epivizfileserver.handler package

Submodules

epivizfileserver.handler.HandlerNoActor module

class epivizfileserver.handler.HandlerNoActor.FileHandlerProcess(fileTime, MAXWORKER, client=None)

Bases: object

Class to manage query, transformation and cache using dask distributed

Parameters:

• fileTime (int) – time to keep file objects in memory
• MAXWORKER (int) – maximum workers that can be used

records

a dictionary of all file objects

client

asynchronous dask server client

binFileData(fileName, data, chr, start, end, bins, columns, metadata)

submit tasks to the dask client

cleanFileOBJ()

automated task to pickle all fileobjects to disk

getRecord(name)

get file object from records by name

Parameters:name (str) – file name Returns:file object

handleFile(fileName, fileType, chr, start, end, bins=2000)

submit tasks to the dask client

Parameters:

• fileName – file location
• fileType – file type
• chr – chromosome
• start – genomic start
• end – genomic end
• points – number of base-pairse to group per bin

handleSearch(fileName, fileType, query, maxResults)

submit tasks to the dask client

Parameters:

• fileName – file location
• fileType – file type
• chr – chromosome
• start – genomic start
• end – genomic end

pickleFileObject(fileName)

automated task to load a pickled file object

Parameters:fileName – file name to load

setRecord(name, fileObj, fileType)

add or update records with new file object

Parameters:

• name (str) – file name
• fileObj – file object
• fileType – file type

epivizfileserver.handler.handler module

class epivizfileserver.handler.handler.FileHandlerProcess(fileTime, MAXWORKER, client=None)

Bases: object

Class to manage query, transformation and cache using dask distributed

Parameters:

• fileTime (int) – time to keep file objects in memory
• MAXWORKER (int) – maximum workers that can be used

records

a dictionary of all file objects

client

asynchronous dask server client

binFileData(fileName, fileType, data, chr, start, end, bins, columns, metadata)

submit tasks to the dask client

cleanFileOBJ()

automated task to pickle all fileobjects to disk

getRecord(name)

get file object from records by name

Parameters:name (str) – file name Returns:file object

get_file_object(fileName, fileType)

handleFile(fileName, fileType, chr, start, end, bins=2000)

submit tasks to the dask client

Parameters:

• fileName – file location
• fileType – file type
• chr – chromosome
• start – genomic start
• end – genomic end
• points – number of base-pairse to group per bin

handleSearch(fileName, fileType, query, maxResults)

submit tasks to the dask client

Parameters:

• fileName – file location
• fileType – file type
• chr – chromosome
• start – genomic start
• end – genomic end

pickleFileObject(fileName)

automated task to load a pickled file object

Parameters:fileName – file name to load

setRecord(name, fileObj, fileType)

add or update records with new file object

Parameters:

• name (str) – file name
• fileObj – file object
• fileType – file type

epivizfileserver.handler.handler.bin_rows(data, chr, start, end, columns=None, metadata=None, bins=400)

epivizfileserver.handler.utils module

epivizfileserver.handler.utils.create_parser_object(format, source)

Create appropriate File class based on file format

Parameters:

• format – Type of file
• request – Other request parameters

Returns:

An instance of parser class

Module contents