PyOpenWorm package¶
PyOpenWorm¶
OpenWorm Unified Data Abstract Layer.
An introduction to PyOpenWorm can be found in the README on our Github page.
Most statements correspond to some action on the database.
Some of these actions may be complex, but intuitively a.B()
, the Query form,
will query against the database for the value or values that are related to a
through B
;
on the other hand, a.B(c)
, the Update form, will add a statement to the database that a
relates to c
through B
. For the Update form, a Statement object describing the
relationship stated is returned as a side-effect of the update.
The Update form can also be accessed through the set() method of a Property and the Query form through the get() method like:
a.B.set(c)
and:
a.B.get()
The get() method also allows for parameterizing the query in ways specific to the Property.
-
PyOpenWorm.
loadData
(conf, data='OpenWormData/WormData.n3', dataFormat='n3', skipIfNewer=False)[source]¶ Load data into the underlying database of this library.
XXX: This is only guaranteed to work with the ZODB database.
Parameters: - data – (Optional) Specify the file to load into the library
- dataFormat – (Optional) Specify the file format to load into the library. Currently n3 is supported
- skipIfNewer – (Optional) Skips loading of data if the database file is newer than the data to be loaded in. This is determined by the modified time on the main database file compared to the modified time on the data file.
-
PyOpenWorm.
connect
(configFile=False, conf=None, do_logging=False, data=False, dataFormat='n3')[source]¶ Load desired configuration and open the database
Parameters: - configFile – (Optional) The configuration file for PyOpenWorm
- conf – (Optional) a configuration object for the connection. Takes precedence over configFile
- do_logging – (Optional) If true, turn on debug level logging
- data – (Optional) specify the file to load into the library
- dataFormat – (Optional) file format of data. Currently n3 is supported
Subpackages¶
- PyOpenWorm.data_trans package
- Submodules
- PyOpenWorm.data_trans.bibtex module
- PyOpenWorm.data_trans.common_data module
- PyOpenWorm.data_trans.connections module
- PyOpenWorm.data_trans.context_datasource module
- PyOpenWorm.data_trans.context_merge module
- PyOpenWorm.data_trans.csv_ds module
- PyOpenWorm.data_trans.data_with_evidence_ds module
- PyOpenWorm.data_trans.excel_ds module
- PyOpenWorm.data_trans.file_ds module
- PyOpenWorm.data_trans.http_ds module
- PyOpenWorm.data_trans.local_file_ds module
- PyOpenWorm.data_trans.neuron_data module
- PyOpenWorm.data_trans.wormatlas module
- PyOpenWorm.data_trans.wormbase module
- Submodules
Submodules¶
- PyOpenWorm.bibtex module
- PyOpenWorm.bibtex_customizations module
- PyOpenWorm.biology module
- PyOpenWorm.bittorrent module
- PyOpenWorm.capabilities module
- PyOpenWorm.capability module
- PyOpenWorm.cell module
- PyOpenWorm.cell_common module
- PyOpenWorm.channel module
- PyOpenWorm.channel_common module
- PyOpenWorm.channelworm module
- PyOpenWorm.cli module
- PyOpenWorm.cli_command_wrapper module
- PyOpenWorm.cli_common module
- PyOpenWorm.cli_hints module
- PyOpenWorm.collections module
- PyOpenWorm.command module
- PyOpenWorm.command_util module
- PyOpenWorm.configure module
- PyOpenWorm.connection module
- PyOpenWorm.context module
- PyOpenWorm.contextDataObject module
- PyOpenWorm.context_common module
- PyOpenWorm.context_store module
- PyOpenWorm.contextualize module
- PyOpenWorm.data module
- PyOpenWorm.dataObject module
- PyOpenWorm.datasource module
- PyOpenWorm.datasource_loader module
- PyOpenWorm.document module
- PyOpenWorm.documentContext module
- PyOpenWorm.evidence module
- PyOpenWorm.experiment module
- PyOpenWorm.git_repo module
- PyOpenWorm.identifier_mixin module
- PyOpenWorm.import_contextualizer module
- PyOpenWorm.import_override module
- PyOpenWorm.inverse_property module
- PyOpenWorm.mapper module
- PyOpenWorm.module_recorder module
- PyOpenWorm.muscle module
- PyOpenWorm.my_neuroml module
- PyOpenWorm.network module
- PyOpenWorm.neuron module
- PyOpenWorm.pProperty module
- PyOpenWorm.package_utils module
- PyOpenWorm.plot module
- PyOpenWorm.rdf_go_modifiers module
- PyOpenWorm.rdf_query_util module
- PyOpenWorm.simpleProperty module
- PyOpenWorm.statement module
- PyOpenWorm.text_util module
- PyOpenWorm.utils module
- PyOpenWorm.website module
- PyOpenWorm.worm module
- PyOpenWorm.worm_common module