agatha.construct.test_semrep_util module¶

agatha.construct.test_semrep_util.test_extract_entitites_and_predicates_with_dask()¶

agatha.construct.test_semrep_util.test_get_all_paths()¶: Tests that getting semrep paths gets all needed paths

agatha.construct.test_semrep_util.test_get_metamap_paths()¶: Tests that getting semrep paths gets all needed paths

agatha.construct.test_semrep_util.test_get_semrep_paths_fails()¶: Tests that if you give semrep paths bad install locations, it fails

agatha.construct.test_semrep_util.test_metamap_server()¶: Tests that we can actually run metamap

agatha.construct.test_semrep_util.test_parse_semrep_end_to_end_difficult()¶

agatha.construct.test_semrep_util.test_semrep_fails_with_bad_sentence()¶: We ran into a problem with the following abstract:

https://pubmed.ncbi.nlm.nih.gov/3624238/

Specifically, the component that includes a list of names:

(Samanta, H., Engel, D. A., Chao, H. M., Thakur, A., Garcia-Blanco, M. A., and Lengyel, P. (1986) J. Biol. Chem. 261, 11849-11858).

Was split into these sentences:

1: (Samanta, H., Engel, D. 2: A., Chao, H. …

The sentence A., Chao, H. causes an error due to an unforseen exception within semrep.

This problematic abstract is represented here and processed in the same way as in the typical dask pipeline.

agatha.construct.test_semrep_util.test_semrep_id_to_agatha_sentence_id_weird_id()¶

agatha.construct.test_semrep_util.test_semrep_paths()¶: Tests that if we just need the semrep paths, we can get those

agatha.construct.test_semrep_util.test_semrep_xml_to_records()¶: Ensures that parsing xml files happens without error

agatha.construct.test_semrep_util.test_sentence_to_semrep_input_filter_newline()¶

agatha.construct.test_semrep_util.test_sentence_to_semrep_input_filter_single_quote()¶

agatha.construct.test_semrep_util.test_sentence_to_semrep_input_filter_unicode()¶