diff options
| -rw-r--r-- | tests/uploader/phenotypes/test_edit_bulk_upload.py | 67 | ||||
| -rw-r--r-- | uploader/publications/__init__.py | 1 | ||||
| -rw-r--r-- | uploader/publications/misc.py | 10 |
3 files changed, 78 insertions, 0 deletions
diff --git a/tests/uploader/phenotypes/test_edit_bulk_upload.py b/tests/uploader/phenotypes/test_edit_bulk_upload.py new file mode 100644 index 0000000..7a52941 --- /dev/null +++ b/tests/uploader/phenotypes/test_edit_bulk_upload.py @@ -0,0 +1,67 @@ +"""Tests for functions used for bulk editing.""" +import pytest + +from uploader.publications.misc import publications_differences + + +@pytest.mark.unit_test +@pytest.mark.parametrize( + "filedata,dbdata,pubmed2pubidmap,expected", + (((), (), {}, tuple()), # no data + + # Same Data + (({"phenotype_id": 1, "xref_id": 10001, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10002, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10003, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10005, "PubMed_ID": 9999999999999}), + ({"PhenotypeId": 1, "xref_id": 10001, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10002, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10003, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": 15, + "PubMed_ID": 9999999999999}), + {9999999999999: 15}, + tuple()), + + # Differences: no new pubmeds (all pubmeds in db) + (({"phenotype_id": 1, "xref_id": 10001, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10002, "PubMed_ID": 9999999999998}, + {"phenotype_id": 1, "xref_id": 10003, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10004, "PubMed_ID": 9999999999997}), + ({"PhenotypeId": 1, "xref_id": 10001, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10002, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10003, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": 15, + "PubMed_ID": None}), + {9999999999999: 15, 9999999999998: 18, 9999999999997: 12}, + ({"PhenotypeId": 1, "xref_id": 10002, "PublicationId": 18, + "PubMed_ID": 9999999999998}, + {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": 12, + "PubMed_ID": 9999999999997})), + + # Differences: Deletions of pubmeds + (({"phenotype_id": 1, "xref_id": 10001, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10002, "PubMed_ID": None}, + {"phenotype_id": 1, "xref_id": 10003, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10004, "PubMed_ID": None}), + ({"PhenotypeId": 1, "xref_id": 10001, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10002, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10003, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": 15, + "PubMed_ID": 9999999999999}), + {9999999999999: 15, 9999999999998: 18, 9999999999997: 12}, + ({"PhenotypeId": 1, "xref_id": 10002, "PublicationId": None, + "PubMed_ID": None}, + {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": None, + "PubMed_ID": None})))) +def test_publications_differences(filedata, dbdata, pubmed2pubidmap, expected): + assert publications_differences( + filedata, dbdata, pubmed2pubidmap) == expected diff --git a/uploader/publications/__init__.py b/uploader/publications/__init__.py new file mode 100644 index 0000000..57c0cbb --- /dev/null +++ b/uploader/publications/__init__.py @@ -0,0 +1 @@ +"""Package for handling publications.""" diff --git a/uploader/publications/misc.py b/uploader/publications/misc.py new file mode 100644 index 0000000..d93ecdd --- /dev/null +++ b/uploader/publications/misc.py @@ -0,0 +1,10 @@ +"""Miscellaneous functions dealing with publications.""" + + +def publications_differences( + filedata: tuple[dict, ...], + dbdata: tuple[dict, ...], + pubmedid2pubidmap: dict[str, int] +) -> tuple[dict, ...]: + """Compute the differences between file data and db data""" + return tuple() |