else:
self._get = self._normal_get
if key is not None:
self.api_key = key
raise DeprecationWarning('this way of passing keys will be deprecated soon')
@property
def api_key(self):
return self._api_key
@api_key.setter
def api_key(self, value):
self._api_key = value
def __del__(self):
self._session.close()
def _safe_url(self, url):
return url.replace(self.api_key, '[secure]') if self.api_key else url
@property
def _last_url(self):
return self._safe_url(self.__last_url)
def _normal_get(self, method, url, params=None, output=None):
s = self._session
if self.api_key is not None:
params['key'] = self.api_key
if method == 'POST':
req = requests.Request(method=method, url=url, data=params)
else:
req = requests.Request(method=method, url=url, params=params)
if output:
req.headers['Accept'] = output
prep = req.prepare()
if self._verbose: print(self._safe_url(prep.url))
try:
resp = s.send(prep)
self.__last_url = resp.url
except requests.exceptions.ConnectionError as e:
host_port = prep.url.split(prep.path_url)[0]
raise ConnectionError(f'Could not connect to {host_port}. '
'Are SciGraph services running?') from e
if resp.status_code == 401:
raise ConnectionError(f'{resp.reason}. '
f'Did you set {self.__class__.__name__}.api_key'
' = my_api_key?')
elif not resp.ok:
if self._do_error:
resp.raise_for_status()
else:
return None
elif resp.headers['content-type'] == 'application/json':
return resp.json()
elif resp.headers['content-type'].startswith('text/plain'):
return resp.text
else:
return resp
def _cache_get(self, method, url, params=None, output=None):
if params:
pkey = '?' + '&'.join(['%s=%s' % (k,v) for k,v in sorted(params.items()) if v is not None])
else:
pkey = ''
key = url + pkey + ' ' + method + ' ' + str(output)
if key in self._cache:
if self._verbose:
print('cache hit', key)
self.__last_url, resp = self._cache[key]
else:
resp = self._normal_get(method, url, params, output)
self._cache[key] = self.__last_url, resp
return resp
def _safe_cache_get(self, *args, **kwargs):
""" If cached values might be used in a context where they
could be mutated, then safe_cache = True should be set
and this wrapper will protect the output """
return copy.deepcopy(self._cache_get(*args, **kwargs)) # prevent mutation of the cache
def _make_rest(self, default=None, **kwargs):
kwargs = {k:v for k, v in kwargs.items() if v}
param_rest = '&'.join(['%s={%s}' % (arg, arg) for arg in kwargs if arg != default])
param_rest = param_rest if param_rest else ''
return param_rest
class Analyzer(restService):
""" Analysis services """
def __init__(self, basePath=None, verbose=False, cache=False, safe_cache=False, key=None, do_error=False):
if basePath is None:
basePath = BASEPATH
self._basePath = basePath
self._verbose = verbose
super().__init__(cache=cache, safe_cache=safe_cache, key=key, do_error=do_error)
def enrich(self, sample, ontologyClass, path, callback=None, output='application/json'):
""" Class Enrichment Service from: /analyzer/enrichment
Arguments:
sample: A list of CURIEs for nodes whose attributes are to be tested for
enrichment. For example, a list of genes.
ontologyClass: CURIE for parent ontology class for the attribute to be tested.
For example, GO biological process
path: A path expression that connects sample nodes to attribute class nodes
callback: Name of the JSONP callback ('fn' by default). Supplying this
parameter or requesting a javascript media type will cause a
JSONP response to be rendered.
outputs:
application/json
"""
kwargs = {'sample': sample, 'ontologyClass': ontologyClass, 'path': path, 'callback': callback}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/analyzer/enrichment').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else None
def enrichPost(self, output='application/json'):
""" from: /analyzer/enrichment
Arguments:
outputs:
application/json
"""
kwargs = {}
# type caste not needed
url = self._basePath + ('/analyzer/enrichment').format(**kwargs)
requests_params = kwargs
output = self._get('POST', url, requests_params, output)
return output if output else []
class Annotations(restService):
""" Annotation services """
def __init__(self, basePath=None, verbose=False, cache=False, safe_cache=False, key=None, do_error=False):
if basePath is None:
basePath = BASEPATH
self._basePath = basePath
self._verbose = verbose
super().__init__(cache=cache, safe_cache=safe_cache, key=key, do_error=do_error)
def annotate(self, content, includeCat=None, excludeCat=None, minLength=None, longestOnly=None, includeAbbrev=None, includeAcronym=None, includeNumbers=None, output='text/plain; charset=utf-8'):
""" Annotate text from: /annotations
Arguments:
content: The content to annotate
includeCat: A set of categories to include
excludeCat: A set of categories to exclude
minLength: The minimum number of characters in annotated entities
longestOnly: Should only the longest entity be returned for an overlapping group
includeAbbrev: Should abbreviations be included
includeAcronym: Should acronyms be included
includeNumbers: Should numbers be included
outputs:
text/plain; charset=utf-8
"""
kwargs = {'content': content, 'includeCat': includeCat, 'excludeCat': excludeCat, 'minLength': minLength, 'longestOnly': longestOnly, 'includeAbbrev': includeAbbrev, 'includeAcronym': includeAcronym, 'includeNumbers': includeNumbers}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/annotations').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else None
def annotatePost(self, content, includeCat=None, excludeCat=None, minLength=None, longestOnly=None, includeAbbrev=None, includeAcronym=None, includeNumbers=None, ignoreTag=None, stylesheet=None, scripts=None, targetId=None, targetClass=None, output='application/json'):
""" Annotate text from: /annotations
Arguments:
content: The content to annotate
includeCat: A set of categories to include
excludeCat: A set of categories to exclude
minLength: The minimum number of characters in annotated entities
longestOnly: Should only the longest entity be returned for an overlapping group
includeAbbrev: Should abbreviations be included
includeAcronym: Should acronyms be included
includeNumbers: Should numbers be included
ignoreTag: HTML tags that should not be annotated
stylesheet: CSS stylesheets to add to the HEAD
scripts: JavaScripts that should to add to the HEAD
targetId: A set of element IDs to annotate
targetClass: A set of CSS class names to annotate
outputs:
application/json
"""
kwargs = {'content': content, 'includeCat': includeCat, 'excludeCat': excludeCat, 'minLength': minLength, 'longestOnly': longestOnly, 'includeAbbrev': includeAbbrev, 'includeAcronym': includeAcronym, 'includeNumbers': includeNumbers, 'ignoreTag': ignoreTag, 'stylesheet': stylesheet, 'scripts': scripts, 'targetId': targetId, 'targetClass': targetClass}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/annotations').format(**kwargs)
requests_params = kwargs
output = self._get('POST', url, requests_params, output)
return output if output else None
def getEntitiesAndContent(self, content, includeCat=None, excludeCat=None, minLength=None, longestOnly=None, includeAbbrev=None, includeAcronym=None, includeNumbers=None, output='application/json'):
""" Get embedded annotations as well as a separate list from: /annotations/complete
Arguments:
content: The content to annotate
includeCat: A set of categories to include
excludeCat: A set of categories to exclude
minLength: The minimum number of characters in annotated entities
longestOnly: Should only the longest entity be returned for an overlapping group
includeAbbrev: Should abbreviations be included
includeAcronym: Should acronyms be included
includeNumbers: Should numbers be included
outputs:
application/json
"""
kwargs = {'content': content, 'includeCat': includeCat, 'excludeCat': excludeCat, 'minLength': minLength, 'longestOnly': longestOnly, 'includeAbbrev': includeAbbrev, 'includeAcronym': includeAcronym, 'includeNumbers': includeNumbers}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/annotations/complete').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else []
def postEntitiesAndContent(self, content, includeCat=None, excludeCat=None, minLength=None, longestOnly=None, includeAbbrev=None, includeAcronym=None, includeNumbers=None, output='application/json'):
""" Get embedded annotations as well as a separate list from: /annotations/complete
Arguments:
content: The content to annotate
includeCat: A set of categories to include
excludeCat: A set of categories to exclude
minLength: The minimum number of characters in annotated entities
longestOnly: Should only the longest entity be returned for an overlapping group
includeAbbrev: Should abbreviations be included
includeAcronym: Should acronyms be included
includeNumbers: Should numbers be included
outputs:
application/json
"""
kwargs = {'content': content, 'includeCat': includeCat, 'excludeCat': excludeCat, 'minLength': minLength, 'longestOnly': longestOnly, 'includeAbbrev': includeAbbrev, 'includeAcronym': includeAcronym, 'includeNumbers': includeNumbers}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/annotations/complete').format(**kwargs)
requests_params = kwargs
output = self._get('POST', url, requests_params, output)
return output if output else []
def getEntities(self, content, includeCat=None, excludeCat=None, minLength=None, longestOnly=None, includeAbbrev=None, includeAcronym=None, includeNumbers=None, output='application/json'):
""" Get entities from text from: /annotations/entities
Arguments:
content: The content to annotate
includeCat: A set of categories to include
excludeCat: A set of categories to exclude
minLength: The minimum number of characters in annotated entities
longestOnly: Should only the longest entity be returned for an overlapping group
includeAbbrev: Should abbreviations be included
includeAcronym: Should acronyms be included
includeNumbers: Should numbers be included
outputs:
application/json
"""
kwargs = {'content': content, 'includeCat': includeCat, 'excludeCat': excludeCat, 'minLength': minLength, 'longestOnly': longestOnly, 'includeAbbrev': includeAbbrev, 'includeAcronym': includeAcronym, 'includeNumbers': includeNumbers}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/annotations/entities').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else []
def postEntities(self, content, includeCat=None, excludeCat=None, minLength=None, longestOnly=None, includeAbbrev=None, includeAcronym=None, includeNumbers=None, output='application/json'):
""" Get entities from text from: /annotations/entities
Arguments:
content: The content to annotate
includeCat: A set of categories to include
excludeCat: A set of categories to exclude
minLength: The minimum number of characters in annotated entities
longestOnly: Should only the longest entity be returned for an overlapping group
includeAbbrev: Should abbreviations be included
includeAcronym: Should acronyms be included
includeNumbers: Should numbers be included
outputs:
application/json
"""
kwargs = {'content': content, 'includeCat': includeCat, 'excludeCat': excludeCat, 'minLength': minLength, 'longestOnly': longestOnly, 'includeAbbrev': includeAbbrev, 'includeAcronym': includeAcronym, 'includeNumbers': includeNumbers}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/annotations/entities').format(**kwargs)
requests_params = kwargs
output = self._get('POST', url, requests_params, output)
return output if output else []
def annotateUrl(self, url, includeCat=None, excludeCat=None, minLength=None, longestOnly=None, includeAbbrev=None, includeAcronym=None, includeNumbers=None, ignoreTag=None, stylesheet=None, scripts=None, targetId=None, targetClass=None, output='text/html'):
""" Annotate a URL from: /annotations/url
Arguments:
url:
includeCat: A set of categories to include
excludeCat: A set of categories to exclude
minLength: The minimum number of characters in annotated entities
longestOnly: Should only the longest entity be returned for an overlapping group
includeAbbrev: Should abbreviations be included
includeAcronym: Should acronyms be included
includeNumbers: Should numbers be included
ignoreTag: HTML tags that should not be annotated
stylesheet: CSS stylesheets to add to the HEAD
scripts: JavaScripts that should to add to the HEAD
targetId: A set of element IDs to annotate
targetClass: A set of CSS class names to annotate
outputs:
text/html
"""
kwargs = {'url': url, 'includeCat': includeCat, 'excludeCat': excludeCat, 'minLength': minLength, 'longestOnly': longestOnly, 'includeAbbrev': includeAbbrev, 'includeAcronym': includeAcronym, 'includeNumbers': includeNumbers, 'ignoreTag': ignoreTag, 'stylesheet': stylesheet, 'scripts': scripts, 'targetId': targetId, 'targetClass': targetClass}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/annotations/url').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else None
class CypherBase(restService):
""" Cypher utility services """
def __init__(self, basePath=None, verbose=False, cache=False, safe_cache=False, key=None, do_error=False):
if basePath is None:
basePath = BASEPATH
self._basePath = basePath
self._verbose = verbose
super().__init__(cache=cache, safe_cache=safe_cache, key=key, do_error=do_error)
def getCuries(self, callback=None, output='application/json'):
""" Get the curie map from: /cypher/curies
Arguments:
callback: Name of the JSONP callback ('fn' by default). Supplying this
parameter or requesting a javascript media type will cause a
JSONP response to be rendered.
outputs:
application/json
"""
kwargs = {'callback': callback}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/cypher/curies').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else {}
def execute(self, cypherQuery, limit, output='text/plain', **kwargs):
""" Execute an arbitrary Cypher query. from: /cypher/execute
Arguments:
cypherQuery: The cypher query to execute
limit: Limit
outputs:
text/plain
application/json
"""
kwargs = {'cypherQuery': cypherQuery, 'limit': limit, **kwargs}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + (f'{"/cypher/execute.json" if output == "application/json" else "/cypher/execute"}').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else None
def resolve(self, cypherQuery, output='text/plain', **kwargs):
""" Cypher query resolver from: /cypher/resolve
Arguments:
cypherQuery: The cypher query to resolve
outputs:
text/plain
"""
kwargs = {'cypherQuery': cypherQuery, **kwargs}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/cypher/resolve').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else None
class Cypher(CypherBase):
@staticmethod
def fix_quotes(string, s1=':["', s2='"],'):
out = []
def subsplit(sstr, s=s2):
#print(s)
if s == '",' and sstr.endswith('"}'): # special case for end of record
s = '"}'
if s:
string, *rest = sstr.rsplit(s, 1)
else:
string = sstr
rest = '',
if rest:
#print('>>>>', string)
#print('>>>>', rest)
r, = rest
if s == '"],':
fixed_string = Cypher.fix_quotes(string, '","', '') + s + r
else:
fixed_string = string.replace('"', r'\"') + s + r
return fixed_string
for sub1 in string.split(s1):
ss = subsplit(sub1)
if ss is None:
if s1 == ':["':
out.append(Cypher.fix_quotes(sub1, ':"', '",'))
else:
out.append(sub1)
else:
out.append(ss)
return s1.join(out)
def fix_cypher(self, record):
rep = re.sub(r'({|, )(\S+)(: "|: \[)', r'\1"\2"\3',
self.fix_quotes(record.strip()).
split(']', 1)[1] .
replace(':"', ': "') .
replace(':[', ': [') .
replace('",', '", ') .
replace('"],', '"], ') .
replace('\n', '\\n') .
replace('xml:lang="en"', r'xml:lang=\"en\"')
)
try:
value = {self.qname(k):v for k, v in literal_eval(rep).items()}
except (ValueError, SyntaxError) as e:
print(repr(record))
print(repr(rep))
raise e
return value
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._setCuries()
def _setCuries(self):
try:
self._curies = self.getCuries()
except ConnectionError:
self._curies = {}
self._inv = {v:k for k, v in self._curies.items()}
@property
def api_key(self):
# note that using properties means that
# if you want to use properties at all in
# a subClass hierarchy you have to reimplement
# them every single time to be aware if the
# parent class value chanes
if isinstance(restService.api_key, str):
return restService.api_key
else:
return self._api_key
@api_key.setter
def api_key(self, value):
old_key = self.api_key
self._api_key = value
if old_key is None and value is not None:
self._setCuries()
def qname(self, iri):
for prefix, curie in self._inv.items():
if iri.startswith(prefix):
return iri.replace(prefix, curie + ':')
else:
return iri
def execute(self, query, limit, output='text/plain', **kwargs):
if output == 'text/plain':
out = super().execute(query, limit, output, **kwargs)
rows = []
if out:
for raw in out.split('|')[3:-1]:
record = raw.strip()
if record:
d = self.fix_cypher(record)
rows.append(d)
return rows
else:
return super().execute(query, limit, output, **kwargs)
class DynamicBase(restService):
""" Dynamic Cypher resources """
def __init__(self, basePath=None, verbose=False, cache=False, safe_cache=False, key=None, do_error=False):
if basePath is None:
basePath = BASEPATH
self._basePath = basePath
self._verbose = verbose
super().__init__(cache=cache, safe_cache=safe_cache, key=key, do_error=do_error)
def demos_apinat_bundles_start_id(self, start_id, output='application/json'):
""" Return the paths to somas from an anatomical region (aka connected-somas) from: /dynamic/demos/apinat/bundles/{start-id}
Arguments:
start_id: ontology id of the starting point
Query:
MATCH path1 = (start:Class{iri: "${start-id}"})
-[:apinatomy:annotates]->(start_housing)
-[:apinatomy:subtypes*0..1]->()
-[:apinatomy:clones*0..1]->(layer_or_end)
-[:apinatomy:layers*0..1]->()
-[:apinatomy:bundles]->(linkStart)
-[:apinatomy:prevChainEndLevels|apinatomy:prev|apinatomy:source*1..]->(link)
-[:apinatomy:targetOf|apinatomy:sourceOf]->(linkSoma) // axon or dendrite root
-[:apinatomy:conveyingLyph]->()
-[:apinatomy:supertype*0..1]->(soma:NamedIndividual)
-[:apinatomy:ontologyTerms]->(c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
WITH path1, link
OPTIONAL MATCH path2 = (link)
-[:apinatomy:fasciculatesIn|apinatomy:endsIn]->(layer_or_end)
-[:apinatomy:layerIn*0..1]->(end)
-[:apinatomy:ontologyTerms]->(external)
RETURN path1, path2
outputs:
application/json
application/graphson
application/xml
application/graphml+xml
application/xgmml
text/gml
text/csv
text/tab-separated-values
image/jpeg
image/png
"""
kwargs = {'start_id': start_id}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/dynamic/demos/apinat/bundles/{start_id}').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else None
def demos_apinat_housing_lyphs(self, output='application/json'):
""" List all the housing lyphs (neuronal processes) for all starting points. from: /dynamic/demos/apinat/housing-lyphs
Arguments:
Query:
MATCH path = (c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
-[:apinatomy:annotates]->(soma:NamedIndividual) // soma lyph
-[:apinatomy:conveys]->(somaLink) // link connecting soma to axon and dendrite
-[:apinatomy:target|apinatomy:source]->(root) // axon or dendrite root
-[:apinatomy:controlNodes|apinatomy:rootOf*1..2]->(chain) // axon or dendrite tree
-[:apinatomy:housingLyphs]->(housing) // list of lyphs housing the trees
-[:apinatomy:ontologyTerms*0..1]->(external) // external ids for the housing lyphs
WHERE soma.`https://apinatomy.org/uris/readable/generated` IS NULL
RETURN path
outputs:
application/json
application/graphson
application/xml
application/graphml+xml
application/xgmml
text/gml
text/csv
text/tab-separated-values
image/jpeg
image/png
"""
kwargs = {}
# type caste not needed
url = self._basePath + ('/dynamic/demos/apinat/housing-lyphs').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else None
def demos_apinat_housing_lyphs_start_id(self, start_id, output='application/json'):
""" List all the housing lyphs for a starting point. from: /dynamic/demos/apinat/housing-lyphs/{start-id}
Arguments:
start_id: ontology id of the starting point
Query:
MATCH path1 = (c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
-[:apinatomy:annotates]->(soma:NamedIndividual) // soma lyph
-[:apinatomy:conveys]->(somaLink) // link connecting soma to axon and dendrite
-[:apinatomy:target|apinatomy:source]->(root) // axon or dendrite root
-[:apinatomy:internalIn]->(layer_or_end)
-[:apinatomy:cloneOf*0..1]->()
-[:apinatomy:supertype*0..1]->()
-[:apinatomy:ontologyTerms]->(layer_or_end_external:Class{iri: '${start-id}'})
WHERE soma.`https://apinatomy.org/uris/readable/generated` IS NULL
WITH path1, root
MATCH path2 = (root)
-[:apinatomy:controlNodes|apinatomy:rootOf*1..2]->(chain) // axon or dendrite tree
-[:apinatomy:housingLyphs]->(housing) // list of lyphs housing the trees
-[:apinatomy:ontologyTerms*0..1]->(external) // external ids for the housing lyphs
RETURN path1, path2
UNION
MATCH path1 = (c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
-[:apinatomy:annotates]->(soma:NamedIndividual) // soma lyph
-[:apinatomy:conveys]->(somaLink) // link connecting soma to axon and dendrite
-[:apinatomy:target|apinatomy:source]->(root) // axon or dendrite root
-[:apinatomy:internalIn]->(layer)
-[:apinatomy:cloneOf*0..1]->()
-[:apinatomy:supertype*0..1]->()
-[:apinatomy:layerIn]->(end_housing)
-[:apinatomy:ontologyTerms]->(end_housing_external:Class{iri: '${start-id}'})
WHERE soma.`https://apinatomy.org/uris/readable/generated` IS NULL
WITH path1, root
MATCH path2 = (root)
-[:apinatomy:rootOf]->(chain) // axon or dendrite tree
-[:apinatomy:housingLyphs]->(housing) // list of lyphs housing the trees
-[:apinatomy:ontologyTerms*0..1]->(external) // external ids for the housing lyphs
RETURN path1, path2
outputs:
application/json
application/graphson
application/xml
application/graphml+xml
application/xgmml
text/gml
text/csv
text/tab-separated-values
image/jpeg
image/png
"""
kwargs = {'start_id': start_id}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/dynamic/demos/apinat/housing-lyphs/{start_id}').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else None
def demos_apinat_modelList(self, output='application/json'):
""" Return the list of all ApiNATOMY models in the database. from: /dynamic/demos/apinat/modelList
Arguments:
Query:
MATCH ({iri: "https://apinatomy.org/uris/elements/Graph"})
<-[:type]-(g)-[:isDefinedBy]->(o:Ontology)
RETURN o
outputs:
application/json
application/graphson
application/xml
application/graphml+xml
application/xgmml
text/gml
text/csv
text/tab-separated-values
image/jpeg
image/png
"""
kwargs = {}
# type caste not needed
url = self._basePath + ('/dynamic/demos/apinat/modelList').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else None
def demos_apinat_modelPopulationsReferences_model_id(self, model_id, output='application/json'):
""" Given an ApiNATOMY model id return the identifiers for the neuronpopulations that are present in the model and the identifiers forreferences that provide supporting evidence. Publications andpopulations can be distingished by checking whether their meta typefield is NamedIndividual or Class. from: /dynamic/demos/apinat/modelPopulationsReferences/{model_id}
Arguments:
model_id: the identifier for an ApiNATOMY model
Query:
MATCH (start:Ontology {iri: $model_id})
<-[:isDefinedBy]-(external:Class)
-[:subClassOf*]->(:Class {iri: "http://uri.interlex.org/tgbugs/uris/readable/NeuronEBM"}) // FIXME
,
(external)
-[e:type]->()
RETURN e
UNION
OPTIONAL MATCH (start:Ontology {iri: $model_id})
<-[:isDefinedBy]-(graph:NamedIndividual)
-[:type]->({iri: "https://apinatomy.org/uris/elements/Graph"}) // elements don't have a superclass right now
,
(graph)
-[:apinatomy:references]->(pub)
-[e:type]->(:Class{iri: "https://apinatomy.org/uris/elements/Reference"})
RETURN e
outputs:
application/json
application/graphson
application/xml
application/graphml+xml
application/xgmml
text/gml
text/csv
text/tab-separated-values
image/jpeg
image/png
"""
kwargs = {'model_id': model_id}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/dynamic/demos/apinat/modelPopulationsReferences/{model_id}').format(**kwargs)
requests_params = {k:v for k, v in kwargs.items() if k != 'model_id'}
output = self._get('GET', url, requests_params, output)
return output if output else None
def demos_apinat_neru_1_neupop_id(self, neupop_id, output='application/json'):
""" Return the housing regions and publications for neurulated groups. from: /dynamic/demos/apinat/neru-1/{neupop-id}
Arguments:
neupop_id: neuron population identifier
Query:
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
// publications
WITH neugrp, a
OPTIONAL MATCH path = (neugrp)
-[:apinatomy:references]->(pub)
-[:type]->(:Class{iri: "https://apinatomy.org/uris/elements/Publication"}) // cannot be curied, dynamic endpoints will not expand it
WITH neugrp, a, path
MATCH (neugrp)
-[b:apinatomy:links]->(link)
-[c:apinatomy:fasciculatesIn|apinatomy:endsIn*0..1]->(lyph_or_layer) // real lyphs convey things, layers do not
-[d:apinatomy:layerIn*0..1]->(lyph)
-[:apinatomy:conveys*0..1]->() // make sure we are at a real lyph
WITH lyph, a, b, c, d, path
MATCH (lyph)
-[e:apinatomy:ontologyTerms]->(region)
RETURN a, b, c, d, e, path
UNION
// this part usually only returns the soma housing lyph
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
-[b:apinatomy:lyphs]->(lyph)
-[c:apinatomy:internalIn]->(e) // e is a hack to get columns to match
-[d:apinatomy:ontologyTerms*0..1]->(region)
// this variant shows the dead end lyphs that correspond to the fasciculatesIn links above
//-[c:apinatomy:internalIn*0..1]->(e)
//-[d:apinatomy:ontologyTerms*0..1]->(region)
return a, b, c, d, null AS e, null AS path
outputs:
application/json
application/graphson
application/xml
application/graphml+xml
application/xgmml
text/gml
text/csv
text/tab-separated-values
image/jpeg
image/png
"""
kwargs = {'neupop_id': neupop_id}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/dynamic/demos/apinat/neru-1/{neupop_id}').format(**kwargs)
requests_params = kwargs
output = self._get('GET', url, requests_params, output)
return output if output else None
def demos_apinat_neru_2_neupop_id(self, neupop_id, output='application/json'):
""" Return the housing regions and publications for neurulated groups. from: /dynamic/demos/apinat/neru-2/{neupop_id}
Arguments:
neupop_id: neuron population identifier
Query:
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
// publications
WITH neugrp, a
OPTIONAL MATCH path = (neugrp)
-[:apinatomy:references]->(pub)
-[:type]->(:Class{iri: "https://apinatomy.org/uris/elements/Publication"}) // cannot be curied, dynamic endpoints will not expand it
WITH neugrp, a, path
MATCH (neugrp)
-[b:apinatomy:links]->(link)
-[c:apinatomy:fasciculatesIn|apinatomy:endsIn*0..1]->(lyph_or_layer) // real lyphs convey things, layers do not
-[d:apinatomy:layerIn*0..1]->(lyph)
-[:apinatomy:conveys*0..1]->() // make sure we are at a real lyph
WITH neugrp, link, lyph, a, b, c, d, path
MATCH (lyph)
-[e:apinatomy:ontologyTerms]->(region)
// use apinatomy:next to extract ordering information
WITH neugrp, link, a, b, c, d, e, path
MATCH (link)
-[f:apinatomy:next*0..]->()
//-[f:apinatomy:next|apinatomy:nextChainStartLevels*0..]->()
// FIXME these should be collapsing into a single relationship
-[g:apinatomy:target*0..1]->()
-[h:apinatomy:rootOf*0..1]->()
-[i:apinatomy:levels*0..1]->()
<-[:apinatomy:links]-(neugrp)
RETURN a, b, c, d, e, f, g,h,i, path
UNION
// this part usually only returns the soma housing lyph
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
-[b:apinatomy:lyphs]->(lyph)
-[c:apinatomy:internalIn]->(e) // e is a hack to get columns to match
-[d:apinatomy:ontologyTerms*0..1]->(region)
// this variant shows the dead end lyphs that correspond to the fasciculatesIn links above
//-[c:apinatomy:internalIn*0..1]->(e)
//-[d:apinatomy:ontologyTerms*0..1]->(region)
RETURN a, b, c, d, null AS e, null AS f, null AS g, null AS h, null AS i, null AS path
outputs:
application/json
application/graphson
application/xml
application/graphml+xml
application/xgmml
text/gml
text/csv
text/tab-separated-values
image/jpeg
image/png
"""
kwargs = {'neupop_id': neupop_id}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/dynamic/demos/apinat/neru-2/{neupop_id}').format(**kwargs)
requests_params = {k:v for k, v in kwargs.items() if k != 'neupop_id'}
output = self._get('GET', url, requests_params, output)
return output if output else None
def demos_apinat_neru_3_neupop_id(self, neupop_id, output='application/json'):
""" Return the housing regions and publications for neurulated groups. from: /dynamic/demos/apinat/neru-3/{neupop_id}
Arguments:
neupop_id: neuron population identifier
Query:
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
// publications
WITH neugrp, a
OPTIONAL MATCH path = (neugrp)
-[:apinatomy:references]->(pub)
-[:type]->(:Class{iri: "https://apinatomy.org/uris/elements/Publication"}) // cannot be curied, dynamic endpoints will not expand it
WITH neugrp, a, path
MATCH (neugrp)
-[b:apinatomy:links]->(link)
-[c:apinatomy:fasciculatesIn|apinatomy:endsIn*0..1]->(lyph_or_layer) // real lyphs convey things, layers do not
-[d:apinatomy:layerIn*0..1]->(lyph)
-[:apinatomy:conveys*0..1]->() // make sure we are at a real lyph
WITH neugrp, link, lyph, a, b, c, d, path // MATCH vs , not all things that match as lyphs have externals
MATCH (lyph)
-[e:apinatomy:ontologyTerms]->(region)
// use apinatomy:next to extract ordering information
WITH neugrp, link, a, b, c, d, e, path
MATCH p2 = (link)
-[:apinatomy:conveyingLyph]->(cl)
-[:apinatomy:topology]->()
WITH neugrp, link, a, b, c, d, e, path, p2, cl
MATCH (cl)
-[x:apinatomy:inheritedOntologyTerms*0..1]->()
WITH neugrp, link, a, b, c, d, e, path, p2, x
MATCH (link)
-[f:apinatomy:next*0..]->()
//-[f:apinatomy:next|apinatomy:nextChainStartLevels*0..]->()
// FIXME these should be collapsing into a single relationship
-[g:apinatomy:target*0..1]->()
-[h:apinatomy:rootOf*0..1]->()
-[i:apinatomy:levels*0..1]->()
<-[:apinatomy:links]-(neugrp)
RETURN a, b, c, d, e, f, g,h,i, path, p2, x
UNION
// this part usually only returns the soma housing lyph
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
-[b:apinatomy:lyphs]->(lyph)
-[c:apinatomy:internalIn]->()
-[d:apinatomy:ontologyTerms*0..1]->(region)
// this variant shows the dead end lyphs that correspond to the fasciculatesIn links above
//-[c:apinatomy:internalIn*0..1]->()
//-[d:apinatomy:ontologyTerms*0..1]->(region)
RETURN a, b, c, d, null AS e, null AS f, null AS g, null AS h, null AS i, null AS path, null as p2, null as x
outputs:
application/json
application/graphson
application/xml
application/graphml+xml
application/xgmml
text/gml
text/csv
text/tab-separated-values
image/jpeg
image/png
"""
kwargs = {'neupop_id': neupop_id}
kwargs = {k:dumps(v) if builtins.type(v) is dict else v for k, v in kwargs.items()}
url = self._basePath + ('/dynamic/demos/apinat/neru-3/{neupop_id}').format(**kwargs)
requests_params = {k:v for k, v in kwargs.items() if k != 'neupop_id'}
output = self._get('GET', url, requests_params, output)
return output if output else None
def demos_apinat_neru_4_neupop_id(self, neupop_id, output='application/json'):
""" Return the housing regions and publications for neurulated groups. from: /dynamic/demos/apinat/neru-4/{neupop_id}
Arguments:
neupop_id: neuron population identifier
Query:
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
, (neugrp)
-[:apinatomy:links]->(link)
-[c:apinatomy:fasciculatesIn|apinatomy:endsIn*0..1]->(lyph_or_layer) // real lyphs convey things, layers do not
-[d:apinatomy:layerIn*0..1]->(lyph)
-[:apinatomy:conveys*0..1]->() // make sure we are at a real lyph