academic_observatory_workflows.pubmed_telescope.tests.test_pubmed_telescope

Module Contents

Classes

TestPubMedTelescope	Tests for the Pubmed telescope
TestPubMedUtils

Functions

query_table(→ List[Dict])

Query a BigQuery table, sorting the results and returning results as a list of dicts.

Attributes

FIXTURES_FOLDER

academic_observatory_workflows.pubmed_telescope.tests.test_pubmed_telescope.FIXTURES_FOLDER

academic_observatory_workflows.pubmed_telescope.tests.test_pubmed_telescope.query_table(table_id: str, select_columns: str, order_by_field: str) → List[Dict]

Query a BigQuery table, sorting the results and returning results as a list of dicts.

Parameters:

• table_id – the table id.

• select_columns – Columns to pull from the table.

• order_by_field – what field or fields to order by.

Returns:

the table rows.

class academic_observatory_workflows.pubmed_telescope.tests.test_pubmed_telescope.TestPubMedTelescope(*args, **kwargs)

Bases: observatory.platform.observatory_environment.ObservatoryTestCase

Tests for the Pubmed telescope

test_dag_structure()

Test PubMed DAG structure.

test_dag_load()

Test that the PubMed DAG can be loaded from a DAG bag.

test_telescope()

Test the PubMed Telescope end to end

class academic_observatory_workflows.pubmed_telescope.tests.test_pubmed_telescope.TestPubMedUtils(*args, **kwargs)

Bases: observatory.platform.observatory_environment.ObservatoryTestCase

test_download_datafiles()

Test that an exmaple PubMed XMLs can be transformed successfully.

test_load_datafile()

Test that a Pubmed datafile can be read in and parsed.

test_save_pubmed_jsonl()

Test that data can be saved from to a json.gz or a .jsonl file correctly.

test_save_pubmed_merged_upserts()

Test if records can be reliably pulled from transformed files and written to file.

test_parse_articles()

Test if PubmedArticle records (upserts) can be pulled out from a data dictionary.

test_parse_deletes()

Test if DeleteCiation records (deletes) can be pulled out from a data dictionary.

test_transform_pubmed()

Test that exmaple PubMed XMLs can be transformed successfully.

test_merge_upserts_and_deletes()

test_add_attributes()

Test that attributes from the Biopython data classes can be reliably pulled out and added to the dictionary.

test_change_pubmed_list_structure()

Test that the data in *list fields can be moved up one level to the parent field.

test_PubMedCustomEncoder()

Test that files are written out as expected using the CustomEncoder for PubMed-like files.