veoibd_synapse package

Subpackages

• veoibd_synapse.cli package
  • Submodules
  • veoibd_synapse.cli.config module
  • veoibd_synapse.cli.main module
  • veoibd_synapse.cli.pull module
  • veoibd_synapse.cli.push module
  • veoibd_synapse.cli.query module
  • veoibd_synapse.cli.syncdb module
  • Module contents
• veoibd_synapse.data package
  • Subpackages
    • veoibd_synapse.data.extract_subids package
      • Subpackages
        • veoibd_synapse.data.extract_subids.utils package
          • Submodules
          • veoibd_synapse.data.extract_subids.utils.bch module
          • Module contents
      • Submodules
      • veoibd_synapse.data.extract_subids.bch module
      • Module contents
    • veoibd_synapse.data.loaders package
      • Submodules
      • veoibd_synapse.data.loaders.vcf module
      • Module contents
    • veoibd_synapse.data.parsers package
      • Submodules
      • veoibd_synapse.data.parsers.GTF module
      • Module contents
    • veoibd_synapse.data.preprocessing package
      • Submodules
      • veoibd_synapse.data.preprocessing.variant_tables module
      • Module contents
  • Submodules
  • veoibd_synapse.data.asset_intake module
  • Module contents
• veoibd_synapse.rules package
  • Module contents
• veoibd_synapse.visualization package
  • Module contents

Submodules

veoibd_synapse.dag_tools module

Provide functions for working with our DAGs.

class veoibd_synapse.dag_tools.ProjectDAG(project_id, synapse_session)

Bases: networkx.classes.digraph.DiGraph

Class to generate and manage our project structure.

__init__(project_id, synapse_session)

Set up instance.

check_children(node_id, func)

Return list of child-ids where func returns True.

follow_path_to_folder(path, origin=None, create=False)

Return terminal folder’s synID after traversing the defined path.

class veoibd_synapse.dag_tools.SynNode(entity_dict, synapse_session=None, is_root=False)

Bases: munch.Munch

Provide methods and attributes to model an entity node in a DAG of Synapse Entities.

__eq__(other)

Return True if equal.

__hash__()

Return hash value.

__init__(entity_dict, synapse_session=None, is_root=False)

Initialize an entity node object.

__ne__(other)

Return True if NOT equal.

__str__()

Override this.

store()

If self.needs_update is True, run sys.store and reset needs_update.

veoibd_synapse.dag_tools.is_folder_named_x(child, name)

Return True if child is a folder named name.

veoibd_synapse.errors module

Provide error classes for veoibd-synapse-data-manager.

exception veoibd_synapse.errors.NoResult

Bases: veoibd_synapse.errors.VEOIBDSynapseError

Raise when an iteration has nothing to return, but normally would.

exception veoibd_synapse.errors.NotImplementedYet(msg=None)

Bases: NotImplementedError, veoibd_synapse.errors.VEOIBDSynapseError

Raise when a section of code that has been left for another time is asked to execute.

__init__(msg=None)

Set up the Exception.

exception veoibd_synapse.errors.VEOIBDSynapseError

Bases: Exception

Base error class for veoibd-synapse-data-manager.

exception veoibd_synapse.errors.ValidationError

Bases: veoibd_synapse.errors.VEOIBDSynapseError

Raise when a validation/sanity check comes back with unexpected value.

veoibd_synapse.interface module

Provide a representation of the interactions between a Synapse Project and other Synapse Entities.

class veoibd_synapse.interface.VEOProject(name=None, annotations=None, synapse_client=None, config_tree=None, **kwargs)

Bases: object

Manage a collection of Synapse Entities common to a single project.

__init__(name=None, annotations=None, synapse_client=None, config_tree=None, **kwargs)

Initialize an empty ProjectData object.

_build_remote_entity_dag()

Build a DAG of the remote project structure.

_get_project_entity()

Set self.project after retrieving the synapse object by name, create the Project if it does not exist.

_get_remote_entity_dicts()

Query Synapse for all entity information related to this Project ID.

_process_annotations(annotations)

Process annotation values.

_process_config_tree(config_tree)

Process configuration values.

veoibd_synapse.misc module

Provide misc common functions to the rest of the CLI.

veoibd_synapse.misc.chunk_md5(path, size=1024000)

Calculate and return the md5-hexdigest of a file in chunks of size.

veoibd_synapse.misc.load_csv(csv, **kwargs)

veoibd_synapse.misc.nan_to_str(x, replacement=None)

Return empty string if pd.isnull(x): replacement otherwise.

Parameters:

• x (unknown) – object to inspect
• replacement (None|str) – string to use as replacement (default: “”)

veoibd_synapse.misc.process_config(config=None)

Prepare single config file.

veoibd_synapse.misc.update_configs(directory, to_update=None)

Collect, combine, and return all *.yaml files in directory.

Module contents

Top-level package for veoibd_synapse.