neo package¶
Submodules¶
neo.neo4j_tools module¶
-
class
vfb_connect.neo.neo4j_tools.
Neo4jConnect
(endpoint='http://pdb.virtualflybrain.org', usr='neo4j', pwd='vfb')[source]¶ Bases:
object
Thin layer over REST API to hold connection details, handle multi-statement POST queries, return results and report errors.
- Parameters
endpoint – a neo4j REST endpoint
usr – username (content ignored if credentials not rqd)
pwd – password (content ignored if credentials not rqd)
-
commit_list
(statements, return_graphs=False)[source]¶ Commit a list of statements to neo4J DB via REST API. Errors prompt warnings (STDERR), not exceptions, and cause return = FALSE.
- Param
statements: A list of cypher statements.
- Param
return_graphs: Optional. Boolean. Returns graphs under ‘graph’ key if True. Default: False
- Return
List of results or False if any errors are encountered.
-
commit_list_in_chunks
(statements, verbose=False, chunk_length=1000)[source]¶ Commit multiple (chunked) commit of statements to neo4J DB via REST API. Errors prompt warnings (STDOUT), not exceptions, and cause return = FALSE.
- Param
statements: A list of cypher statements.
- Param
verbose: Boolean. Optionally print periodic reports of progress to STDOUT
- Param
chunk_length. Int. Optional. Set chunk size. Default = 1000.
- Return
List of results or False if any errors are encountered. Chunking is not reflected in results.
-
get_lookup
(limit_by_prefix=None, include_individuals=False, limit_properties_by_prefix=('RO', 'BFO', 'VFBext'))[source]¶ Generate a name:ID lookup from a VFB neo4j DB, optionally restricted by a list of prefixes.
- Parameters
limit_by_prefix – Optional list of id prefixes for limiting lookup of classes & individuals
include_individuals – If True, individuals included in lookup.
limit_properties_by_prefix – Optional list of id prefixes for limiting lookup of properties.
-
vfb_connect.neo.neo4j_tools.
chunks
(l, n)[source]¶ Yield successive n-sized chunks from l.
- Parameters
l – a list
- Param
n, chunk size
-
vfb_connect.neo.neo4j_tools.
cli_credentials
()[source]¶ Parses command line credentials for Neo4J rest connection; Optionally specify additional args as a list of dicts with args required by argparse.add_argument(). Order in list specified arg order
neo.query_wrapper module¶
-
class
vfb_connect.neo.query_wrapper.
QueryWrapper
(*args, **kwargs)[source]¶ Bases:
vfb_connect.neo.neo4j_tools.Neo4jConnect
-
get_DataSet_TermInfo
(short_forms, summary=False)[source]¶ Generate JSON reports for types from a list of VFB IDs (short_forms) of DataSets.
- Parameters
short_forms – An iterable (e.g. a list) of VFB IDs (short_forms) of types
summary – Optional. Returns summary reports if True. Default False
- Return type
list of VFB_json or summary_report_json
-
get_TermInfo
(short_forms)[source]¶ Generate JSON report for terms specified by a list of IDs
- Parameters
short_forms (
iter
) – An iterable (e.g. a list) of VFB IDs (short_forms)db – optionally specify the VFB id (short_form) of external DB.
id_type – optionally specify an external id_type
- Returns
list of term metadata as VFB_json
-
get_anatomical_individual_TermInfo
(short_forms, summary=False)[source]¶ Generate JSON reports for anatomical individuals from a list of VFB IDs (short_forms)
- Parameters
short_forms – An iterable (e.g. a list) of VFB IDs (short_forms) of anatomical individuals
summary – Optional. Returns summary reports if True. Default False
- Return type
list of VFB_json or summary_report_json
-
get_datasets
(summary=False)[source]¶ Generate JSON report of all datsets.
- Parameters
summary – Optional. Returns summary reports if True. Default False
- Returns
Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
- Return type
list of VFB_json or summary_report_json
-
get_images
(short_forms, template, image_folder, image_type='swc', stomp=False)[source]¶ Given an iterable of short_forms for instances, find all images of specified image_type registered to template. Save these to image_folder along with a manifest.tsv. Return manifest as pandas DataFrame.
- Parameters
short_forms (
iter
) – iterable (e.g. list) of VFB IDs of Individuals with imagestemplate – template name
image_folder – folder to save image files & manifest to.
image_type – image type (file extension)
stomp – Overwrite image_folder if already exists.
- Returns
Manifest as Pandas DataFrame
-
get_images_by_filename
(filenames, dataset=None)[source]¶ Takes a list of filenames as input and returns a list of image terminfo. Optionally restrict by dataset (improves speed)
-
get_template_TermInfo
(short_forms)[source]¶ Generate JSON reports for types from a list of VFB IDs (short_forms) of templates.
- Parameters
short_forms – An iterable (e.g. a list) of VFB IDs (short_forms) of types
summary – Optional. Returns summary reports if True. Default False
- Return type
list of VFB_json or summary_report_json
-
get_templates
(summary=False)[source]¶ Generate JSON report of all available templates.
- Parameters
summary – Optional. Returns summary reports if True. Default False
- Returns
Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
- Return type
list of VFB_json or summary_report_json
-
get_terms_by_xref
(acc, db='', id_type='')[source]¶ Generate JSON report for terms specified by a list of IDs
- Parameters
short_forms – An iterable (e.g. a list) of VFB IDs (short_forms)
- Returns
list of term metadata as VFB_json
-
get_type_TermInfo
(short_forms, summary=False)[source]¶ Generate JSON reports for types from a list of VFB IDs (short_forms) of classes/types.
- Parameters
short_forms – An iterable (e.g. a list) of VFB IDs (short_forms) of types
summary – Optional. Returns summary reports if True. Default False
- Return type
list of VFB_json or summary_report_json
-
vfb_id_2_xrefs
(vfb_id, db='', id_type='', reverse_return=False)[source]¶ Map a list of short_form IDs in VFB to external DB IDs
- Parameters
vfb_id (
iter
) – An iterable (e.g. a list) of VFB short_form IDs.db – optional specify the VFB id (short_form) of an external DB to map to. (use get_dbs to find options)
id_type – optionally specify an external id_type
reverse_return – Boolean: Optional (see return)
- Returns
- if reverse_return is False:
dict { VFB_id : [{ db: <db> : acc : <acc> }
- Return if reverse_return is True:
dict { acc : [{ db: <db> : vfb_id : <VFB_id> }
-
xref_2_vfb_id
(acc=None, db='', id_type='', reverse_return=False)[source]¶ Map a list external DB IDs to VFB IDs
- Parameters
acc – An iterable (e.g. a list) of external IDs (e.g. neuprint bodyIDs).
db – optional specify the VFB id (short_form) of an external DB to map to. (use get_dbs to find options)
id_type – optionally specify an external id_type
reverse_return – Boolean: Optional (see return)
- Returns
- if reverse_return is False:
dict { acc : [{ db: <db> : vfb_id : <VFB_id> }
- Return if reverse_return is True:
dict { VFB_id : [{ db: <db> : acc : <acc> }
-