Python store_entity Examples

Example #1

File: run_info.py Project: hshujia/bcbio-nextgen

def _add_provenance(items, dirs, config):
    p = programs.write_versions(dirs, config)
    versioncheck.testall(items)
    p_db = diagnostics.initialize(dirs)
    out = []
    for item in items:
        entity_id = diagnostics.store_entity(item)
        item["config"]["resources"]["program_versions"] = p
        item["provenance"] = {"programs": p, "entity": entity_id, "db": p_db}
        out.append([item])
    return out

Example #2

File: main.py Project: hlkfoz/bcbio-nextgen

def _add_provenance(items, dirs, parallel, config):
    p = programs.write_versions(dirs, config, is_wrapper=parallel.get("wrapper") is not None)
    p_db = diagnostics.initialize(dirs)
    system.write_info(dirs, parallel, config)
    out = []
    for item in items:
        entity_id = diagnostics.store_entity(item)
        item["config"]["resources"]["program_versions"] = p
        item["provenance"] = {"programs": p, "entity": entity_id, "db": p_db}
        out.append([item])
    return out

Example #3

File: run_info.py Project: tenxcloud/bcbio-nextgen

def _add_provenance(items, dirs, config):
    p = programs.write_versions(dirs, config=config)
    versioncheck.testall(items)
    p_db = diagnostics.initialize(dirs)
    out = []
    for item in items:
        entity_id = diagnostics.store_entity(item)
        item["config"]["resources"]["program_versions"] = p
        item["provenance"] = {"programs": p, "entity": entity_id,
                              "db": p_db}
        out.append([item])
    return out

Example #4

def _add_provenance(items, dirs, parallel, config):
    p = programs.write_versions(dirs,
                                config,
                                is_wrapper=parallel.get("wrapper") is not None)
    p_db = diagnostics.initialize(dirs)
    system.write_info(dirs, parallel, config)
    out = []
    for item in items:
        entity_id = diagnostics.store_entity(item)
        item["config"]["resources"]["program_versions"] = p
        item["provenance"] = {"programs": p, "entity": entity_id, "db": p_db}
        out.append([item])
    return out