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Resolve missing germplasm cvterms in automated testing environment #2288

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Merged
merged 5 commits into from
Sep 22, 2025
Merged

Resolve missing germplasm cvterms in automated testing environment #2288

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47a1c82
Update PBO details to match those used in extension modules.
laceysanderson Sep 16, 2025
4ecd60a
Add missing germplasm terms to the test chado SQL file.
laceysanderson Sep 16, 2025
c78491b
Revert URLs to old onces based on @dsenalik comment indicating the ne…
laceysanderson Sep 22, 2025
e042e1f
Merge remote-tracking branch 'origin/4.x' into tv4g9-2287-missingGerm…
laceysanderson Sep 22, 2025
92d8f01
Obo importer test now checks num changed in mviews
dsenalik Sep 22, 2025
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2 changes: 1 addition & 1 deletion tripal_chado/config/install/tripal.tripal_content_terms.chado_content_terms.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -988,7 +988,7 @@ vocabularies:
url: 'https://agroportal.lirmm.fr/ontologies/PBO'
idSpaces:
- name: 'PBO'
description: 'Plant Breeding Ontology'
description: 'Plant Breeding Ontology (PBO): an ontology for the plant breeding community which captures more than 2200 entries where 80 represent the core terms.'
urlPrefix: 'https://agroportal.lirmm.fr/ontologies/PBO/PBO_{accession}'
terms:
- id: 'PBO:0000065'
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18 changes: 14 additions & 4 deletions tripal_chado/tests/fixtures/fill_chado_test_prepare.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,7 @@ INSERT INTO chado.cv VALUES (29, 'sep', 'A structured controlled vocabulary for
INSERT INTO chado.cv VALUES (30, 'SIO', 'The Semanticscience Integrated Ontology (SIO) provides a simple, integrated ontology of types and relations for rich description of objects, processes and their attributes.');
INSERT INTO chado.cv VALUES (31, 'cellular_component', NULL);
INSERT INTO chado.cv VALUES (32, 'synonym_type', NULL);
INSERT INTO chado.cv VALUES (33, 'PBO', 'Plant Breeding Ontology');
INSERT INTO chado.db VALUES (19, 'UO', 'Units of Measurement Ontology', 'http://purl.obolibrary.org/obo/UO_{accession}', 'http://purl.obolibrary.org/obo/uo');
INSERT INTO chado.db VALUES (2, 'CO_010', 'Crop Germplasm Ontology', 'http://www.cropontology.org/terms/CO_010:{accession}', 'http://www.cropontology.org/get-ontology/CO_010');
INSERT INTO chado.db VALUES (11, 'OBCS', 'Ontology of Biological and Clinical Statistics', 'http://purl.obolibrary.org/obo/{db}_{accession}', 'https://github.com/obcs/obcs');
Expand Down Expand Up @@ -163,6 +164,7 @@ INSERT INTO chado.db VALUES (35, 'BS', '', NULL, '');
INSERT INTO chado.db VALUES (36, 'RNAMOD', '', NULL, '');
INSERT INTO chado.db VALUES (37, 'MOD', '', NULL, '');
INSERT INTO chado.db VALUES (38, 'wikipedia', '', NULL, '');
INSERT INTO chado.db VALUES (41, 'PBO', 'Plant Breeding Ontology (PBO): an ontology for the plant breeding community which captures more than 2200 entries where 80 represent the core terms.', 'https://agroportal.lirmm.fr/ontologies/PBO/PBO_{accession}', 'https://agroportal.lirmm.fr/ontologies/PBO');
INSERT INTO chado.dbxref VALUES (1, 1, 'local:null', '', NULL);
INSERT INTO chado.dbxref VALUES (2, 1, 'chado_properties:version', '', NULL);
INSERT INTO chado.dbxref VALUES (3, 2, '0000044', '', NULL);
Expand Down Expand Up @@ -3652,6 +3654,10 @@ INSERT INTO chado.dbxref VALUES (3486, 15, 'lineageex', '', NULL);
INSERT INTO chado.dbxref VALUES (3487, 20, 'C16493', '', NULL);
INSERT INTO chado.dbxref VALUES (3488, 31, '001377', '', NULL);
INSERT INTO chado.dbxref VALUES (3489, 4, '1122', '', NULL);
INSERT INTO chado.dbxref VALUES (3490, 8, '0007059', '', NULL);
INSERT INTO chado.dbxref VALUES (3491, 8, '0005136', '', NULL);
INSERT INTO chado.dbxref VALUES (3492, 12, '0002076', '', NULL);
INSERT INTO chado.dbxref VALUES (3493, 41, '0000065', '', NULL);
INSERT INTO chado.cvterm VALUES (1, 1, 'null', NULL, 1, 0, 0);
INSERT INTO chado.cvterm VALUES (2, 4, 'version', 'Chado schema version', 2, 0, 0);
INSERT INTO chado.cvterm VALUES (3, 5, 'accession', '', 3, 0, 0);
Expand Down Expand Up @@ -6834,6 +6840,10 @@ INSERT INTO chado.cvterm VALUES (3179, 2, 'lineageex', '', 3486, 0, 0);
INSERT INTO chado.cvterm VALUES (3180, 19, 'Data Source', 'The person or authoritative body who provided the information.', 3487, 0, 0);
INSERT INTO chado.cvterm VALUES (3181, 30, 'versioned dataset', 'a versioned dataset is a dataset with a particular release date or release number.', 3488, 0, 0);
INSERT INTO chado.cvterm VALUES (3182, 7, 'Phylogenetic tree type', 'Phylogenetic tree type | A label (text token) describing the type of a phylogenetic tree. [http://edamontology.org]', 3489, 0, 0);
INSERT INTO chado.cvterm VALUES (3183, 8, 'germplasm', 'Germplasm is the living genetic resources such as seeds or tissue that is maintained for the purpose of animal and plant breeding, preservation, and other research uses. These resources may take the form of seed collections stored in seed banks, trees growing in nurseries, animal breeding lines maintained in animal breeding programs or gene banks, etc. Germplasm collections can range from collections of wild species to elite, domesticated breeding lines that have undergone extensive human selection.', 3490, 0, 0);
INSERT INTO chado.cvterm VALUES (3184, 8, 'cultivar', 'A cultivated plant variety selected and given a name because it has desirable characteristics that distinguish it from otherwise similar plants of the same species.', 3491, 0, 0);
INSERT INTO chado.cvterm VALUES (3185, 12, 'collection of specimens', 'A material entity that has two or more specimens as its parts.', 3492, 0, 0);
INSERT INTO chado.cvterm VALUES (3186, 33, 'progeny', '', 3493, 0, 0);
INSERT INTO chado.contact VALUES (1, NULL, 'null', 'null');
INSERT INTO chado.pub VALUES (1, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'null', 'null', 1, false, NULL, NULL);
INSERT INTO chado.chadoprop VALUES (1, 2, '1.3', 0);
Expand Down Expand Up @@ -16525,12 +16535,12 @@ INSERT INTO chado.db2cv_mview VALUES (29, 'sep', 30, 'sep', 2);
INSERT INTO chado.db2cv_mview VALUES (32, 'synonym_type', 33, 'synonym_type', 4);
SELECT pg_catalog.setval('chado.chadoprop_chadoprop_id_seq', 1, true);
SELECT pg_catalog.setval('chado.contact_contact_id_seq', 1, true);
SELECT pg_catalog.setval('chado.cv_cv_id_seq', 32, true);
SELECT pg_catalog.setval('chado.cvterm_cvterm_id_seq', 3182, true);
SELECT pg_catalog.setval('chado.cv_cv_id_seq', 33, true);
SELECT pg_catalog.setval('chado.cvterm_cvterm_id_seq', 3186, true);
SELECT pg_catalog.setval('chado.cvterm_dbxref_cvterm_dbxref_id_seq', 308, true);
SELECT pg_catalog.setval('chado.cvterm_relationship_cvterm_relationship_id_seq', 3435, true);
SELECT pg_catalog.setval('chado.cvtermprop_cvtermprop_id_seq', 1346, true);
SELECT pg_catalog.setval('chado.cvtermsynonym_cvtermsynonym_id_seq', 4559, true);
SELECT pg_catalog.setval('chado.db_db_id_seq', 40, true);
SELECT pg_catalog.setval('chado.dbxref_dbxref_id_seq', 3489, true);
SELECT pg_catalog.setval('chado.db_db_id_seq', 41, true);
SELECT pg_catalog.setval('chado.dbxref_dbxref_id_seq', 3493, true);
SELECT pg_catalog.setval('chado.pub_pub_id_seq', 1, true);
8 changes: 4 additions & 4 deletions tripal_chado/tests/src/Kernel/Plugin/TripalImporter/OboImporter-TestInfo.yml
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Expand Up @@ -7,8 +7,8 @@ scenarios:
name: 'TO'
path: '{tripal_chado}/tests/fixtures/obo_loader/test_to.obo'
expect_message: 'a lookup will be performed with the EBI Ontology Lookup Service'
expect_db2cv_count: 31
expect_cv_root_count: 10
expect_db2cv_count: 3
expect_cv_root_count: 1
expect:
- table: 'db'
column: 'name'
Expand Down Expand Up @@ -51,8 +51,8 @@ scenarios:
tripal_cv_obo:
name: 'EDAM'
path: '{tripal_chado}/tests/fixtures/obo_loader/test_EDAM.obo'
expect_db2cv_count: 31
expect_cv_root_count: 9
expect_db2cv_count: 3
expect_cv_root_count: 0
expect:
- table: 'cvterm'
column: 'name'
Expand Down
21 changes: 12 additions & 9 deletions tripal_chado/tests/src/Kernel/Plugin/TripalImporter/OboImporterTest.php
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Expand Up @@ -308,19 +308,22 @@ public function testOboImporter(int $current_scenario_key, string $current_scena
$this->assertEquals($expected_count, $count, 'Did not create a ' . $expect['table'] . '.' . $expect['column'] . ' record with the expected value');
}

$db_query = $this->chado_connection->select('1:db2cv_mview', 't');
$db_query->fields('t', ['cv_id', 'cvname', 'db_id', 'dbname', 'num_terms']);
$db_initial_count = $db_query->countQuery()->execute()->fetchField();
$cv_query = $this->chado_connection->select('1:cv_root_mview', 't');
$cv_query->fields('t', ['name', 'cvterm_id', 'cv_id', 'name']);
$cv_initial_count = $cv_query->countQuery()->execute()->fetchField();

// Postrun of the obo importer populates materialized views.
$obo_importer->postRun();

// Test that the materialized views have been populated.
$query = $this->chado_connection->select('1:db2cv_mview', 't');
$query->fields('t', ['cv_id', 'cvname', 'db_id', 'dbname', 'num_terms']);
$count = $query->countQuery()->execute()->fetchField();
$this->assertEquals($current_scenario['expect_db2cv_count'], $count, 'Expected number of records in db2cv_mview not found');

$query = $this->chado_connection->select('1:cv_root_mview', 't');
$query->fields('t', ['name', 'cvterm_id', 'cv_id', 'name']);
$count = $query->countQuery()->execute()->fetchField();
$this->assertEquals($current_scenario['expect_cv_root_count'], $count, 'Expected number of records in cv_root_mview not found');
$db_num_added = $db_query->countQuery()->execute()->fetchField() - $db_initial_count;
$this->assertEquals($current_scenario['expect_db2cv_count'], $db_num_added, 'Expected number of records in db2cv_mview not found');

$cv_num_added = $cv_query->countQuery()->execute()->fetchField() - $cv_initial_count;
$this->assertEquals($current_scenario['expect_cv_root_count'], $cv_num_added, 'Expected number of records in cv_root_mview not found');

}

Expand Down