BoghdadyJR/codesearch_python · Datasets at Hugging Face

text stringlengths 75 104k
def _add_to_ref(self, rec_curr, line, lnum): """Add new fields to the current reference.""" # Written by DV Klopfenstein # Examples of record lines containing ':' include: # id: GO:0000002 # name: mitochondrial genome maintenance # namespace: biological_process ...
def update_rec(self, rec, name, value): """Update current GOTerm with optional record.""" # 'def' is a reserved word in python, do not use it as a Class attr. if name == "def": name = "defn" # If we have a relationship, then we will split this into a further # dictio...
def _add_to_typedef(self, typedef_curr, line, lnum): """Add new fields to the current typedef.""" mtch = re.match(r'^(\S+):\s(\S.)$', line) if mtch: field_name = mtch.group(1) field_value = mtch.group(2).split('!')[0].rstrip() if field_name == "id": ...
def _add_nested(self, rec, name, value): """Adds a term's nested attributes.""" # Remove comments and split term into typedef / target term. (typedef, target_term) = value.split('!')[0].rstrip().split(' ') # Save the nested term. getattr(rec, name)[typedef].append(target_term)
def _init_optional_attrs(self, optional_attrs): """Prepare to store data from user-desired optional fields. Not loading these optional fields by default saves in space and speed. But allow the possibility for saving these fields, if the user desires, Including: com...
def _die(self, msg, lnum): """Raise an Exception if file read is unexpected.""" raise Exception("**FATAL {FILE}({LNUM}): {MSG}\n".format( FILE=self.obo_file, LNUM=lnum, MSG=msg))
def write_hier_rec(self, gos_printed, out=sys.stdout, len_dash=1, max_depth=None, num_child=None, short_prt=False, include_only=None, go_marks=None, depth=1, dp="-"): """Write hierarchy for a GO Term record.""" # Added by DV Klopfenstein ...
def write_hier_all(self, out=sys.stdout, len_dash=1, max_depth=None, num_child=None, short_prt=False): """Write hierarchy for all GO Terms in obo file.""" # Print: [biological_process, molecular_function, and cellular_component] for go_id in ['GO:0008150', 'GO:0003674', 'GO...
def write_hier(self, GO_id, out=sys.stdout, len_dash=1, max_depth=None, num_child=None, short_prt=False, include_only=None, go_marks=None): """Write hierarchy for a GO Term.""" gos_printed = set() self[GO_id].write_hier_rec(gos_printed, out, len_dash...
def paths_to_top(self, term): """ Returns all possible paths to the root node Each path includes the term given. The order of the path is top -> bottom, i.e. it starts with the root and ends with the given term (inclusively). Parameters: ----------- ...
def make_graph_pydot(self, recs, nodecolor, edgecolor, dpi, draw_parents=True, draw_children=True): """draw AMIGO style network, lineage containing one query record.""" import pydot G = pydot.Dot(graph_type='digraph', dpi="{}".format(dpi)) # Directed Gra...
def sqliteRowsToDicts(sqliteRows): """ Unpacks sqlite rows as returned by fetchall into an array of simple dicts. :param sqliteRows: array of rows returned from fetchall DB call :return: array of dicts, keyed by the column names. """ return map(lambda r: dict(zip(r.keys(), r)), sqliteRows)
def limitsSql(startIndex=0, maxResults=0): """ Construct a SQL LIMIT clause """ if startIndex and maxResults: return " LIMIT {}, {}".format(startIndex, maxResults) elif startIndex: raise Exception("startIndex was provided, but maxResults was not") elif maxResults: return ...
def iterativeFetch(query, batchSize=default_batch_size): """ Returns rows of a sql fetch query on demand """ while True: rows = query.fetchmany(batchSize) if not rows: break rowDicts = sqliteRowsToDicts(rows) for rowDict in rowDicts: yield rowDict
def _parsePageToken(pageToken, numValues): """ Parses the specified pageToken and returns a list of the specified number of values. Page tokens are assumed to consist of a fixed number of integers seperated by colons. If the page token does not conform to this specification, raise a InvalidPageToken...
def _parseIntegerArgument(args, key, defaultValue): """ Attempts to parse the specified key in the specified argument dictionary into an integer. If the argument cannot be parsed, raises a BadRequestIntegerException. If the key is not present, return the specified default value. """ ret = de...
def _initialiseIteration(self): """ Starts a new iteration. """ self._searchIterator = self._search( self._request.start, self._request.end if self._request.end != 0 else None) self._currentObject = next(self._searchIterator, None) if self._current...
def _pickUpIteration(self, searchAnchor, objectsToSkip): """ Picks up iteration from a previously provided page token. There are two different phases here: 1) We are iterating over the initial set of intervals in which start is < the search start coorindate. 2) We are ite...
def next(self): """ Returns the next (object, nextPageToken) pair. """ if self._currentObject is None: raise StopIteration() nextPageToken = None if self._nextObject is not None: start = self._getStart(self._nextObject) # If start > the...
def filterVariantAnnotation(self, vann): """ Returns true when an annotation should be included. """ # TODO reintroduce feature ID search ret = False if len(self._effects) != 0 and not vann.transcript_effects: return False elif len(self._effects) == 0:...
def filterEffect(self, teff): """ Returns true when any of the transcript effects are present in the request. """ ret = False for effect in teff.effects: ret = self._matchAnyEffects(effect) or ret return ret
def _checkIdEquality(self, requestedEffect, effect): """ Tests whether a requested effect and an effect present in an annotation are equal. """ return self._idPresent(requestedEffect) and ( effect.term_id == requestedEffect.term_id)
def ga4ghImportGlue(): """ Call this method before importing a ga4gh module in the scripts dir. Otherwise, you will be using the installed package instead of the development package. Assumes a certain directory structure. """ path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))...
def _update(self, dataFile, handle): """ Update the priority of the file handle. The element is first removed and then added to the left of the deque. """ self._cache.remove((dataFile, handle)) self._add(dataFile, handle)
def _removeLru(self): """ Remove the least recently used file handle from the cache. The pop method removes an element from the right of the deque. Returns the name of the file that has been removed. """ (dataFile, handle) = self._cache.pop() handle.close() ...
def getFileHandle(self, dataFile, openMethod): """ Returns handle associated to the filename. If the file is already opened, update its priority in the cache and return its handle. Otherwise, open the file using openMethod, store it in the cache and return the corresponding handl...
def join(cls, splits): """ Join an array of ids into a compound id string """ segments = [] for split in splits: segments.append('"{}",'.format(split)) if len(segments) > 0: segments[-1] = segments[-1][:-1] jsonString = '[{}]'.format(''.joi...
def parse(cls, compoundIdStr): """ Parses the specified compoundId string and returns an instance of this CompoundId class. :raises: An ObjectWithIdNotFoundException if parsing fails. This is because this method is a client-facing method, and if a malformed identifier (u...
def obfuscate(cls, idStr): """ Mildly obfuscates the specified ID string in an easily reversible fashion. This is not intended for security purposes, but rather to dissuade users from depending on our internal ID structures. """ return unicode(base64.urlsafe_b64encode( ...
def deobfuscate(cls, data): """ Reverses the obfuscation done by the :meth:`obfuscate` method. If an identifier arrives without correct base64 padding this function will append it to the end. """ # the str() call is necessary to convert the unicode string # to an ...
def serializeAttributes(self, msg): """ Sets the attrbutes of a message during serialization. """ attributes = self.getAttributes() for key in attributes: protocol.setAttribute( msg.attributes.attr[key].values, attributes[key]) return msg
def _scanDataFiles(self, dataDir, patterns): """ Scans the specified directory for files with the specified globbing pattern and calls self._addDataFile for each. Raises an EmptyDirException if no data files are found. """ numDataFiles = 0 for pattern in patterns:...
def getInitialPeerList(filePath, logger=None): """ Attempts to get a list of peers from a file specified in configuration. This file has one URL per line and can contain newlines and comments. # Main ga4gh node http://1kgenomes.ga4gh.org # Local intranet peer https://192.16...
def insertInitialPeer(dataRepository, url, logger=None): """ Takes the datarepository, a url, and an optional logger and attempts to add the peer into the repository. """ insertPeer = dataRepository.insertPeer try: peer = datamodel.peers.Peer(url) insertPeer(peer) except exce...
def isUrl(urlString): """ Attempts to return whether a given URL string is valid by checking for the presence of the URL scheme and netloc using the urlparse module, and then using a regex. From http://stackoverflow.com/questions/7160737/ """ parsed = urlparse.urlparse(urlString) urlpar...
def setUrl(self, url): """ Attempt to safely set the URL by string. """ if isUrl(url): self._url = url else: raise exceptions.BadUrlException(url) return self
def setAttributesJson(self, attributesJson): """ Sets the attributes dictionary from a JSON string. """ try: self._attributes = json.loads(attributesJson) except: raise exceptions.InvalidJsonException(attributesJson) return self
def populateFromRow(self, peerRecord): """ This method accepts a model record and sets class variables. """ self.setUrl(peerRecord.url) \ .setAttributesJson(peerRecord.attributes) return self
def _topLevelObjectGenerator(self, request, numObjects, getByIndexMethod): """ Returns a generator over the results for the specified request, which is over a set of objects of the specified size. The objects are returned by call to the specified method, which must take a single ...
def _protocolObjectGenerator(self, request, numObjects, getByIndexMethod): """ Returns a generator over the results for the specified request, from a set of protocol objects of the specified size. The objects are returned by call to the specified method, which must take a single ...
def _protocolListGenerator(self, request, objectList): """ Returns a generator over the objects in the specified list using _protocolObjectGenerator to generate page tokens. """ return self._protocolObjectGenerator( request, len(objectList), lambda index: objectList[i...
def _objectListGenerator(self, request, objectList): """ Returns a generator over the objects in the specified list using _topLevelObjectGenerator to generate page tokens. """ return self._topLevelObjectGenerator( request, len(objectList), lambda index: objectList[ind...
def datasetsGenerator(self, request): """ Returns a generator over the (dataset, nextPageToken) pairs defined by the specified request """ return self._topLevelObjectGenerator( request, self.getDataRepository().getNumDatasets(), self.getDataRepository().ge...
def phenotypeAssociationSetsGenerator(self, request): """ Returns a generator over the (phenotypeAssociationSet, nextPageToken) pairs defined by the specified request """ dataset = self.getDataRepository().getDataset(request.dataset_id) return self._topLevelObjectGenerato...
def readGroupSetsGenerator(self, request): """ Returns a generator over the (readGroupSet, nextPageToken) pairs defined by the specified request. """ dataset = self.getDataRepository().getDataset(request.dataset_id) return self._readGroupSetsGenerator( request...
def _readGroupSetsGenerator(self, request, numObjects, getByIndexMethod): """ Returns a generator over the results for the specified request, which is over a set of objects of the specified size. The objects are returned by call to the specified method, which must take a single i...
def referenceSetsGenerator(self, request): """ Returns a generator over the (referenceSet, nextPageToken) pairs defined by the specified request. """ results = [] for obj in self.getDataRepository().getReferenceSets(): include = True if request.md5...
def referencesGenerator(self, request): """ Returns a generator over the (reference, nextPageToken) pairs defined by the specified request. """ referenceSet = self.getDataRepository().getReferenceSet( request.reference_set_id) results = [] for obj in r...
def variantSetsGenerator(self, request): """ Returns a generator over the (variantSet, nextPageToken) pairs defined by the specified request. """ dataset = self.getDataRepository().getDataset(request.dataset_id) return self._topLevelObjectGenerator( request, d...
def variantAnnotationSetsGenerator(self, request): """ Returns a generator over the (variantAnnotationSet, nextPageToken) pairs defined by the specified request. """ compoundId = datamodel.VariantSetCompoundId.parse( request.variant_set_id) dataset = self.getD...
def readsGenerator(self, request): """ Returns a generator over the (read, nextPageToken) pairs defined by the specified request """ if not request.reference_id: raise exceptions.UnmappedReadsNotSupported() if len(request.read_group_ids) < 1: raise...
def variantsGenerator(self, request): """ Returns a generator over the (variant, nextPageToken) pairs defined by the specified request. """ compoundId = datamodel.VariantSetCompoundId \ .parse(request.variant_set_id) dataset = self.getDataRepository().getDatas...
def variantAnnotationsGenerator(self, request): """ Returns a generator over the (variantAnnotaitons, nextPageToken) pairs defined by the specified request. """ compoundId = datamodel.VariantAnnotationSetCompoundId.parse( request.variant_annotation_set_id) dat...
def featuresGenerator(self, request): """ Returns a generator over the (features, nextPageToken) pairs defined by the (JSON string) request. """ compoundId = None parentId = None if request.feature_set_id != "": compoundId = datamodel.FeatureSetCompoun...
def continuousGenerator(self, request): """ Returns a generator over the (continuous, nextPageToken) pairs defined by the (JSON string) request. """ compoundId = None if request.continuous_set_id != "": compoundId = datamodel.ContinuousSetCompoundId.parse( ...
def phenotypesGenerator(self, request): """ Returns a generator over the (phenotypes, nextPageToken) pairs defined by the (JSON string) request """ # TODO make paging work using SPARQL? compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse( request.ph...
def genotypesPhenotypesGenerator(self, request): """ Returns a generator over the (phenotypes, nextPageToken) pairs defined by the (JSON string) request """ # TODO make paging work using SPARQL? compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse( r...
def callSetsGenerator(self, request): """ Returns a generator over the (callSet, nextPageToken) pairs defined by the specified request. """ compoundId = datamodel.VariantSetCompoundId.parse( request.variant_set_id) dataset = self.getDataRepository().getDataset...
def featureSetsGenerator(self, request): """ Returns a generator over the (featureSet, nextPageToken) pairs defined by the specified request. """ dataset = self.getDataRepository().getDataset(request.dataset_id) return self._topLevelObjectGenerator( request, d...
def continuousSetsGenerator(self, request): """ Returns a generator over the (continuousSet, nextPageToken) pairs defined by the specified request. """ dataset = self.getDataRepository().getDataset(request.dataset_id) return self._topLevelObjectGenerator( requ...
def rnaQuantificationSetsGenerator(self, request): """ Returns a generator over the (rnaQuantificationSet, nextPageToken) pairs defined by the specified request. """ dataset = self.getDataRepository().getDataset(request.dataset_id) return self._topLevelObjectGenerator( ...
def rnaQuantificationsGenerator(self, request): """ Returns a generator over the (rnaQuantification, nextPageToken) pairs defined by the specified request. """ if len(request.rna_quantification_set_id) < 1: raise exceptions.BadRequestException( "Rna Qu...
def expressionLevelsGenerator(self, request): """ Returns a generator over the (expressionLevel, nextPageToken) pairs defined by the specified request. Currently only supports searching over a specified rnaQuantification """ rnaQuantificationId = request.rna_quantificati...
def runGetRequest(self, obj): """ Runs a get request by converting the specified datamodel object into its protocol representation. """ protocolElement = obj.toProtocolElement() jsonString = protocol.toJson(protocolElement) return jsonString
def runSearchRequest( self, requestStr, requestClass, responseClass, objectGenerator): """ Runs the specified request. The request is a string containing a JSON representation of an instance of the specified requestClass. We return a string representation of an instance of th...
def runListReferenceBases(self, requestJson): """ Runs a listReferenceBases request for the specified ID and request arguments. """ # In the case when an empty post request is made to the endpoint # we instantiate an empty ListReferenceBasesRequest. if not request...
def runGetCallSet(self, id_): """ Returns a callset with the given id """ compoundId = datamodel.CallSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) variantSet = dataset.getVariantSet(compoundId.variant_set_id) callSet...
def runGetInfo(self, request): """ Returns information about the service including protocol version. """ return protocol.toJson(protocol.GetInfoResponse( protocol_version=protocol.version))
def runAddAnnouncement(self, flaskrequest): """ Takes a flask request from the frontend and attempts to parse into an AnnouncePeerRequest. If successful, it will log the announcement to the `announcement` table with some other metadata gathered from the request. """ ...
def runListPeers(self, request): """ Takes a ListPeersRequest and returns a ListPeersResponse using a page_token and page_size if provided. """ return self.runSearchRequest( request, protocol.ListPeersRequest, protocol.ListPeersResponse, ...
def runGetVariant(self, id_): """ Returns a variant with the given id """ compoundId = datamodel.VariantCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) variantSet = dataset.getVariantSet(compoundId.variant_set_id) gaVaria...
def runGetBiosample(self, id_): """ Runs a getBiosample request for the specified ID. """ compoundId = datamodel.BiosampleCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) biosample = dataset.getBiosample(id_) return self.r...
def runGetIndividual(self, id_): """ Runs a getIndividual request for the specified ID. """ compoundId = datamodel.BiosampleCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) individual = dataset.getIndividual(id_) return se...
def runGetFeature(self, id_): """ Returns JSON string of the feature object corresponding to the feature compoundID passed in. """ compoundId = datamodel.FeatureCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) featureSet =...
def runGetReadGroupSet(self, id_): """ Returns a readGroupSet with the given id_ """ compoundId = datamodel.ReadGroupSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) readGroupSet = dataset.getReadGroupSet(id_) return se...
def runGetReadGroup(self, id_): """ Returns a read group with the given id_ """ compoundId = datamodel.ReadGroupCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) readGroupSet = dataset.getReadGroupSet(compoundId.read_group_set_id) ...
def runGetReference(self, id_): """ Runs a getReference request for the specified ID. """ compoundId = datamodel.ReferenceCompoundId.parse(id_) referenceSet = self.getDataRepository().getReferenceSet( compoundId.reference_set_id) reference = referenceSet.getRe...
def runGetReferenceSet(self, id_): """ Runs a getReferenceSet request for the specified ID. """ referenceSet = self.getDataRepository().getReferenceSet(id_) return self.runGetRequest(referenceSet)
def runGetVariantSet(self, id_): """ Runs a getVariantSet request for the specified ID. """ compoundId = datamodel.VariantSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) variantSet = dataset.getVariantSet(id_) return s...
def runGetFeatureSet(self, id_): """ Runs a getFeatureSet request for the specified ID. """ compoundId = datamodel.FeatureSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) featureSet = dataset.getFeatureSet(id_) return s...
def runGetContinuousSet(self, id_): """ Runs a getContinuousSet request for the specified ID. """ compoundId = datamodel.ContinuousSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) continuousSet = dataset.getContinuousSet(id_) ...
def runGetDataset(self, id_): """ Runs a getDataset request for the specified ID. """ dataset = self.getDataRepository().getDataset(id_) return self.runGetRequest(dataset)
def runGetVariantAnnotationSet(self, id_): """ Runs a getVariantSet request for the specified ID. """ compoundId = datamodel.VariantAnnotationSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) variantSet = dataset.getVariantSet(c...
def runGetRnaQuantification(self, id_): """ Runs a getRnaQuantification request for the specified ID. """ compoundId = datamodel.RnaQuantificationCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) rnaQuantificationSet = dataset.getR...
def runGetRnaQuantificationSet(self, id_): """ Runs a getRnaQuantificationSet request for the specified ID. """ compoundId = datamodel.RnaQuantificationSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) rnaQuantificationSet = dat...
def runGetExpressionLevel(self, id_): """ Runs a getExpressionLevel request for the specified ID. """ compoundId = datamodel.ExpressionLevelCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) rnaQuantificationSet = dataset.getRnaQuan...
def runSearchReadGroupSets(self, request): """ Runs the specified SearchReadGroupSetsRequest. """ return self.runSearchRequest( request, protocol.SearchReadGroupSetsRequest, protocol.SearchReadGroupSetsResponse, self.readGroupSetsGenerator)
def runSearchIndividuals(self, request): """ Runs the specified search SearchIndividualsRequest. """ return self.runSearchRequest( request, protocol.SearchIndividualsRequest, protocol.SearchIndividualsResponse, self.individualsGenerator)
def runSearchBiosamples(self, request): """ Runs the specified SearchBiosamplesRequest. """ return self.runSearchRequest( request, protocol.SearchBiosamplesRequest, protocol.SearchBiosamplesResponse, self.biosamplesGenerator)
def runSearchReads(self, request): """ Runs the specified SearchReadsRequest. """ return self.runSearchRequest( request, protocol.SearchReadsRequest, protocol.SearchReadsResponse, self.readsGenerator)
def runSearchReferenceSets(self, request): """ Runs the specified SearchReferenceSetsRequest. """ return self.runSearchRequest( request, protocol.SearchReferenceSetsRequest, protocol.SearchReferenceSetsResponse, self.referenceSetsGenerator)
def runSearchReferences(self, request): """ Runs the specified SearchReferenceRequest. """ return self.runSearchRequest( request, protocol.SearchReferencesRequest, protocol.SearchReferencesResponse, self.referencesGenerator)
def runSearchVariantSets(self, request): """ Runs the specified SearchVariantSetsRequest. """ return self.runSearchRequest( request, protocol.SearchVariantSetsRequest, protocol.SearchVariantSetsResponse, self.variantSetsGenerator)
def runSearchVariantAnnotationSets(self, request): """ Runs the specified SearchVariantAnnotationSetsRequest. """ return self.runSearchRequest( request, protocol.SearchVariantAnnotationSetsRequest, protocol.SearchVariantAnnotationSetsResponse, self.var...
def runSearchVariants(self, request): """ Runs the specified SearchVariantRequest. """ return self.runSearchRequest( request, protocol.SearchVariantsRequest, protocol.SearchVariantsResponse, self.variantsGenerator)
def runSearchVariantAnnotations(self, request): """ Runs the specified SearchVariantAnnotationsRequest. """ return self.runSearchRequest( request, protocol.SearchVariantAnnotationsRequest, protocol.SearchVariantAnnotationsResponse, self.variantAnnotati...
def runSearchCallSets(self, request): """ Runs the specified SearchCallSetsRequest. """ return self.runSearchRequest( request, protocol.SearchCallSetsRequest, protocol.SearchCallSetsResponse, self.callSetsGenerator)
def runSearchDatasets(self, request): """ Runs the specified SearchDatasetsRequest. """ return self.runSearchRequest( request, protocol.SearchDatasetsRequest, protocol.SearchDatasetsResponse, self.datasetsGenerator)
def runSearchFeatureSets(self, request): """ Returns a SearchFeatureSetsResponse for the specified SearchFeatureSetsRequest object. """ return self.runSearchRequest( request, protocol.SearchFeatureSetsRequest, protocol.SearchFeatureSetsResponse, ...
def runSearchFeatures(self, request): """ Returns a SearchFeaturesResponse for the specified SearchFeaturesRequest object. :param request: JSON string representing searchFeaturesRequest :return: JSON string representing searchFeatureResponse """ return self.runSe...

def _add_to_ref(self, rec_curr, line, lnum): """Add new fields to the current reference.""" # Written by DV Klopfenstein # Examples of record lines containing ':' include: # id: GO:0000002 # name: mitochondrial genome maintenance # namespace: biological_process ...

def update_rec(self, rec, name, value): """Update current GOTerm with optional record.""" # 'def' is a reserved word in python, do not use it as a Class attr. if name == "def": name = "defn" # If we have a relationship, then we will split this into a further # dictio...

def _add_to_typedef(self, typedef_curr, line, lnum): """Add new fields to the current typedef.""" mtch = re.match(r'^(\S+):\s*(\S.*)$', line) if mtch: field_name = mtch.group(1) field_value = mtch.group(2).split('!')[0].rstrip() if field_name == "id": ...

def _add_nested(self, rec, name, value): """Adds a term's nested attributes.""" # Remove comments and split term into typedef / target term. (typedef, target_term) = value.split('!')[0].rstrip().split(' ') # Save the nested term. getattr(rec, name)[typedef].append(target_term)

def _init_optional_attrs(self, optional_attrs): """Prepare to store data from user-desired optional fields. Not loading these optional fields by default saves in space and speed. But allow the possibility for saving these fields, if the user desires, Including: com...

def _die(self, msg, lnum): """Raise an Exception if file read is unexpected.""" raise Exception("**FATAL {FILE}({LNUM}): {MSG}\n".format( FILE=self.obo_file, LNUM=lnum, MSG=msg))

def write_hier_rec(self, gos_printed, out=sys.stdout, len_dash=1, max_depth=None, num_child=None, short_prt=False, include_only=None, go_marks=None, depth=1, dp="-"): """Write hierarchy for a GO Term record.""" # Added by DV Klopfenstein ...

def write_hier_all(self, out=sys.stdout, len_dash=1, max_depth=None, num_child=None, short_prt=False): """Write hierarchy for all GO Terms in obo file.""" # Print: [biological_process, molecular_function, and cellular_component] for go_id in ['GO:0008150', 'GO:0003674', 'GO...

def write_hier(self, GO_id, out=sys.stdout, len_dash=1, max_depth=None, num_child=None, short_prt=False, include_only=None, go_marks=None): """Write hierarchy for a GO Term.""" gos_printed = set() self[GO_id].write_hier_rec(gos_printed, out, len_dash...

def paths_to_top(self, term): """ Returns all possible paths to the root node Each path includes the term given. The order of the path is top -> bottom, i.e. it starts with the root and ends with the given term (inclusively). Parameters: ----------- ...

def make_graph_pydot(self, recs, nodecolor, edgecolor, dpi, draw_parents=True, draw_children=True): """draw AMIGO style network, lineage containing one query record.""" import pydot G = pydot.Dot(graph_type='digraph', dpi="{}".format(dpi)) # Directed Gra...

def sqliteRowsToDicts(sqliteRows): """ Unpacks sqlite rows as returned by fetchall into an array of simple dicts. :param sqliteRows: array of rows returned from fetchall DB call :return: array of dicts, keyed by the column names. """ return map(lambda r: dict(zip(r.keys(), r)), sqliteRows)

def limitsSql(startIndex=0, maxResults=0): """ Construct a SQL LIMIT clause """ if startIndex and maxResults: return " LIMIT {}, {}".format(startIndex, maxResults) elif startIndex: raise Exception("startIndex was provided, but maxResults was not") elif maxResults: return ...

def iterativeFetch(query, batchSize=default_batch_size): """ Returns rows of a sql fetch query on demand """ while True: rows = query.fetchmany(batchSize) if not rows: break rowDicts = sqliteRowsToDicts(rows) for rowDict in rowDicts: yield rowDict

def _parsePageToken(pageToken, numValues): """ Parses the specified pageToken and returns a list of the specified number of values. Page tokens are assumed to consist of a fixed number of integers seperated by colons. If the page token does not conform to this specification, raise a InvalidPageToken...

def _parseIntegerArgument(args, key, defaultValue): """ Attempts to parse the specified key in the specified argument dictionary into an integer. If the argument cannot be parsed, raises a BadRequestIntegerException. If the key is not present, return the specified default value. """ ret = de...

def _initialiseIteration(self): """ Starts a new iteration. """ self._searchIterator = self._search( self._request.start, self._request.end if self._request.end != 0 else None) self._currentObject = next(self._searchIterator, None) if self._current...

def _pickUpIteration(self, searchAnchor, objectsToSkip): """ Picks up iteration from a previously provided page token. There are two different phases here: 1) We are iterating over the initial set of intervals in which start is < the search start coorindate. 2) We are ite...

def next(self): """ Returns the next (object, nextPageToken) pair. """ if self._currentObject is None: raise StopIteration() nextPageToken = None if self._nextObject is not None: start = self._getStart(self._nextObject) # If start > the...

def filterVariantAnnotation(self, vann): """ Returns true when an annotation should be included. """ # TODO reintroduce feature ID search ret = False if len(self._effects) != 0 and not vann.transcript_effects: return False elif len(self._effects) == 0:...

def filterEffect(self, teff): """ Returns true when any of the transcript effects are present in the request. """ ret = False for effect in teff.effects: ret = self._matchAnyEffects(effect) or ret return ret

def _checkIdEquality(self, requestedEffect, effect): """ Tests whether a requested effect and an effect present in an annotation are equal. """ return self._idPresent(requestedEffect) and ( effect.term_id == requestedEffect.term_id)

def ga4ghImportGlue(): """ Call this method before importing a ga4gh module in the scripts dir. Otherwise, you will be using the installed package instead of the development package. Assumes a certain directory structure. """ path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))...

def _update(self, dataFile, handle): """ Update the priority of the file handle. The element is first removed and then added to the left of the deque. """ self._cache.remove((dataFile, handle)) self._add(dataFile, handle)

def _removeLru(self): """ Remove the least recently used file handle from the cache. The pop method removes an element from the right of the deque. Returns the name of the file that has been removed. """ (dataFile, handle) = self._cache.pop() handle.close() ...

def getFileHandle(self, dataFile, openMethod): """ Returns handle associated to the filename. If the file is already opened, update its priority in the cache and return its handle. Otherwise, open the file using openMethod, store it in the cache and return the corresponding handl...

def join(cls, splits): """ Join an array of ids into a compound id string """ segments = [] for split in splits: segments.append('"{}",'.format(split)) if len(segments) > 0: segments[-1] = segments[-1][:-1] jsonString = '[{}]'.format(''.joi...

def parse(cls, compoundIdStr): """ Parses the specified compoundId string and returns an instance of this CompoundId class. :raises: An ObjectWithIdNotFoundException if parsing fails. This is because this method is a client-facing method, and if a malformed identifier (u...

def obfuscate(cls, idStr): """ Mildly obfuscates the specified ID string in an easily reversible fashion. This is not intended for security purposes, but rather to dissuade users from depending on our internal ID structures. """ return unicode(base64.urlsafe_b64encode( ...

def deobfuscate(cls, data): """ Reverses the obfuscation done by the :meth:`obfuscate` method. If an identifier arrives without correct base64 padding this function will append it to the end. """ # the str() call is necessary to convert the unicode string # to an ...

def serializeAttributes(self, msg): """ Sets the attrbutes of a message during serialization. """ attributes = self.getAttributes() for key in attributes: protocol.setAttribute( msg.attributes.attr[key].values, attributes[key]) return msg

def _scanDataFiles(self, dataDir, patterns): """ Scans the specified directory for files with the specified globbing pattern and calls self._addDataFile for each. Raises an EmptyDirException if no data files are found. """ numDataFiles = 0 for pattern in patterns:...

def getInitialPeerList(filePath, logger=None): """ Attempts to get a list of peers from a file specified in configuration. This file has one URL per line and can contain newlines and comments. # Main ga4gh node http://1kgenomes.ga4gh.org # Local intranet peer https://192.16...

def insertInitialPeer(dataRepository, url, logger=None): """ Takes the datarepository, a url, and an optional logger and attempts to add the peer into the repository. """ insertPeer = dataRepository.insertPeer try: peer = datamodel.peers.Peer(url) insertPeer(peer) except exce...

def isUrl(urlString): """ Attempts to return whether a given URL string is valid by checking for the presence of the URL scheme and netloc using the urlparse module, and then using a regex. From http://stackoverflow.com/questions/7160737/ """ parsed = urlparse.urlparse(urlString) urlpar...

def setUrl(self, url): """ Attempt to safely set the URL by string. """ if isUrl(url): self._url = url else: raise exceptions.BadUrlException(url) return self

def setAttributesJson(self, attributesJson): """ Sets the attributes dictionary from a JSON string. """ try: self._attributes = json.loads(attributesJson) except: raise exceptions.InvalidJsonException(attributesJson) return self

def populateFromRow(self, peerRecord): """ This method accepts a model record and sets class variables. """ self.setUrl(peerRecord.url) \ .setAttributesJson(peerRecord.attributes) return self

def _topLevelObjectGenerator(self, request, numObjects, getByIndexMethod): """ Returns a generator over the results for the specified request, which is over a set of objects of the specified size. The objects are returned by call to the specified method, which must take a single ...

def _protocolObjectGenerator(self, request, numObjects, getByIndexMethod): """ Returns a generator over the results for the specified request, from a set of protocol objects of the specified size. The objects are returned by call to the specified method, which must take a single ...

def _protocolListGenerator(self, request, objectList): """ Returns a generator over the objects in the specified list using _protocolObjectGenerator to generate page tokens. """ return self._protocolObjectGenerator( request, len(objectList), lambda index: objectList[i...

def _objectListGenerator(self, request, objectList): """ Returns a generator over the objects in the specified list using _topLevelObjectGenerator to generate page tokens. """ return self._topLevelObjectGenerator( request, len(objectList), lambda index: objectList[ind...

def datasetsGenerator(self, request): """ Returns a generator over the (dataset, nextPageToken) pairs defined by the specified request """ return self._topLevelObjectGenerator( request, self.getDataRepository().getNumDatasets(), self.getDataRepository().ge...

def phenotypeAssociationSetsGenerator(self, request): """ Returns a generator over the (phenotypeAssociationSet, nextPageToken) pairs defined by the specified request """ dataset = self.getDataRepository().getDataset(request.dataset_id) return self._topLevelObjectGenerato...

def readGroupSetsGenerator(self, request): """ Returns a generator over the (readGroupSet, nextPageToken) pairs defined by the specified request. """ dataset = self.getDataRepository().getDataset(request.dataset_id) return self._readGroupSetsGenerator( request...

def _readGroupSetsGenerator(self, request, numObjects, getByIndexMethod): """ Returns a generator over the results for the specified request, which is over a set of objects of the specified size. The objects are returned by call to the specified method, which must take a single i...

def referenceSetsGenerator(self, request): """ Returns a generator over the (referenceSet, nextPageToken) pairs defined by the specified request. """ results = [] for obj in self.getDataRepository().getReferenceSets(): include = True if request.md5...

def referencesGenerator(self, request): """ Returns a generator over the (reference, nextPageToken) pairs defined by the specified request. """ referenceSet = self.getDataRepository().getReferenceSet( request.reference_set_id) results = [] for obj in r...

def variantSetsGenerator(self, request): """ Returns a generator over the (variantSet, nextPageToken) pairs defined by the specified request. """ dataset = self.getDataRepository().getDataset(request.dataset_id) return self._topLevelObjectGenerator( request, d...

def variantAnnotationSetsGenerator(self, request): """ Returns a generator over the (variantAnnotationSet, nextPageToken) pairs defined by the specified request. """ compoundId = datamodel.VariantSetCompoundId.parse( request.variant_set_id) dataset = self.getD...

def readsGenerator(self, request): """ Returns a generator over the (read, nextPageToken) pairs defined by the specified request """ if not request.reference_id: raise exceptions.UnmappedReadsNotSupported() if len(request.read_group_ids) < 1: raise...

def variantsGenerator(self, request): """ Returns a generator over the (variant, nextPageToken) pairs defined by the specified request. """ compoundId = datamodel.VariantSetCompoundId \ .parse(request.variant_set_id) dataset = self.getDataRepository().getDatas...

def variantAnnotationsGenerator(self, request): """ Returns a generator over the (variantAnnotaitons, nextPageToken) pairs defined by the specified request. """ compoundId = datamodel.VariantAnnotationSetCompoundId.parse( request.variant_annotation_set_id) dat...

def featuresGenerator(self, request): """ Returns a generator over the (features, nextPageToken) pairs defined by the (JSON string) request. """ compoundId = None parentId = None if request.feature_set_id != "": compoundId = datamodel.FeatureSetCompoun...

def continuousGenerator(self, request): """ Returns a generator over the (continuous, nextPageToken) pairs defined by the (JSON string) request. """ compoundId = None if request.continuous_set_id != "": compoundId = datamodel.ContinuousSetCompoundId.parse( ...

def phenotypesGenerator(self, request): """ Returns a generator over the (phenotypes, nextPageToken) pairs defined by the (JSON string) request """ # TODO make paging work using SPARQL? compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse( request.ph...

def genotypesPhenotypesGenerator(self, request): """ Returns a generator over the (phenotypes, nextPageToken) pairs defined by the (JSON string) request """ # TODO make paging work using SPARQL? compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse( r...

def callSetsGenerator(self, request): """ Returns a generator over the (callSet, nextPageToken) pairs defined by the specified request. """ compoundId = datamodel.VariantSetCompoundId.parse( request.variant_set_id) dataset = self.getDataRepository().getDataset...

def featureSetsGenerator(self, request): """ Returns a generator over the (featureSet, nextPageToken) pairs defined by the specified request. """ dataset = self.getDataRepository().getDataset(request.dataset_id) return self._topLevelObjectGenerator( request, d...

def continuousSetsGenerator(self, request): """ Returns a generator over the (continuousSet, nextPageToken) pairs defined by the specified request. """ dataset = self.getDataRepository().getDataset(request.dataset_id) return self._topLevelObjectGenerator( requ...

def rnaQuantificationSetsGenerator(self, request): """ Returns a generator over the (rnaQuantificationSet, nextPageToken) pairs defined by the specified request. """ dataset = self.getDataRepository().getDataset(request.dataset_id) return self._topLevelObjectGenerator( ...

def rnaQuantificationsGenerator(self, request): """ Returns a generator over the (rnaQuantification, nextPageToken) pairs defined by the specified request. """ if len(request.rna_quantification_set_id) < 1: raise exceptions.BadRequestException( "Rna Qu...

def expressionLevelsGenerator(self, request): """ Returns a generator over the (expressionLevel, nextPageToken) pairs defined by the specified request. Currently only supports searching over a specified rnaQuantification """ rnaQuantificationId = request.rna_quantificati...

def runGetRequest(self, obj): """ Runs a get request by converting the specified datamodel object into its protocol representation. """ protocolElement = obj.toProtocolElement() jsonString = protocol.toJson(protocolElement) return jsonString

def runSearchRequest( self, requestStr, requestClass, responseClass, objectGenerator): """ Runs the specified request. The request is a string containing a JSON representation of an instance of the specified requestClass. We return a string representation of an instance of th...

def runListReferenceBases(self, requestJson): """ Runs a listReferenceBases request for the specified ID and request arguments. """ # In the case when an empty post request is made to the endpoint # we instantiate an empty ListReferenceBasesRequest. if not request...

def runGetCallSet(self, id_): """ Returns a callset with the given id """ compoundId = datamodel.CallSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) variantSet = dataset.getVariantSet(compoundId.variant_set_id) callSet...

def runGetInfo(self, request): """ Returns information about the service including protocol version. """ return protocol.toJson(protocol.GetInfoResponse( protocol_version=protocol.version))

def runAddAnnouncement(self, flaskrequest): """ Takes a flask request from the frontend and attempts to parse into an AnnouncePeerRequest. If successful, it will log the announcement to the `announcement` table with some other metadata gathered from the request. """ ...

def runListPeers(self, request): """ Takes a ListPeersRequest and returns a ListPeersResponse using a page_token and page_size if provided. """ return self.runSearchRequest( request, protocol.ListPeersRequest, protocol.ListPeersResponse, ...

def runGetVariant(self, id_): """ Returns a variant with the given id """ compoundId = datamodel.VariantCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) variantSet = dataset.getVariantSet(compoundId.variant_set_id) gaVaria...

def runGetBiosample(self, id_): """ Runs a getBiosample request for the specified ID. """ compoundId = datamodel.BiosampleCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) biosample = dataset.getBiosample(id_) return self.r...

def runGetIndividual(self, id_): """ Runs a getIndividual request for the specified ID. """ compoundId = datamodel.BiosampleCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) individual = dataset.getIndividual(id_) return se...

def runGetFeature(self, id_): """ Returns JSON string of the feature object corresponding to the feature compoundID passed in. """ compoundId = datamodel.FeatureCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) featureSet =...

def runGetReadGroupSet(self, id_): """ Returns a readGroupSet with the given id_ """ compoundId = datamodel.ReadGroupSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) readGroupSet = dataset.getReadGroupSet(id_) return se...

def runGetReadGroup(self, id_): """ Returns a read group with the given id_ """ compoundId = datamodel.ReadGroupCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) readGroupSet = dataset.getReadGroupSet(compoundId.read_group_set_id) ...

def runGetReference(self, id_): """ Runs a getReference request for the specified ID. """ compoundId = datamodel.ReferenceCompoundId.parse(id_) referenceSet = self.getDataRepository().getReferenceSet( compoundId.reference_set_id) reference = referenceSet.getRe...

def runGetReferenceSet(self, id_): """ Runs a getReferenceSet request for the specified ID. """ referenceSet = self.getDataRepository().getReferenceSet(id_) return self.runGetRequest(referenceSet)

def runGetVariantSet(self, id_): """ Runs a getVariantSet request for the specified ID. """ compoundId = datamodel.VariantSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) variantSet = dataset.getVariantSet(id_) return s...

def runGetFeatureSet(self, id_): """ Runs a getFeatureSet request for the specified ID. """ compoundId = datamodel.FeatureSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) featureSet = dataset.getFeatureSet(id_) return s...

def runGetContinuousSet(self, id_): """ Runs a getContinuousSet request for the specified ID. """ compoundId = datamodel.ContinuousSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) continuousSet = dataset.getContinuousSet(id_) ...

def runGetDataset(self, id_): """ Runs a getDataset request for the specified ID. """ dataset = self.getDataRepository().getDataset(id_) return self.runGetRequest(dataset)

def runGetVariantAnnotationSet(self, id_): """ Runs a getVariantSet request for the specified ID. """ compoundId = datamodel.VariantAnnotationSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) variantSet = dataset.getVariantSet(c...

def runGetRnaQuantification(self, id_): """ Runs a getRnaQuantification request for the specified ID. """ compoundId = datamodel.RnaQuantificationCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) rnaQuantificationSet = dataset.getR...

def runGetRnaQuantificationSet(self, id_): """ Runs a getRnaQuantificationSet request for the specified ID. """ compoundId = datamodel.RnaQuantificationSetCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) rnaQuantificationSet = dat...

def runGetExpressionLevel(self, id_): """ Runs a getExpressionLevel request for the specified ID. """ compoundId = datamodel.ExpressionLevelCompoundId.parse(id_) dataset = self.getDataRepository().getDataset(compoundId.dataset_id) rnaQuantificationSet = dataset.getRnaQuan...

def runSearchReadGroupSets(self, request): """ Runs the specified SearchReadGroupSetsRequest. """ return self.runSearchRequest( request, protocol.SearchReadGroupSetsRequest, protocol.SearchReadGroupSetsResponse, self.readGroupSetsGenerator)

def runSearchIndividuals(self, request): """ Runs the specified search SearchIndividualsRequest. """ return self.runSearchRequest( request, protocol.SearchIndividualsRequest, protocol.SearchIndividualsResponse, self.individualsGenerator)

def runSearchBiosamples(self, request): """ Runs the specified SearchBiosamplesRequest. """ return self.runSearchRequest( request, protocol.SearchBiosamplesRequest, protocol.SearchBiosamplesResponse, self.biosamplesGenerator)

def runSearchReads(self, request): """ Runs the specified SearchReadsRequest. """ return self.runSearchRequest( request, protocol.SearchReadsRequest, protocol.SearchReadsResponse, self.readsGenerator)

def runSearchReferenceSets(self, request): """ Runs the specified SearchReferenceSetsRequest. """ return self.runSearchRequest( request, protocol.SearchReferenceSetsRequest, protocol.SearchReferenceSetsResponse, self.referenceSetsGenerator)

def runSearchReferences(self, request): """ Runs the specified SearchReferenceRequest. """ return self.runSearchRequest( request, protocol.SearchReferencesRequest, protocol.SearchReferencesResponse, self.referencesGenerator)

def runSearchVariantSets(self, request): """ Runs the specified SearchVariantSetsRequest. """ return self.runSearchRequest( request, protocol.SearchVariantSetsRequest, protocol.SearchVariantSetsResponse, self.variantSetsGenerator)

def runSearchVariantAnnotationSets(self, request): """ Runs the specified SearchVariantAnnotationSetsRequest. """ return self.runSearchRequest( request, protocol.SearchVariantAnnotationSetsRequest, protocol.SearchVariantAnnotationSetsResponse, self.var...

def runSearchVariants(self, request): """ Runs the specified SearchVariantRequest. """ return self.runSearchRequest( request, protocol.SearchVariantsRequest, protocol.SearchVariantsResponse, self.variantsGenerator)

def runSearchVariantAnnotations(self, request): """ Runs the specified SearchVariantAnnotationsRequest. """ return self.runSearchRequest( request, protocol.SearchVariantAnnotationsRequest, protocol.SearchVariantAnnotationsResponse, self.variantAnnotati...

def runSearchCallSets(self, request): """ Runs the specified SearchCallSetsRequest. """ return self.runSearchRequest( request, protocol.SearchCallSetsRequest, protocol.SearchCallSetsResponse, self.callSetsGenerator)

def runSearchDatasets(self, request): """ Runs the specified SearchDatasetsRequest. """ return self.runSearchRequest( request, protocol.SearchDatasetsRequest, protocol.SearchDatasetsResponse, self.datasetsGenerator)

def runSearchFeatureSets(self, request): """ Returns a SearchFeatureSetsResponse for the specified SearchFeatureSetsRequest object. """ return self.runSearchRequest( request, protocol.SearchFeatureSetsRequest, protocol.SearchFeatureSetsResponse, ...

def runSearchFeatures(self, request): """ Returns a SearchFeaturesResponse for the specified SearchFeaturesRequest object. :param request: JSON string representing searchFeaturesRequest :return: JSON string representing searchFeatureResponse """ return self.runSe...