pybiocfilecache package

Subpackages

• pybiocfilecache.db package
  • Submodules
  • pybiocfilecache.db.db_config module
    • Metadata
      • Metadata.key
      • Metadata.value
    • Resource
      • Resource.access_time
      • Resource.create_time
      • Resource.etag
      • Resource.expires
      • Resource.fpath
      • Resource.id
      • Resource.last_modified_time
      • Resource.rid
      • Resource.rname
      • Resource.rpath
      • Resource.rtype
    • add_metadata()
    • create_schema()
  • Module contents

Submodules

pybiocfilecache.BiocFileCache module

Python Implementation of BiocFileCache.

class pybiocfilecache.BiocFileCache.BiocFileCache(cacheDirOrPath: str | Path = '/tmp/tmp1m9194ak')

Bases: object

Class to manage and cache files.

add(rname: str, fpath: str | Path, rtype: Literal['local', 'web', 'relative'] = 'local', action: Literal['copy', 'move', 'asis'] = 'copy', ext: bool = False) → Resource

Add a resource from the provided fpath to cache as rname.

Parameters:

• rname – Name of the resource to add to cache.

• fpath – Location of the resource.

• rtype – One of local, web, or relative. Defaults to local.

• action – Either copy, move or asis. Defaults to copy.

• ext – Whether to use filepath extension when storing in cache. Defaults to False.

Raises:

• NoFpathError – When the fpath does not exist.

• RnameExistsError – When the rname already exists in the cache. sqlalchemy exceptions: When something is up with the cache.

Returns:

Database record of the new resource in cache.

get(rname: str) → Resource | None

Get resource by name from cache.

Parameters:

rname – Name of the file to search.

Returns:

Matched Resource from cache if exists.

purge()

Remove all files from cache.

query(query: str, field: str = 'rname') → List[Resource]

Search cache for a resource.

Parameters:

• query – Query string or keywords to search.

• field – Field to search. Defaults to “rname”.

Returns:

List of matching resources from cache.

remove(rname: str) → None

Remove a resource from cache by name.

Parameters:

rname – Name of the resource to remove.

update(rname: str, fpath: str | Path, action: Literal['copy', 'move', 'asis'] = 'copy') → Resource

Update a resource in cache.

Parameters:

• rname – Name of the resource in cache.

• fpath – New resource to replace existing file in cache.

• action –

  Either copy, move or asis.

  Defaults to copy.

Returns:

Updated resource record in cache.

pybiocfilecache.const module

pybiocfilecache.utils module

pybiocfilecache.utils.copy_or_move(source: str | Path, target: str | Path, rname: str, action: Literal['copy', 'move', 'asis'] = 'copy') → None

Copy or move a resource from source to target.

Parameters:

• source – Source location of the resource to copy of move.

• target – Destination to copy of move to.

• rname – Name of resource to add to cache.

• action – Copy of move file from source. Defaults to copy.

Raises:

• ValueError – If action is not copy, move or asis.

• Exception – Error storing resource in the cache directory.

pybiocfilecache.utils.create_tmp_dir() → str

Create a temporary directory.

Returns:

Temporary path to the directory.

pybiocfilecache.utils.generate_id() → str

Generate uuid.

Returns:

Unique string for use as id.

pybiocfilecache.utils.setup_logging(loglevel)

Setup basic logging.

Parameters:

loglevel (int) – minimum loglevel for emitting messages

Module contents