Python File.annotations方法代码示例

# 需要导入模块: from synapseclient import File [as 别名]
# 或者: from synapseclient.File import annotations [as 别名]
def upload(args,syn):
	if args.dataType == "rnaseq":
		parentId = "syn6034916"
		pipeline = "syn6126122"
		dataType = "RNASeq"
	elif args.dataType == "dnaseq":
		parentId = "syn6034751"
		pipeline = "syn6126123"
		dataType = "TargDNASeq"
	elif args.dataType == "snparray":
		parentId = "syn6038475"
		pipeline = "syn6126121"
		dataType = "SNParray"
	elif args.dataType == "exparray":
		parentId = "syn6038915"
		pipeline = "syn6126120"
		dataType = "expression_microarray"
	elif args.dataType == "exome":
		parentId = "syn6115597"
		dataType = "exome"
		pipeline = ""
	else:
		raise ValueError("dataType needs to be rnaseq/dnaseq/snparray/exparray/exome")
	if args.workflow is not None:
		workflow = syn.get(pipeline,downloadFile=False)
		workflow.path = args.workflow
		workflow.name = os.path.basename(args.workflow)
		workflow = syn.store(workflow)
		pipeline = workflow.id
	fileEnt = File(args.input,parent=parentId)
	fileEnt.annotations = temp.to_dict('index').values()[0]
	fileEnt.dataType = dataType
	fileEnt.sampleId = sampleId
	fileEnt = syn.store(fileEnt,used = pipeline)
	return(fileEnt.id)

# 需要导入模块: from synapseclient import File [as 别名]
# 或者: from synapseclient.File import annotations [as 别名]
def _copyFile(syn, entity, destinationId, version=None, updateExisting=False, setProvenance="traceback",
              skipCopyAnnotations=False):
    """
    Copies most recent version of a file to a specified synapse ID.

    :param entity:              A synapse ID of a File entity

    :param destinationId:       Synapse ID of a folder/project that the file wants to be copied to

    :param version:             Can specify version of a file. 
                                Default to None

    :param updateExisting:      Can choose to update files that have the same name 
                                Default to False
    
    :param setProvenance:       Has three values to set the provenance of the copied entity:
                                    traceback: Sets to the source entity
                                    existing: Sets to source entity's original provenance (if it exists)
                                    None: No provenance is set
    :param skipCopyAnnotations: Skips copying the annotations
                                Default is False
    """
    ent = syn.get(entity, downloadFile=False, version=version, followLink=False)
    # CHECK: If File is in the same parent directory (throw an error) (Can choose to update files)
    if not updateExisting:
        existingEntity = syn.findEntityId(ent.name, parent=destinationId)
        if existingEntity is not None:
            raise ValueError('An entity named "%s" already exists in this location. File could not be copied'
                             % ent.name)
    profile = syn.getUserProfile()
    # get provenance earlier to prevent errors from being called in the end
    # If traceback, set activity to old entity
    if setProvenance == "traceback":
        act = Activity("Copied file", used=ent)
    # if existing, check if provenance exists
    elif setProvenance == "existing":
        try:
            act = syn.getProvenance(ent.id)
        except SynapseHTTPError as e:
            if e.response.status_code == 404:
                act = None
            else:
                raise e
    elif setProvenance is None or setProvenance.lower() == 'none':
        act = None
    else:
        raise ValueError('setProvenance must be one of None, existing, or traceback')
    # Grab entity bundle
    bundle = syn._getEntityBundle(ent.id, version=ent.versionNumber, bitFlags=0x800 | 0x1)
    fileHandle = synapseclient.utils.find_data_file_handle(bundle)
    createdBy = fileHandle['createdBy']
    # CHECK: If the user created the file, copy the file by using fileHandleId else copy the fileHandle
    if profile.ownerId == createdBy:
        newdataFileHandleId = ent.dataFileHandleId
    else:
        copiedFileHandle = copyFileHandles(syn, [fileHandle], ["FileEntity"], [bundle['entity']['id']],
                                           [fileHandle['contentType']], [fileHandle['fileName']])
        # Check if failurecodes exist
        copyResult = copiedFileHandle['copyResults'][0]
        if copyResult.get("failureCode") is not None:
            raise ValueError("%s dataFileHandleId: %s" % (copyResult["failureCode"],
                                                          copyResult['originalFileHandleId']))
        newdataFileHandleId = copyResult['newFileHandle']['id']

    new_ent = File(dataFileHandleId=newdataFileHandleId,  name=ent.name, parentId=destinationId)
    # Set annotations here
    if not skipCopyAnnotations:
        new_ent.annotations = ent.annotations
    # Store provenance if act is not None
    if act is not None:
        new_ent = syn.store(new_ent, activity=act)
    else:
        new_ent = syn.store(new_ent)
    # Leave this return statement for test
    return new_ent['id']

# 需要导入模块: from synapseclient import File [as 别名]
# 或者: from synapseclient.File import annotations [as 别名]
def _copyFile(syn, entity, destinationId, version=None, update=False, setProvenance="traceback"):
    """
    Copies most recent version of a file to a specified synapse ID.

    :param entity:          A synapse ID of a File entity

    :param destinationId:   Synapse ID of a folder/project that the file wants to be copied to

    :param version:         Can specify version of a file. 
                            Default to None

    :param update:          Can choose to update files that have the same name 
                            Default to False
    
    :param setProvenance:   Has three values to set the provenance of the copied entity:
                                traceback: Sets to the source entity
                                existing: Sets to source entity's original provenance (if it exists)
                                None: No provenance is set
    """
    ent = syn.get(entity, downloadFile=False, version=version, followLink=False)
    #CHECK: If File is in the same parent directory (throw an error) (Can choose to update files)
    if not update:
        search = syn.query('select name from entity where parentId =="%s"'%destinationId)
        for i in search['results']:
            if i['entity.name'] == ent.name:
                raise ValueError('An item named "%s" already exists in this location. File could not be copied'%ent.name)
    profile = syn.getUserProfile()
    # get provenance earlier to prevent errors from being called in the end
    # If traceback, set activity to old entity
    if setProvenance == "traceback":
        act = Activity("Copied file", used=ent)
    # if existing, check if provenance exists
    elif setProvenance == "existing":
        try:
            act = syn.getProvenance(ent.id)
        except SynapseHTTPError as e:
            # Should catch the 404
            act = None
    elif setProvenance is None or setProvenance.lower() == 'none':
        act = None
    else:
        raise ValueError('setProvenance must be one of None, existing, or traceback')
    #Grab file handle createdBy annotation to see the user that created fileHandle
    fileHandleList = syn.restGET('/entity/%s/version/%s/filehandles'%(ent.id,ent.versionNumber))
    #NOTE: May not always be the first index (need to filter to make sure not PreviewFileHandle)
    #Loop through to check which dataFileHandles match and return createdBy
    # Look at convenience function
    for fileHandle in fileHandleList['list']:
        if fileHandle['id'] == ent.dataFileHandleId:
            createdBy = fileHandle['createdBy']
            break
    else:
        createdBy = None
    #CHECK: If the user created the file, copy the file by using fileHandleId else hard copy
    if profile.ownerId == createdBy:
        new_ent = File(name=ent.name, parentId=destinationId)
        new_ent.dataFileHandleId = ent.dataFileHandleId
    else:
        #CHECK: If the synapse entity is an external URL, change path and store
        if ent.externalURL is None: #and ent.path == None:
            #####If you have never downloaded the file before, the path is None
            store = True
            #This needs to be here, because if the file has never been downloaded before
            #there wont be a ent.path
            ent = syn.get(entity,downloadFile=store,version=version)
            path = ent.path
        else:
            store = False
            ent = syn.get(entity,downloadFile=store,version=version)
            path = ent.externalURL

        new_ent = File(path, name=ent.name, parentId=destinationId, synapseStore=store)
    #Set annotations here
    new_ent.annotations = ent.annotations
    #Store provenance if act is not None
    if act is not None:
        new_ent = syn.store(new_ent, activity=act)
    else:
        new_ent = syn.store(new_ent)
    #Leave this return statement for test
    return new_ent['id']