epivizfileserver.handler package

Submodules

epivizfileserver.handler.HandlerNoActor module

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

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)[source]

submit tasks to the dask client

cleanFileOBJ()[source]

automated task to pickle all fileobjects to disk

getRecord(name)[source]

get file object from records by name

Parameters:name (str) – file name
Returns:file object
handleFile(fileName, fileType, chr, start, end, bins=2000)[source]

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)[source]

submit tasks to the dask client

Parameters:
  • fileName – file location
  • fileType – file type
  • chr – chromosome
  • start – genomic start
  • end – genomic end
pickleFileObject(fileName)[source]

automated task to load a pickled file object

Parameters:fileName – file name to load
setRecord(name, fileObj, fileType)[source]

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)[source]

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)[source]

submit tasks to the dask client

cleanFileOBJ()[source]

automated task to pickle all fileobjects to disk

getRecord(name)[source]

get file object from records by name

Parameters:name (str) – file name
Returns:file object
get_file_object(fileName, fileType)[source]
handleFile(fileName, fileType, chr, start, end, bins=2000)[source]

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)[source]

submit tasks to the dask client

Parameters:
  • fileName – file location
  • fileType – file type
  • chr – chromosome
  • start – genomic start
  • end – genomic end
pickleFileObject(fileName)[source]

automated task to load a pickled file object

Parameters:fileName – file name to load
setRecord(name, fileObj, fileType)[source]

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)[source]

epivizfileserver.handler.utils module

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