Source code for civic

import requests
from requests.packages.urllib3.util.retry import Retry
import importlib
import logging
import pandas as pd
import pickle
import os
from pathlib import Path
from collections import defaultdict, namedtuple
from civicpy import REMOTE_CACHE_URL, LOCAL_CACHE_PATH, CACHE_TIMEOUT_DAYS
import requests
from civicpy import exports
import deprecation
from civicpy.__version__ import __version__
from datetime import datetime, timedelta
from backports.datetime_fromisoformat import MonkeyPatch
MonkeyPatch.patch_fromisoformat()
import re


CACHE = dict()

COORDINATE_TABLE = None
COORDINATE_TABLE_START = None
COORDINATE_TABLE_STOP = None
COORDINATE_TABLE_CHR = None

HPO_TERMS = dict()

FRESH_DELTA = timedelta(days=CACHE_TIMEOUT_DAYS)

MODULE = importlib.import_module('civicpy.civic')

API_URL = 'https://civicdb.org/api/graphql'

LINKS_URL = 'https://civicdb.org/links'

UNMARKED_PLURALS = {'evidence'}

CIVIC_TO_PYCLASS = {
    'evidence_items': 'evidence'
}


_CoordinateQuery = namedtuple('CoordinateQuery', ['chr', 'start', 'stop', 'alt', 'ref', 'build', 'key'])
_CoordinateQuery.__new__.__defaults__ = (None, None, "GRCh37", None)


[docs]class CoordinateQuery(_CoordinateQuery): # Wrapping for documentation """ A namedtuple with preset fields describing a genomic coordinate, for use with coordinate-based queries of CIViC Variants. :param str chr: A chromosome of value 1-23, X, Y :param int start: The chromosomal start position in base coordinates (1-based) :param int stop: The chromosomal stop position in base coordinates (1-based) :param str optional alt: The alternate nucleotide(s) at the designated coordinates :param str optional ref: The reference nucleotide(s) at the designated coordinates :param NCBI36,GRCh37,GRCh38 build: The reference build version of the coordinates :param Any optional key: A user-defined object linked to the coordinate """ pass
def pluralize(string): if string in UNMARKED_PLURALS: return '{}_items'.format(string) if string.endswith('s'): return string return string + 's' def singularize(string): string = string.rstrip('s') if string == 'evidence_item': string = 'evidence' return string def search_url(element, use_search_meta): element = pluralize(element).lower() components = [API_URL, element] if use_search_meta: components.append('search') return '/'.join(components) def snake_to_camel(snake_string): words = snake_string.split('_') cap_words = [x.capitalize() for x in words] return ''.join(cap_words) def element_lookup_by_id(element_type, element_id): e = _request_by_ids(element_type, [int(element_id)])[0] e = _postprocess_response_element(e, element_type) return e def get_class(element_type): e_string = singularize(element_type) class_string = snake_to_camel(e_string) cls = getattr(MODULE, class_string, CivicAttribute) return cls def download_remote_cache(remote_cache_url=REMOTE_CACHE_URL, local_cache_path=LOCAL_CACHE_PATH): """ Retrieve a remote cache file from URL and save to local filepath. :param remote_cache_url: A URL string to a remote cache for retrieval. This parameter defaults to REMOTE_CACHE_URL. :param local_cache_path: A filepath destination string for the retrieved remote cache. This parameter defaults to LOCAL_CACHE_PATH. :return: Returns True on success. """ logging.warning( 'Downloading remote cache from {}.'.format(remote_cache_url) ) _make_local_cache_path_if_missing(local_cache_path) r = requests.get(remote_cache_url) r.raise_for_status() with open(local_cache_path, 'wb') as local_cache: local_cache.write(r.content) return True def save_cache(local_cache_path=LOCAL_CACHE_PATH): """ Save in-memory cache to local file. :param local_cache_path: A filepath destination string for storing the cache. This parameter defaults to LOCAL_CACHE_PATH. :return: Returns True on success. """ with open(local_cache_path, 'wb') as pf: pickle.dump(CACHE, pf) return True def cache_file_present(local_cache_path=LOCAL_CACHE_PATH): """ Determines if a file exists at a given path. :param local_cache_path: A filepath where cache is expected. This parameter defaults to LOCAL_CACHE_PATH. :return: Returns True on success. """ return os.path.isfile(local_cache_path) def delete_local_cache(local_cache_path=LOCAL_CACHE_PATH): """ Deletes local cache file. :param local_cache_path: A filepath destination string for the cache to be deleted. This parameter defaults to LOCAL_CACHE_PATH. :return: Returns True on success. """ return os.unlink(local_cache_path) def load_cache(local_cache_path=LOCAL_CACHE_PATH, on_stale='auto'): """ Load local file to in-memory cache. :param local_cache_path: A filepath destination string for loading the cache. This parameter defaults to LOCAL_CACHE_PATH. :param on_stale: ['auto', 'reject', 'ignore', 'update'] auto: If cache_path matches the filepath in LOCAL_CACHE_PATH, follows 'update' behavior. Otherwise, follows 'reject' behavior. reject: Clear loaded cache from memory if stale. ignore: Keep loaded cache in memory if stale. update: Run update_cache and save fresh cache to cache_path. This parameter defaults to 'auto'. :return: Returns True if content is loaded to in-memory cache. """ downloaded_remote = False remote_url = REMOTE_CACHE_URL if local_cache_path == LOCAL_CACHE_PATH: if not cache_file_present(): download_remote_cache(remote_cache_url=remote_url) downloaded_remote = True elif not cache_file_present(local_cache_path): raise FileNotFoundError("No cache found at {}".format(local_cache_path)) with open(local_cache_path, 'rb') as pf: loaded_cache = pickle.load(pf) c = dict() variants = set() for k, v in loaded_cache.items(): if isinstance(k, str): c[k] = v elif isinstance(k, int): c[hash(v)] = v if v.type == 'variant': variants.add(v) else: raise ValueError old_cache = MODULE.CACHE MODULE.CACHE = c for k, v in MODULE.CACHE.items(): if isinstance(k, str): continue v.update() if _has_full_cached_fresh() or on_stale == 'ignore': _build_coordinate_table(variants) return True elif (on_stale == 'auto' and local_cache_path == LOCAL_CACHE_PATH) or on_stale == 'update': MODULE.CACHE = old_cache if downloaded_remote: logging.error( 'Remote cache at {} is stale. Consider running `update_cache(from_remote_cache=False)` ' "to create cache from API query (slow), or `load_cache(on_stale='ignore')` " "to load stale local cache (if present). " 'Please create an issue at https://github.com/griffithlab/civicpy/issues ' 'if this is unexpected behavior.'.format(remote_url) ) raise SystemError else: logging.warning( 'Local cache at {} is stale, updating from remote.'.format(local_cache_path) ) update_cache(local_cache_path=local_cache_path) return True elif on_stale == 'reject' or on_stale == 'auto': MODULE.CACHE = old_cache logging.warning( 'Local cache at {} is stale and was not loaded. To load anyway, re-run ' '`load_cache` with `on_stale` parameter set to desired behavior.'.format(local_cache_path) ) return False raise NotImplementedError # An unexpected condition occurred. def update_cache(from_remote_cache=True, remote_cache_url=REMOTE_CACHE_URL, local_cache_path=LOCAL_CACHE_PATH): """ Update local cache file. :param from_remote_cache: If set to True, update_cache will first download the remote cache designated by REMOTE_CACHE_URL, store it to LOCAL_CACHE_PATH, and then load the downloaded cache into memory. This parameter defaults to True. :param remote_cache_url: A URL string to a remote cache for retrieval. This parameter defaults to REMOTE_CACHE_URL. :param local_cache_path: A filepath destination string for the retrieved remote cache. This parameter defaults to LOCAL_CACHE_PATH. :return: Returns True on success. """ _make_local_cache_path_if_missing(local_cache_path) if from_remote_cache: download_remote_cache(local_cache_path=local_cache_path, remote_cache_url=remote_cache_url) load_cache(local_cache_path=local_cache_path) else: molecular_profiles = _get_elements_by_ids('molecular_profile', allow_cached=False, get_all=True) genes = _get_elements_by_ids('gene', allow_cached=False, get_all=True) variants = _get_elements_by_ids('variant', allow_cached=False, get_all=True) evidence = _get_elements_by_ids('evidence', allow_cached=False, get_all=True) assertions = _get_elements_by_ids('assertion', allow_cached=False, get_all=True) variant_groups = _get_elements_by_ids('variant_group', allow_cached=False, get_all=True) for e in evidence: e.assertions = [a for a in assertions if a.id in e.assertion_ids] e._partial = False CACHE[hash(e)] = e for g in genes: g.variants = [v for v in variants if v.gene_id == g.id] g._partial = False CACHE[hash(g)] = g for v in variants: v.variant_groups = [vg for vg in variant_groups if v.id in vg.variant_ids] v.molecular_profiles = [mp for mp in molecular_profiles if v.id in mp.variant_ids] v._partial = False CACHE[hash(v)] = v for a in assertions: a.evidence_items = [e for e in evidence if e.id in a.evidence_ids] CACHE[hash(a)] = a for vg in variant_groups: vg.variants = [v for v in variants if v.id in vg.variant_ids] vg._partial = False CACHE[hash(vg)] = vg for mp in molecular_profiles: mp.evidence_items = [e for e in evidence if e.molecular_profile_id == mp.id] mp.variants = [v for v in variants if v.id in mp.variant_ids] mp.assertions = [a for a in assertions if a.molecular_profile_id == mp.id] mp._partial = False CACHE[hash(mp)] = mp CACHE['full_cached'] = datetime.now() _build_coordinate_table(variants) save_cache(local_cache_path=local_cache_path) def _make_local_cache_path_if_missing(local_cache_path): p = Path(local_cache_path) if not p.parent.is_dir(): os.makedirs(p.parent)
[docs]class CivicRecord: """ As a base class, :class:`CivicRecord` is used to define the characteristic of all records in CIViC. This class is not intended to be invoked directly by the end user, but provided for documentation of shared methods and variables in child classes. """ _SIMPLE_FIELDS = {'id', 'type'} _COMPLEX_FIELDS = set() _OPTIONAL_FIELDS = set()
[docs] def __init__(self, partial=False, **kwargs): """ The record object may be initialized by the user, though the practice is discouraged. To do so, values for each of the object attributes (except ``type``) must be specified as keyword arguments, or the ``partial`` parameter must be set to **True**. If ``partial`` is set to **True**, the ``id`` keyword argument is still required. Users are encouraged to use the functions for `getting records`_ in lieu of directly initializing record objects. :param bool partial: Indicates whether the the set of object attributes passed is incomplete. If set to **True** the ``id`` keyword is required. """ self._incomplete = set() self._partial = partial simple_fields = sorted(self._SIMPLE_FIELDS, reverse=True) simple_fields = sorted(simple_fields, key=lambda x: x in CivicRecord._SIMPLE_FIELDS, reverse=True) for field in simple_fields: try: self.__setattr__(field, kwargs[field]) except KeyError: try: object.__getattribute__(self, field) except AttributeError: if (partial and field not in CivicRecord._SIMPLE_FIELDS) or field in self._OPTIONAL_FIELDS: self._incomplete.add(field) # Allow for incomplete data when partial flag set else: raise AttributeError('Expected {} attribute for {}, none found.'.format(field, self.type)) for field in self._COMPLEX_FIELDS: try: v = kwargs[field] if v is None: v = dict() except KeyError: if partial or field in self._OPTIONAL_FIELDS: self._incomplete.add(field) continue else: raise AttributeError('Expected {} attribute for {}, none found.'.format(field, self.type)) is_compound = isinstance(v, list) cls = get_class(field) if is_compound: result = list() for data in v: if isinstance(data, dict): data['type'] = data.get('type', singularize(field)) result.append(cls(partial=True, **data)) else: result.append(data) self.__setattr__(field, result) else: t = v.get('type', field) v['type'] = CIVIC_TO_PYCLASS.get(t, t) if v.keys() == {'type'}: self.__setattr__(field, {}) else: self.__setattr__(field, cls(partial=True, **v)) self._partial = bool(self._incomplete) if not isinstance(self, CivicAttribute) and not self._partial and self.__class__.__name__ != 'CivicRecord': CACHE[hash(self)] = self self._include_status = ['accepted','submitted','rejected']
def __dir__(self): return [attribute for attribute in super().__dir__() if not attribute.startswith('_')] def __repr__(self): return '<CIViC {} {}>'.format(self.type, self.id) def __getattr__(self, item): if self._partial and item in self._incomplete: self.update() return object.__getattribute__(self, item) def __hash__(self): return hash('{}:{}'.format(self.type, self.id)) def __eq__(self, other): return hash(self) == hash(other) def __setstate__(self, state): self.__dict__ = state
[docs] def update(self, allow_partial=True, force=False, **kwargs): """ Updates the record object from the cache or the server. Keyword arguments may be passed to ``kwargs``, which will update the corresponding attributes of the :class:`CivicRecord` instance. :param bool allow_partial: Flag to indicate whether the record will be updated according to the contents of CACHE, without requiring all attributes to be assigned. :param bool force: Flag to indicate whether to force an update from the server, even if a full record ecists in the cache. :return: True if record is complete after update, else False. """ if kwargs: self.__init__(partial=allow_partial, force=force, **kwargs) return not self._partial if not force and CACHE.get(hash(self)): cached = CACHE[hash(self)] for field in self._SIMPLE_FIELDS | self._COMPLEX_FIELDS: v = getattr(cached, field) setattr(self, field, v) self._partial = False logging.info('Loading {} from cache'.format(str(self))) return True resp_dict = element_lookup_by_id(self.type, self.id) self.__init__(partial=False, **resp_dict) return True
@property def site_link(self): """Returns a URL to the record on the CIViC web application.""" return '/'.join([LINKS_URL, self.type, str(self.id)])
[docs]class MolecularProfile(CivicRecord): _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union({ 'description', 'molecular_profile_score', 'name', 'variant_ids', }) _COMPLEX_FIELDS = CivicRecord._COMPLEX_FIELDS.union({ 'aliases', 'assertions', 'evidence_items', 'sources', 'variants', }) def __init__(self, **kwargs): self._evidence_items = [] self._assertions = [] self._variants = [] super().__init__(**kwargs) @property def evidence_sources(self): sources = set() for evidence in self.evidence_items: if evidence.source is not None: sources.add(evidence.source) return sources @property def summary(self): return self.description @summary.setter def summary(self, value): self.description = value @property def evidence(self): return self.evidence_items @property def evidence_items(self): return [e for e in self._evidence_items if e.status in self._include_status] @evidence_items.setter def evidence_items(self, value): self._evidence_items = value @property def assertions(self): return [a for a in self._assertions if a.status in self._include_status] @assertions.setter def assertions(self, value): self._assertions = value @property def variants(self): return self._variants @variants.setter def variants(self, value): self._variants = value def sanitized_name(self): name = self.name words = [] for word in name.split(' '): regex = re.compile(r"^([A-Z]+)([0-9]+)(=)(.*)$") match = regex.match(word) if match is not None: word = "".join([match.group(1), match.group(2), match.group(1), match.group(4)]) words.append(word) return ' '.join(words)
[docs]class Variant(CivicRecord): _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union({ 'allele_registry_id', 'gene_id', 'name', 'single_variant_molecular_profile_id', 'entrez_name', 'entrez_id' }) _COMPLEX_FIELDS = CivicRecord._COMPLEX_FIELDS.union({ 'clinvar_entries', 'coordinates', # 'errors', 'hgvs_expressions', #'lifecycle_actions', # 'provisional_values', 'variant_aliases', 'variant_groups', 'variant_types'}) def __init__(self, **kwargs): # Handle overloaded evidence_items from some advanced search views kwargs['type'] = 'variant' self._variant_groups = [] self._molecular_profiles = [] coordinates = kwargs.get('coordinates') if coordinates: if coordinates.get('reference_bases') in ['', '-']: coordinates['reference_bases'] = None if coordinates.get('variant_bases') in ['', '-']: coordinates['variant_bases'] = None super().__init__(**kwargs) @property def aliases(self): return self.variant_aliases @property def groups(self): return self.variant_groups @property def types(self): return self.variant_types @property def variant_groups(self): return self._variant_groups @variant_groups.setter def variant_groups(self, value): self._variant_groups = value @property def molecular_profiles(self): for mp in self._molecular_profiles: mp._include_status = self._include_status return [mp for mp in self._molecular_profiles if mp.evidence] @molecular_profiles.setter def molecular_profiles(self, value): self._molecular_profiles = value @property def gene(self): return _get_element_by_id('gene', self.gene_id) @property def single_variant_molecular_profile(self): mp = _get_element_by_id('molecular_profile', self.single_variant_molecular_profile_id) mp._include_status = self._include_status return mp @property def is_insertion(self): ref = self.coordinates.reference_bases alt = self.coordinates.variant_bases return (ref is None and alt is not None) or (ref is not None and alt is not None and len(ref) < len(alt)) @property def is_deletion(self): ref = self.coordinates.reference_bases alt = self.coordinates.variant_bases if alt is not None and (alt == '-' or alt == ''): alt = None return (ref is not None and alt is None) or (ref is not None and alt is not None and len(ref) > len(alt)) def is_valid_for_vcf(self, emit_warnings=False): if self.coordinates.chromosome2 or self.coordinates.start2 or self.coordinates.stop2: warning = "Variant {} has a second set of coordinates. Skipping".format(self.id) elif self.coordinates.chromosome and self.coordinates.start and (self.coordinates.reference_bases or self.coordinates.variant_bases): if self._valid_ref_bases(): if self._valid_alt_bases(): return True else: warning = "Unsupported variant base(s) for variant {}. Skipping.".format(self.id) else: warning = "Unsupported reference base(s) for variant {}. Skipping.".format(self.id) else: warning = "Incomplete coordinates for variant {}. Skipping.".format(self.id) if emit_warnings: logging.warning(warning) return False def _valid_ref_bases(self): if self.coordinates.reference_bases is not None: return all([c.upper() in ['A', 'C', 'G', 'T', 'N'] for c in self.coordinates.reference_bases]) else: return True def _valid_alt_bases(self): if self.coordinates.variant_bases is not None: return all([c.upper() in ['A', 'C', 'G', 'T', 'N'] for c in self.coordinates.variant_bases]) else: return True def vcf_coordinates(self): ensembl_server = "https://grch37.rest.ensembl.org" if self.coordinates.reference_build != 'GRCh37': return if self.is_insertion: if not self.coordinates.representative_transcript: return else: start = self.coordinates.start ext = "/sequence/region/human/{}:{}-{}".format(self.coordinates.chromosome, start, start) r = requests.get(ensembl_server+ext, headers={ "Content-Type" : "text/plain"}) if self.coordinates.reference_bases == None or self.coordinates.reference_bases == '-' or self.coordinates.reference_bases == '': ref = r.text else: ref = "{}{}".format(r.text, self.coordinates.reference_bases) alt = "{}{}".format(r.text, self.coordinates.variant_bases) elif self.is_deletion: if not self.coordinates.representative_transcript: return else: start = self.coordinates.start - 1 ext = "/sequence/region/human/{}:{}-{}".format(self.coordinates.chromosome, start, start) r = requests.get(ensembl_server+ext, headers={ "Content-Type" : "text/plain"}) ref = "{}{}".format(r.text, self.coordinates.reference_bases) if self.coordinates.variant_bases == None or self.coordinates.variant_bases == '-' or self.coordinates.variant_bases == '': alt = r.text else: alt = "{}{}".format(r.text, self.coordinates.variant_bases) else: start = self.coordinates.start ref = self.coordinates.reference_bases alt = self.coordinates.variant_bases return (start, ref, alt) def csq_alt(self): if self.coordinates.reference_build != 'GRCh37': return if self.is_insertion: if not self.coordinates.representative_transcript: return else: return self.coordinates.variant_bases elif self.is_deletion: if not self.coordinates.representative_transcript: return else: return "-" else: return self.coordinates.variant_bases def hgvs_c(self): if self.coordinates.representative_transcript: hgvs_cs = [e for e in self.hgvs_expressions if (':c.' in e) and (self.coordinates.representative_transcript in e)] return hgvs_cs[0] if len(hgvs_cs) == 1 else '' else: return '' def hgvs_p(self): if self.coordinates.representative_transcript: hgvs_ps = [e for e in self.hgvs_expressions if (':p.' in e) and (self.coordinates.representative_transcript in e)] return hgvs_ps[0] if len(hgvs_ps) == 1 else '' else: return '' def sanitized_name(self): name = self.name regex = re.compile(r"^([A-Z]+)([0-9]+)(=)(.*)$") match = regex.match(name) if match is not None: name = "".join([match.group(1), match.group(2), match.group(1), match.group(4)]) return name def csq(self, include_status=None): if self.csq_alt() is None: return [] else: csq = [] for mp in self.molecular_profiles: for evidence in mp.evidence: if include_status is not None and evidence.status not in include_status: continue special_character_table = str.maketrans(exports.VCFWriter.SPECIAL_CHARACTERS) csq.append('|'.join([ self.csq_alt(), '&'.join(map(lambda t: t.name, self.variant_types)), self.gene.name, str(self.gene.entrez_id), 'transcript', str(self.coordinates.representative_transcript), self.hgvs_c(), self.hgvs_p(), self.sanitized_name(), str(self.id), '&'.join(map(lambda a: a.translate(special_character_table), self.variant_aliases)), "https://civicdb.org/links/variants/{}".format(self.id), mp.sanitized_name(), str(mp.id), '&'.join(map(lambda a: a.translate(special_character_table), mp.aliases)), "https://civicdb.org/links/molecular-profiles/{}".format(mp.id), '&'.join(map(lambda e: e.translate(special_character_table), self.hgvs_expressions)), str(self.allele_registry_id), '&'.join(self.clinvar_entries), str(mp.molecular_profile_score), "evidence", str(evidence.id), "https://civicdb.org/links/evidence/{}".format(evidence.id), "{} ({})".format(evidence.source.citation_id, evidence.source.source_type), str(evidence.variant_origin), evidence.status, str(evidence.significance or ''), str(evidence.evidence_direction or ''), str(evidence.disease), '&'.join([str(therapy) for therapy in evidence.therapies]), str(evidence.therapy_interaction_type or ""), '&'.join(["{} (HPO ID {})".format(phenotype.name, phenotype.hpo_id) for phenotype in evidence.phenotypes]), evidence.evidence_level, str(evidence.rating), "", "", "", "", "", ])) for assertion in mp.assertions: if include_status is not None and assertion.status not in include_status: continue csq.append('|'.join([ self.csq_alt(), '&'.join(map(lambda t: t.name, self.variant_types)), self.gene.name, str(self.gene.entrez_id), 'transcript', str(self.coordinates.representative_transcript), self.hgvs_c(), self.hgvs_p(), self.sanitized_name(), str(self.id), '&'.join(map(lambda a: a.translate(special_character_table), self.variant_aliases)), "https://civicdb.org/links/variants/{}".format(self.id), mp.sanitized_name(), str(mp.id), '&'.join(map(lambda a: a.translate(special_character_table), mp.aliases)), "https://civicdb.org/links/molecular-profiles/{}".format(mp.id), '&'.join(map(lambda e: e.translate(special_character_table), self.hgvs_expressions)), str(self.allele_registry_id), '&'.join(self.clinvar_entries), str(mp.molecular_profile_score), "assertion", str(assertion.id), "https://civicdb.org/links/assertion/{}".format(assertion.id), "", str(assertion.variant_origin), assertion.status, assertion.significance, assertion.assertion_direction, str(assertion.disease), '&'.join([str(therapy) for therapy in assertion.therapies]), str(assertion.therapy_interaction_type or ''), "", "", "", "&".join([acmg_code.code for acmg_code in assertion.acmg_codes]), str(assertion.amp_level or ''), assertion.format_nccn_guideline(), str(assertion.fda_regulatory_approval or ''), str(assertion.fda_companion_test or ''), ])) return csq
class VariantGroup(CivicRecord): _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union( {'description', 'name', 'variant_ids'}) _COMPLEX_FIELDS = CivicRecord._COMPLEX_FIELDS.union({ # 'errors', # TODO: Add support for these fields in advanced search endpoint # 'lifecycle_actions', # 'provisional_values', 'sources', 'variants' }) def __init__(self, **kwargs): self._variants = [] super().__init__(**kwargs) @property def variants(self): for variant in self._variants: variant._include_status = self._include_status return self._variants @variants.setter def variants(self, value): self._variants = value
[docs]class Gene(CivicRecord): _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union( {'description', 'entrez_id', 'name'}) _COMPLEX_FIELDS = CivicRecord._COMPLEX_FIELDS.union({ 'aliases', # 'errors', # TODO: Add support for these fields in advanced search endpoint # /'lifecycle_actions', # 'provisional_values', 'sources', 'variants', 'assertions', }) def __init__(self, **kwargs): self._variants = [] self._assertions = [] super().__init__(**kwargs) @property def variants(self): for variant in self._variants: variant._include_status = self._include_status return [v for v in self._variants if v.molecular_profiles] @variants.setter def variants(self, value): self._variants = value @property def assertions(self): return [a for a in self._assertions if a.status in self._include_status] @assertions.setter def assertions(self, value): self._assertions = value
[docs]class Evidence(CivicRecord): _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union({ 'significance', 'description', 'therapy_interaction_type', 'evidence_direction', 'evidence_level', 'evidence_type', 'name', # 'open_change_count', 'rating', 'status', 'molecular_profile_id', 'variant_origin', 'assertion_ids', }) _COMPLEX_FIELDS = CivicRecord._COMPLEX_FIELDS.union({ 'assertions', 'disease', 'therapies', # 'errors', # 'fields_with_pending_changes', #'lifecycle_actions', 'phenotypes', 'source'}) def __init__(self, **kwargs): self._assertions = [] super().__init__(**kwargs) @property def molecular_profile(self): return get_molecular_profile_by_id(self.molecular_profile_id) @property def assertions(self): return [a for a in self._assertions if a.status in self._include_status] @assertions.setter def assertions(self, value): self._assertions = value @property def statement(self): return self.description @statement.setter def statement(self, value): self.description = value
[docs]class Assertion(CivicRecord): _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union({ 'amp_level', 'significance', 'description', 'therapy_interaction_type', 'assertion_direction', # 'evidence_item_count', 'assertion_type', 'fda_companion_test', 'fda_regulatory_approval', 'name', 'nccn_guideline', 'nccn_guideline_version', # 'open_change_count', # 'pending_evidence_count', 'status', 'summary', 'variant_origin', 'molecular_profile_id', 'evidence_ids', }) _COMPLEX_FIELDS = CivicRecord._COMPLEX_FIELDS.union({ 'acmg_codes', 'clingen_codes', 'disease', 'therapies', 'evidence_items', #'lifecycle_actions', 'phenotypes', }) def __init__(self, **kwargs): self._evidence_items = [] super().__init__(**kwargs) @property def evidence(self): return self.evidence_items @property def evidence_items(self): return [e for e in self._evidence_items if e.status in self._include_status] @evidence_items.setter def evidence_items(self, value): self._evidence_items = value @property def molecular_profile(self): return get_molecular_profile_by_id(self.molecular_profile_id) @property def hpo_ids(self): return [x.hpo_id for x in self.phenotypes if x.hpo_id] def format_nccn_guideline(self): if self.nccn_guideline is None: return "" else: return "{} (v{})".format(self.nccn_guideline, self.nccn_guideline_version)
class User(CivicRecord): _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union({ 'name', 'username', 'role', 'avatar_url', 'area_of_expertise', 'orcid', 'display_name', 'created_at', 'url', 'twitter_handle', 'facebook_profile', 'linkedin_profile', 'bio', 'featured_expert', # 'accepted_license', # 'signup_complete', # 'affiliation' }) _OPTIONAL_FIELDS = CivicRecord._OPTIONAL_FIELDS.union({ 'country', 'organization', 'conflict_of_interest' }) _COMPLEX_FIELDS = CivicRecord._COMPLEX_FIELDS.union(_OPTIONAL_FIELDS) def __init__(self, **kwargs): self._created_at = None super().__init__(**kwargs) @property def created_at(self): assert self._created_at[-1] == 'Z' return datetime.fromisoformat(self._created_at[:-1]) @created_at.setter def created_at(self, value): self._created_at = value class Organization(CivicRecord): _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union({ 'name', 'url', 'description' }) _COMPLEX_FIELDS = CivicRecord._COMPLEX_FIELDS.union({ 'profile_image', 'parent' })
[docs]class CivicAttribute(CivicRecord, dict): _SIMPLE_FIELDS = {'type'} _COMPLEX_FIELDS = set() def __repr__(self): try: _id = self.id except AttributeError: return '<CIViC Attribute {}>'.format(self.type) else: return '<CIViC Attribute {} {}>'.format(self.type, self.id) def __init__(self, **kwargs): kwargs['partial'] = False for k, v in kwargs.items(): self.__setattr__(k, v) super().__init__(**kwargs) def __hash__(self): try: _id = self.id except AttributeError: raise NotImplementedError if _id is not None: return CivicRecord.__hash__(self) else: raise ValueError @property def site_link(self): return None def update(self): return NotImplementedError
class Therapy(CivicAttribute): _SIMPLE_FIELDS = CivicAttribute._SIMPLE_FIELDS.union({'ncit_id', 'therapy_url', 'name'}) _COMPLEX_FIELDS = CivicAttribute._COMPLEX_FIELDS.union({'aliases'}) def __str__(self): if self.ncit_id is None: return self.name else: return "{} (NCIt ID {})".format(self.name, self.ncit_id) class Disease(CivicAttribute): _SIMPLE_FIELDS = CivicAttribute._SIMPLE_FIELDS.union({'display_name', 'doid', 'disease_url'}) _COMPLEX_FIELDS = CivicAttribute._COMPLEX_FIELDS.union({'aliases'}) def __str__(self): if self.doid is None: return self.name else: return "{} (DOID {})".format(self.name, self.doid) class Phenotype(CivicAttribute): _SIMPLE_FIELDS = CivicAttribute._SIMPLE_FIELDS.union({'hpo_id', 'url', 'name'}) def __str__(self): return "{} (HPO ID {})".format(self.name, self.hpo_id) class Source(CivicAttribute): _SIMPLE_FIELDS = CivicAttribute._SIMPLE_FIELDS.union({ 'citation', 'citation_id', 'source_type', 'abstract', 'asco_abstract_id', 'author_string', 'full_journal_title', 'journal', 'pmc_id', 'publication_date', 'source_url', 'title' }) _COMPLEX_FIELDS = CivicAttribute._COMPLEX_FIELDS.union({'clinical_trials'}) def __str__(self): return "{} ({} {})".format(self.citation, self.source_type, self.citation_id) class Country(CivicAttribute): _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union({'iso', 'name'}) class LifecycleAction(CivicAttribute): _OPTIONAL_FIELDS = CivicAttribute._OPTIONAL_FIELDS.union({ 'submitted', 'last_modified', 'last_reviewed', 'accepted' }) _COMPLEX_FIELDS = CivicAttribute._COMPLEX_FIELDS.union(_OPTIONAL_FIELDS) class BaseLifecycleAction(CivicAttribute): _SIMPLE_FIELDS = CivicAttribute._SIMPLE_FIELDS.union({ 'timestamp' }) _COMPLEX_FIELDS = CivicAttribute._COMPLEX_FIELDS.union({ 'user' }) def __init__(self, **kwargs): self._timestamp = None super().__init__(**kwargs) @property def timestamp(self): assert self._timestamp[-1] == 'Z' return datetime.fromisoformat(self._timestamp[:-1]) @timestamp.setter def timestamp(self, value): self._timestamp = value class Submitted(BaseLifecycleAction): pass class LastModified(BaseLifecycleAction): pass class LastReviewed(BaseLifecycleAction): pass class Accepted(BaseLifecycleAction): pass def get_cached(element_type, element_id): klass = get_class(element_type) r = klass(type=element_type, id=element_id, partial=True) return CACHE.get(hash(r), False) def _has_full_cached_fresh(delta=FRESH_DELTA): s = 'full_cached' if CACHE.get(s, False): return CACHE[s] + delta > datetime.now() return False def _get_elements_by_ids(element, id_list=[], allow_cached=True, get_all=False): if allow_cached: if not CACHE: load_cache() if not get_all: cached = [get_cached(element, element_id) for element_id in id_list] if all(cached): logging.info('Loading {} from cache'.format(pluralize(element))) return cached else: cached = [get_cached(element, element_id) for element_id in CACHE['{}_all_ids'.format(pluralize(element))]] logging.info('Loading {} from cache'.format(pluralize(element))) return cached if id_list and get_all: raise ValueError('Please pass list of ids or use the get_all flag, not both.') if get_all: logging.warning('Getting all {}. This may take a couple of minutes...'.format(pluralize(element))) response_elements = _request_all(element) else: response_elements = _request_by_ids(element, id_list) for e in response_elements: e = _postprocess_response_element(e, element) cls = get_class(element) elements = [cls(**x, partial=True) for x in response_elements] cache = [x['id'] for x in response_elements] CACHE['{}_all_ids'.format(pluralize(element))] = cache return elements def _postprocess_response_element(e, element): e['type'] = element if element == 'assertion': e['molecular_profile_id'] = e['molecular_profile']['id'] e['evidence_ids'] = [evidence['id'] for evidence in e['evidenceItems']] e['status'] = e['status'].lower() elif element == 'evidence': e['molecular_profile_id'] = e['molecular_profile']['id'] e['assertion_ids'] = [a['id'] for a in e['assertions']] e['status'] = e['status'].lower() elif element == 'variant': e['gene_id'] = e['gene']['id'] e['entrez_name'] = e['gene']['name'] e['entrez_id'] = e['gene']['entrezId'] build = e['referenceBuild'] if build == 'GRCH37': build = 'GRCh37' elif build == 'GRCH38': build = 'GRCh38' e['coordinates'] = { 'ensembl_version': e['ensemblVersion'], 'reference_build': build, 'reference_bases': e['referenceBases'], 'variant_bases': e['variantBases'], 'representative_transcript': None if e['primaryCoordinates'] is None else e['primaryCoordinates']['representativeTranscript'], 'chromosome': None if e['primaryCoordinates'] is None else e['primaryCoordinates']['chromosome'], 'start': None if e['primaryCoordinates'] is None else e['primaryCoordinates']['start'], 'stop': None if e['primaryCoordinates'] is None else e['primaryCoordinates']['stop'], 'representative_transcript2': None if e['secondaryCoordinates'] is None else e['secondaryCoordinates']['representativeTranscript'], 'chromosome2': None if e['secondaryCoordinates'] is None else e['secondaryCoordinates']['chromosome'], 'start2': None if e['secondaryCoordinates'] is None else e['secondaryCoordinates']['start'], 'stop2': None if e['secondaryCoordinates'] is None else e['secondaryCoordinates']['stop'], } elif element == 'variant_group': e['variant_ids'] = [v['id'] for v in e['variants']['nodes']] del e['variants'] elif element == 'molecular_profile': e['variant_ids'] = [v['id'] for v in e['variants']] del e['variants'] return e def _get_element_by_id(element, id, allow_cached=True): return _get_elements_by_ids(element, [id], allow_cached)[0] def _request_by_ids(element, ids): payload_methods = { 'evidence': _construct_get_evidence_payload, 'gene': _construct_get_gene_payload, 'variant': _construct_get_variant_payload, 'assertion': _construct_get_assertion_payload, 'variant_group': _construct_get_variant_group_payload, 'molecular_profile': _construct_get_molecular_profile_payload, } payload_method = payload_methods[element] payload = payload_method() response_elements = [] for i in ids: resp = requests.post(API_URL, json={'query': payload, 'variables': {'id': i}}, timeout=(10,200)) resp.raise_for_status() response = resp.json()['data'][element] response_elements.append(response) return response_elements def _request_all(element): payload_methods = { 'evidence': _construct_get_all_evidence_payload, 'gene': _construct_get_all_genes_payload, 'variant': _construct_get_all_variants_payload, 'assertion': _construct_get_all_assertions_payload, 'variant_group': _construct_get_all_variant_groups_payload, 'molecular_profile': _construct_get_all_molecular_profiles_payload, } payload_method = payload_methods[element] payload = payload_method() after_cursor = None variables = { "after": after_cursor } resp = requests.post(API_URL, json={'query': payload, 'variables': variables}, timeout=(10,200)) resp.raise_for_status() response = resp.json()['data'][pluralize(element)] response_elements = response['nodes'] has_next_page = response['pageInfo']['hasNextPage'] after_cursor = response['pageInfo']['endCursor'] while has_next_page: variables = { "after": after_cursor } resp = requests.post(API_URL, json={'query': payload, 'variables': variables}, timeout=(10,200)) resp.raise_for_status() response = resp.json()['data'][pluralize(element)] response_elements.extend(response['nodes']) has_next_page = response['pageInfo']['hasNextPage'] after_cursor = response['pageInfo']['endCursor'] return response_elements def _construct_get_gene_payload(): return """ query gene($id: Int!) { gene(id: $id) { id name description entrez_id: entrezId aliases: geneAliases sources { id name title citation citation_id: citationId source_type: sourceType abstract asco_abstract_id: ascoAbstractId author_string: authorString full_journal_title: fullJournalTitle journal pmc_id: pmcId publication_date: publicationDate source_url: sourceUrl clinical_trials: clinicalTrials { id name description nctId url } } } }""" def _construct_get_all_genes_payload(): return """ query genes($after: String) { genes(after: $after) { totalCount pageInfo { hasNextPage endCursor } nodes { id name description entrez_id: entrezId aliases: geneAliases sources { id name title citation citation_id: citationId source_type: sourceType abstract asco_abstract_id: ascoAbstractId author_string: authorString full_journal_title: fullJournalTitle journal pmc_id: pmcId publication_date: publicationDate source_url: sourceUrl clinical_trials: clinicalTrials { id name description nctId url } } } } }""" def _construct_get_molecular_profile_payload(): return """ query molecularProfile($id: Int!) { molecular_profile: molecularProfile(id: $id) { id description molecular_profile_score: molecularProfileScore name variants { id } aliases: molecularProfileAliases sources { id name title citation citation_id: citationId source_type: sourceType abstract asco_abstract_id: ascoAbstractId author_string: authorString full_journal_title: fullJournalTitle journal pmc_id: pmcId publication_date: publicationDate source_url: sourceUrl clinical_trials: clinicalTrials { id name description nctId url } } } }""" def _construct_get_all_molecular_profiles_payload(): return """ query molecularProfiles($after: String) { molecular_profiles: molecularProfiles(after: $after, evidenceStatusFilter: ALL) { totalCount pageInfo { hasNextPage endCursor } nodes { id description molecular_profile_score: molecularProfileScore name variants { id } aliases: molecularProfileAliases sources { id name title citation citation_id: citationId source_type: sourceType abstract asco_abstract_id: ascoAbstractId author_string: authorString full_journal_title: fullJournalTitle journal pmc_id: pmcId publication_date: publicationDate source_url: sourceUrl clinical_trials: clinicalTrials { id name description nctId url } } } } }""" def _construct_get_variant_payload(): return """ query variant($id: Int!) { variant(id: $id) { id name allele_registry_id: alleleRegistryId gene { id name entrezId } single_variant_molecular_profile_id: singleVariantMolecularProfileId clinvar_entries: clinvarIds hgvs_expressions: hgvsDescriptions variant_aliases: variantAliases variant_types: variantTypes { id name so_id: soid description url } variantBases referenceBases referenceBuild primaryCoordinates { chromosome representativeTranscript start stop } secondaryCoordinates { chromosome representativeTranscript start stop } ensemblVersion } }""" def _construct_get_all_variants_payload(): return """ query variants($after: String) { variants(after: $after) { totalCount pageInfo { hasNextPage endCursor } nodes { id name allele_registry_id: alleleRegistryId gene { id name entrezId } single_variant_molecular_profile_id: singleVariantMolecularProfileId clinvar_entries: clinvarIds hgvs_expressions: hgvsDescriptions variant_aliases: variantAliases variant_types: variantTypes { id name so_id: soid description url } variantBases referenceBases referenceBuild primaryCoordinates { chromosome representativeTranscript start stop } secondaryCoordinates { chromosome representativeTranscript start stop } ensemblVersion } } }""" def _construct_get_evidence_payload(): return """ query evidenceItem($id: Int!) { evidence: evidenceItem(id: $id) { id name significance description therapy_interaction_type: therapyInteractionType evidence_direction: evidenceDirection evidence_level: evidenceLevel evidence_type: evidenceType status variant_origin: variantOrigin molecular_profile: molecularProfile { id } disease { id name display_name: displayName doid disease_url: diseaseUrl aliases: diseaseAliases } therapies { id name ncit_id: ncitId therapy_url: therapyUrl aliases: therapyAliases } phenotypes { id name hpo_id: hpoId url } assertions { id } source { id name title citation citation_id: citationId source_type: sourceType abstract asco_abstract_id: ascoAbstractId author_string: authorString full_journal_title: fullJournalTitle journal pmc_id: pmcId publication_date: publicationDate source_url: sourceUrl clinical_trials: clinicalTrials { id name description nctId url } } rating: evidenceRating } }""" def _construct_get_all_evidence_payload(): return """ query evidenceItems($after: String) { evidence_items: evidenceItems(after: $after, status: ALL) { totalCount pageInfo { hasNextPage endCursor } nodes { id name significance description therapy_interaction_type: therapyInteractionType evidence_direction: evidenceDirection evidence_level: evidenceLevel evidence_type: evidenceType status variant_origin: variantOrigin molecular_profile: molecularProfile { id } disease { id name display_name: displayName doid disease_url: diseaseUrl aliases: diseaseAliases } therapies { id name ncit_id: ncitId therapy_url: therapyUrl aliases: therapyAliases } phenotypes { id name hpo_id: hpoId url } assertions { id } source { id name title citation citation_id: citationId source_type: sourceType abstract asco_abstract_id: ascoAbstractId author_string: authorString full_journal_title: fullJournalTitle journal pmc_id: pmcId publication_date: publicationDate source_url: sourceUrl clinical_trials: clinicalTrials { id name description nctId url } } rating: evidenceRating } } }""" def _construct_get_assertion_payload(): return """ query assertion($id: Int!) { assertion(id: $id) { id name amp_level: ampLevel significance description therapy_interaction_type: therapyInteractionType assertion_direction: assertionDirection assertion_type: assertionType fda_companion_test: fdaCompanionTest fda_regulatory_approval: regulatoryApproval name nccn_guideline: nccnGuideline { name } nccn_guideline_version: nccnGuidelineVersion status summary variant_origin: variantOrigin molecular_profile: molecularProfile { id } acmg_codes: acmgCodes { id code description } clingen_codes: clingenCodes { id code description } disease { id name display_name: displayName doid disease_url: diseaseUrl aliases: diseaseAliases } therapies { id name ncit_id: ncitId therapy_url: therapyUrl aliases: therapyAliases } evidenceItems { id } phenotypes { id name hpo_id: hpoId url } } }""" def _construct_get_all_assertions_payload(): return """ query assertions($after: String) { assertions(after: $after, status: ALL) { totalCount pageInfo { hasNextPage endCursor } nodes { id name amp_level: ampLevel significance description therapy_interaction_type: therapyInteractionType assertion_direction: assertionDirection assertion_type: assertionType fda_companion_test: fdaCompanionTest fda_regulatory_approval: regulatoryApproval name nccn_guideline: nccnGuideline { name } nccn_guideline_version: nccnGuidelineVersion status summary variant_origin: variantOrigin molecular_profile: molecularProfile { id } acmg_codes: acmgCodes { id code description } clingen_codes: clingenCodes { id code description } disease { id name display_name: displayName doid disease_url: diseaseUrl aliases: diseaseAliases } therapies { id name ncit_id: ncitId therapy_url: therapyUrl aliases: therapyAliases } evidenceItems { id } phenotypes { id name hpo_id: hpoId url } } } }""" def _construct_get_variant_group_payload(): return """ query variantGroup($id: Int!) { variant_group: variantGroup(id: $id) { id name description variants(first: 100) { nodes { id } } sources { id name title citation citation_id: citationId source_type: sourceType abstract asco_abstract_id: ascoAbstractId author_string: authorString full_journal_title: fullJournalTitle journal pmc_id: pmcId publication_date: publicationDate source_url: sourceUrl clinical_trials: clinicalTrials { id name description nctId url } } } }""" def _construct_get_all_variant_groups_payload(): return """ query variantGroups($after: String) { variant_groups: variantGroups(after: $after) { totalCount pageInfo { hasNextPage endCursor } nodes { id name description variants(first: 100) { nodes { id } } sources { id name title citation citation_id: citationId source_type: sourceType abstract asco_abstract_id: ascoAbstractId author_string: authorString full_journal_title: fullJournalTitle journal pmc_id: pmcId publication_date: publicationDate source_url: sourceUrl clinical_trials: clinicalTrials { id name description nctId url } } } } }"""
[docs]def get_evidence_by_ids(evidence_id_list): logging.info('Getting evidence...') evidence = _get_elements_by_ids('evidence', evidence_id_list) logging.info('Caching evidence details...') for e in evidence: e._include_status = ['accepted', 'submitted', 'rejected'] mp_ids = [x.molecular_profile.id for x in evidence] # Add molecular profiles to cache _get_elements_by_ids('molecular_profile', mp_ids) for e in evidence: # Load from cache e.molecular_profile.update() return evidence
[docs]def get_evidence_by_id(evidence_id): return get_evidence_by_ids([evidence_id])[0]
[docs]def get_molecular_profile_by_id(mp_id): return get_molecular_profiles_by_ids([mp_id])[0]
[docs]def get_molecular_profiles_by_ids(mp_id_list): logging.info('Getting molecular profiles...') mps = _get_elements_by_ids('molecular_profile', mp_id_list) for mp in mps: mp._include_status = ['accepted', 'submitted', 'rejected'] #logging.info('Caching molecular profile details...') return mps
[docs]def get_assertions_by_ids(assertion_id_list=[], get_all=False): logging.info('Getting assertions...') assertions = _get_elements_by_ids('assertion', assertion_id_list, get_all=get_all) for a in assertions: a._include_status = ['accepted', 'submitted', 'rejected'] logging.info('Caching variant details...') mp_ids = [x.molecular_profile.id for x in assertions] # Add molecular profile to cache _get_elements_by_ids('molecular_profile', mp_ids) for assertion in assertions: # Load from cache assertion.molecular_profile.update() return assertions
[docs]def get_assertion_by_id(assertion_id): return get_assertions_by_ids([assertion_id])[0]
[docs]def get_all_assertions(include_status=['accepted','submitted','rejected'], allow_cached=True): assertions = _get_elements_by_ids('assertion', allow_cached=allow_cached, get_all=True) return [a for a in assertions if a.status in include_status]
[docs]def search_assertions_by_coordinates(coordinates, search_mode='any'): variants = search_variants_by_coordinates(coordinates, search_mode=search_mode) assertions = set() for v in variants: if v.single_variant_molecular_profile.assertions: assertions.update(v.single_variant_molecular_profile.assertions) return list(assertions)
[docs]def get_variants_by_ids(variant_id_list): logging.info('Getting variants...') variants = _get_elements_by_ids('variant', variant_id_list) gene_ids = set() for variant in variants: gene_ids.add(variant.gene_id) variant._include_status = ['accepted', 'submitted', 'rejected'] if gene_ids: logging.info('Caching gene details...') _get_elements_by_ids('gene', gene_ids) return variants
[docs]def get_variant_by_id(variant_id): return get_variants_by_ids([variant_id])[0]
def get_variant_groups_by_ids(variant_group_id_list): logging.info('Getting variant groups...') vgs = _get_elements_by_ids('variant_group', variant_group_id_list) for vg in vgs: vg._include_status = ['accepted', 'submitted', 'rejected'] return vgs def get_variant_group_by_id(variant_group_id): return get_variant_groups_by_ids([variant_group_id])[0] def _build_coordinate_table(variants): variant_records = list() for v in variants: c = v.coordinates start = getattr(c, 'start', None) stop = getattr(c, 'stop', None) chr = getattr(c, 'chromosome', None) alt = getattr(c, 'variant_bases', None) ref = getattr(c, 'reference_bases', None) if all([start, stop, chr]): variant_records.append([chr, start, stop, alt, ref, hash(v)]) else: continue start = getattr(c, 'start2', None) stop = getattr(c, 'stop2', None) chr = getattr(c, 'chromosome2', None) if all([start, stop, chr]): variant_records.append([chr, start, stop, None, None, hash(v)]) df = pd.DataFrame.from_records( variant_records, columns=['chr', 'start', 'stop', 'alt', 'ref', 'v_hash'] ).sort_values(by=['chr', 'start', 'stop', 'alt', 'ref']) MODULE.COORDINATE_TABLE = df MODULE.COORDINATE_TABLE_START = df.start.sort_values() MODULE.COORDINATE_TABLE_STOP = df.stop.sort_values() MODULE.COORDINATE_TABLE_CHR = df.chr.sort_values()
[docs]def get_all_molecular_profiles(include_status=['accepted', 'submitted', 'rejected'], allow_cached=True): mps = _get_elements_by_ids('molecular_profile', allow_cached=allow_cached, get_all=True) if include_status: assert CACHE.get('evidence_items_all_ids', False) resp = list() for mp in mps: mp._include_status = include_status if mp.evidence: resp.append(mp) return resp else: return mps
[docs]def get_all_variants(include_status=['accepted', 'submitted', 'rejected'], allow_cached=True): variants = _get_elements_by_ids('variant', allow_cached=allow_cached, get_all=True) if include_status: assert CACHE.get('evidence_items_all_ids', False) assert CACHE.get('assertions_all_ids', False) resp = list() for v in variants: v._include_status = include_status if v.molecular_profiles: resp.append(v) return resp else: return variants
def get_all_variant_groups(allow_cached=True): variant_groups = _get_elements_by_ids('variant_group', allow_cached=allow_cached, get_all=True) return variant_groups
[docs]def search_variants_by_allele_registry_id(caid): """ Search the cache for variants matching the queried Allele Registry ID (CAID) :param String caid: Allele Registry ID to query :return: Returns a list of variant hashes matching the Allele Registry ID """ return search_variants_by_attribute('allele_registry_id', caid)
[docs]def search_variants_by_name(name): """ Search the cache for variants matching the queried name :param String name: Variant name to query :return: Returns a list of variant hashes matching the name """ return search_variants_by_attribute('name', name)
[docs]def search_variants_by_hgvs(hgvs): """ Search the cache for variants matching the queried HGVS expression :param String name: HGVS expression to query :return: Returns a list of variant hashes matching the HGVS expression """ return search_variants_by_list_field('hgvs_expressions', hgvs)
def search_variants_by_attribute(attribute, value): variants = get_all_variants() return [v for v in variants if getattr(v, attribute) == value] def search_variants_by_list_field(field, value): variants = get_all_variants() matched_variants = [] return [v for v in variants if value in getattr(v, field)]
[docs]def search_variants_by_coordinates(coordinate_query, search_mode='any'): """ Search the cache for variants matching provided coordinates using the corresponding search mode. :param CoordinateQuery coordinate_query: Coordinates to query :param any,query_encompassing,variant_encompassing,exact search_mode: *any* : any overlap between a query and a variant is a match\n *query_encompassing* : CIViC variant records must fit within the coordinates of the query\n *record_encompassing* : CIViC variant records must encompass the coordinates of the query\n *exact* : variants must match coordinates precisely, as well as reference allele(s) and alternate allele(s). Use ``'*'`` in the coordinate_query as a wildcard for reference and/or alternate alleles. Using ``None`` in the coordinate_query for reference or alternate alleles will only match variants that have no reference or alternate alleles, respectively (e.g. indels) \n search_mode is *any* by default :return: Returns a list of variant hashes matching the coordinates and search_mode """ get_all_variants() if coordinate_query.build == 'GRCh37': ct = COORDINATE_TABLE start_idx = COORDINATE_TABLE_START stop_idx = COORDINATE_TABLE_STOP chr_idx = COORDINATE_TABLE_CHR start = int(coordinate_query.start) stop = int(coordinate_query.stop) chromosome = str(coordinate_query.chr) # overlapping = (start <= ct.stop) & (stop >= ct.start) left_idx = chr_idx.searchsorted(chromosome) right_idx = chr_idx.searchsorted(chromosome, side='right') chr_ct_idx = chr_idx[left_idx:right_idx].index right_idx = start_idx.searchsorted(stop, side='right') start_ct_idx = start_idx[:right_idx].index left_idx = stop_idx.searchsorted(start) stop_ct_idx = stop_idx[left_idx:].index match_idx = chr_ct_idx & start_ct_idx & stop_ct_idx m_df = ct.loc[match_idx, ] if search_mode == 'any': var_digests = m_df.v_hash.to_list() return [CACHE[v] for v in var_digests] elif search_mode == 'query_encompassing': match_idx = (start <= m_df.start) & (stop >= m_df.stop) elif search_mode == 'variant_encompassing': match_idx = (start >= m_df.start) & (stop <= m_df.stop) elif search_mode == 'exact': match_idx = (start == m_df.start) & (stop == m_df.stop) if coordinate_query.alt is not None and coordinate_query.alt != '*': if coordinate_query.alt == '-': raise ValueError("Unexpected alt `-` in coordinate query. Did you mean `None`?") match_idx = match_idx & (coordinate_query.alt == m_df.alt) elif coordinate_query.alt is None: match_idx = match_idx & pd.isnull(m_df.alt) if (coordinate_query.ref is not None and coordinate_query.ref != '*'): if coordinate_query.ref == '-': raise ValueError("Unexpected ref `-` in coordinate query. Did you mean `None`?") match_idx = match_idx & (coordinate_query.ref == m_df.ref) elif coordinate_query.ref is None: match_idx = match_idx & pd.isnull(m_df.ref) else: raise ValueError("unexpected search mode") var_digests = m_df.loc[match_idx,].v_hash.to_list() return [CACHE[v] for v in var_digests] else: if search_mode == 'exact': if coordinate_query.alt or coordinate_query.ref: if coordinate_query.alt == '*' or coordinate_query.ref == '*': raise ValueError("Can't use wildcard when searching for non-GRCh37 coordinates") if coordinate_query.alt == '-': raise ValueError("Unexpected alt `-` in coordinate query. Did you mean `None`?") if coordinate_query.ref == '-': raise ValueError("Unexpected ref `-` in coordinate query. Did you mean `None`?") hgvs = _construct_hgvs_for_coordinate_query(coordinate_query) if hgvs is not None: s = requests.Session() retry = Retry( total=5, read=5, connect=5, backoff_factor=0.3, status_forcelist=(500, 502, 504), ) adapter = requests.adapters.HTTPAdapter(max_retries=retry) s.mount('http://', adapter) r = s.get(url=_allele_registry_url(), params={'hgvs': hgvs}) data = r.json() if '@id' in data: allele_registry_id = data['@id'].split('/')[-1] if not allele_registry_id == '_:CA': return search_variants_by_allele_registry_id(allele_registry_id) else: raise ValueError("alt or ref required for non-GRCh37 coordinate queries") else: raise ValueError("Only exact search mode is supported for non-GRCh37 coordinate queries")
def _allele_registry_url(): return "http://reg.genome.network/allele" def _construct_hgvs_for_coordinate_query(coordinate_query): if coordinate_query.build == 'GRCh38': chromosome = _refseq_sequence_b38(coordinate_query.chr) elif coordinate_query.build == 'NCBI36': chromosome = _refseq_sequence_b36(coordinate_query.chr) else: raise ValueError("unexpected reference build") if chromosome is None: return None base_hgvs = "{}:g.{}".format(chromosome, coordinate_query.start) variant_type = _variant_type(coordinate_query) if variant_type == "deletion": if len(coordinate_query.ref) > 1: return"{}_{}del".format(base_hgvs, coordinate_query.stop) else: return "{}del".format(base_hgvs) elif variant_type == "substitution": return "{}{}>{}".format(base_hgvs, coordinate_query.ref, coordinate_query.alt) elif variant_type == "insertion": return "{}_{}ins{}".format(base_hgvs, coordinate_query.stop, coordinate_query.alt) elif variant_type == "indel": if len(coordinate_query.ref) > 1: return "{}_{}delins{}".format(base_hgvs, coordinate_query.stop, coordinate_query.alt) else: return "{}delins{}".format(base_hgvs, coordinate_query.alt) else: return None def _variant_type(coordinate_query): if not coordinate_query.ref and not coordinate_query.alt: return None elif coordinate_query.ref and not coordinate_query.alt: return "deletion" elif not coordinate_query.ref and coordinate_query.alt: return "insertion" elif len(coordinate_query.ref) == 1 and len(coordinate_query.alt) == 1: return "substitution" elif len(coordinate_query.ref) > 1 and len(coordinate_query.alt) > 1: return "indel" else: return None def _refseq_sequence_b36(chromosome): chromosome = chromosome.replace('chr', '') sequences = { '1' : 'NC_000001.9', '2' : 'NC_000002.10', '3' : 'NC_000003.10', '4' : 'NC_000004.10', '5' : 'NC_000005.8', '6' : 'NC_000006.10', '7' : 'NC_000007.12', '8' : 'NC_000008.9', '9' : 'NC_000009.10', '10' : 'NC_000010.9', '11' : 'NC_000011.8', '12' : 'NC_000012.10', '13' : 'NC_000013.9', '14' : 'NC_000014.7', '15' : 'NC_000015.8', '16' : 'NC_000016.8', '17' : 'NC_000017.9', '18' : 'NC_000018.8', '19' : 'NC_000019.8', '20' : 'NC_000020.9', '21' : 'NC_000021.7', '22' : 'NC_000022.9', 'X' : 'NC_000023.9', 'Y' : 'NC_000024.8', } if chromosome not in sequences: return None return sequences[chromosome] def _refseq_sequence_b38(chromosome): chromosome = chromosome.replace('chr', '') sequences = { '1' : 'NC_000001.11', '2' : 'NC_000002.12', '3' : 'NC_000003.12', '4' : 'NC_000004.12', '5' : 'NC_000005.10', '6' : 'NC_000006.12', '7' : 'NC_000007.14', '8' : 'NC_000008.11', '9' : 'NC_000009.12', '10' : 'NC_000010.11', '11' : 'NC_000011.10', '12' : 'NC_000012.12', '13' : 'NC_000013.11', '14' : 'NC_000014.9', '15' : 'NC_000015.10', '16' : 'NC_000016.10', '17' : 'NC_000017.11', '18' : 'NC_000018.10', '19' : 'NC_000019.10', '20' : 'NC_000020.11', '21' : 'NC_000021.9', '22' : 'NC_000022.11', 'X' : 'NC_000023.11', 'Y' : 'NC_000024.10', } if chromosome not in sequences: return None return sequences[chromosome] # TODO: Refactor this method
[docs]def bulk_search_variants_by_coordinates(sorted_queries, search_mode='any'): """ An interator to search the cache for variants matching the set of sorted coordinates and yield matches corresponding to the search mode. :param list[CoordinateQuery] sorted_queries: Sorted list of coordinates to query :param any,query_encompassing,variant_encompassing,exact search_mode: *any* : any overlap between a query and a variant is a match\n *query_encompassing* : CIViC variant records must fit within the coordinates of the query\n *record_encompassing* : CIViC variant records must encompass the coordinates of the query\n *exact* : variants must match coordinates precisely, as well as reference allele(s) and alternate allele(s). Use ``'*'`` in the coordinate_query as a wildcard for reference and/or alternate alleles. Using ``None`` in the coordinate_query for reference or alternate alleles will only match variants that have no reference or alternate alleles, respectively (e.g. indels) \n search_mode is *any* by default :return: returns a dictionary of Match lists, keyed by query """ def is_sorted(prev_q, current_q): if prev_q['chr'] < current_q['chr']: return True if prev_q['chr'] > current_q['chr']: return False if prev_q['start'] < current_q['start']: return True if prev_q['start'] > current_q['start']: return False if prev_q['stop'] < current_q['stop']: return True if prev_q['stop'] > current_q['stop']: return False return True ct_pointer = 0 query_pointer = 0 last_query_pointer = -1 match_start = None ct = MODULE.COORDINATE_TABLE matches = defaultdict(list) Match = namedtuple('Match', ct.columns) def append_match(matches_list, query, ct_row): matches_list[query].append(Match(**ct_row.to_dict())) while query_pointer < len(sorted_queries) and ct_pointer < len(ct): if last_query_pointer != query_pointer: q = sorted_queries[query_pointer] if q.build != 'GRCh37': raise ValueError("Bulk coordinate search only supports build GRCh37") if match_start is not None: ct_pointer = match_start match_start = None last_query_pointer = query_pointer c = ct.iloc[ct_pointer] q_chr = str(q.chr) c_chr = c.chr if q_chr < c_chr: query_pointer += 1 continue if q_chr > c_chr: ct_pointer += 1 continue q_start = int(q.start) c_start = c.start q_stop = int(q.stop) c_stop = c.stop if q_start > c_stop: ct_pointer += 1 continue if q_stop < c_start: query_pointer += 1 continue if search_mode == 'any': append_match(matches, q, c) elif search_mode == 'exact' and q_start == c_start and q_stop == c_stop: q_alt = q.alt c_alt = c.alt q_ref = q.ref c_ref = c.ref if q_alt == '-': raise ValueError("Unexpected alt `-` in coordinate query. Did you mean `None`?") if q_ref == '-': raise ValueError("Unexpected ref `-` in coordinate query. Did you mean `None`?") if (not (q_alt != '*' and q_alt != c_alt)) and (not (q_ref != '*' and q_ref != c_ref)): append_match(matches, q, c) elif search_mode == 'query_encompassing' and q_start <= c_start and q_stop >= c_stop: append_match(matches, q, c) elif search_mode == 'record_encompassing' and c_start <= q_start and c_stop >= q_stop: append_match(matches, q, c) if match_start is None: match_start = ct_pointer ct_pointer += 1 return dict(matches)
[docs]def get_genes_by_ids(gene_id_list): """ :param list gene_id_list: A list of CIViC gene IDs to query against to cache and (as needed) CIViC. :returns: A list of :class:`Gene` objects. """ logging.info('Getting genes...') genes = _get_elements_by_ids('gene', gene_id_list) # Advanced search results are incomplete variant_ids = set() for gene in genes: gene._include_status = ['accepted', 'submitted', 'rejected'] for variant in gene.variants: variant_ids.add(variant.id) if variant_ids: logging.info('Caching variant details...') _get_elements_by_ids('variant', variant_ids) for gene in genes: for variant in gene.variants: variant.update() return genes
[docs]def get_gene_by_id(gene_id): """ :param int gene_id: A single CIViC gene ID. :returns: A :class:`Gene` object. """ return get_genes_by_ids([gene_id])[0]
[docs]def get_all_genes(include_status=['accepted','submitted','rejected'], allow_cached=True): """ Queries CIViC for all genes. :param list include_status: A list of statuses. Only genes and their associated entities matching the given statuses will be returned. :param bool allow_cached: Indicates whether or not object retrieval from CACHE is allowed. If **False** it will query the CIViC database directly. :returns: A list of :class:`Gene` objects. """ genes = _get_elements_by_ids('gene', get_all=True, allow_cached=allow_cached) if include_status: assert CACHE.get('variants_all_ids', False) assert CACHE.get('evidence_items_all_ids', False) resp = list() for g in genes: g._include_status = include_status if g.variants: resp.append(g) return resp else: return genes
[docs]def get_all_evidence(include_status=['accepted','submitted','rejected'], allow_cached=True): evidence = _get_elements_by_ids('evidence', get_all=True, allow_cached=allow_cached) return [e for e in evidence if e.status in include_status]
def get_HPO_terms_by_ids(hpo_id_list): if not HPO_TERMS: _load_HPO() return [HPO_TERMS[x] for x in hpo_id_list] def _load_HPO(): url = 'https://civicdb.org/api/phenotypes?count=100000' resp = requests.get(url) resp.raise_for_status() for h in resp.json(): HPO_TERMS[h['id']] = h