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add original data and explanation
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@thanh-nguyen-dang
thanh-nguyen-dang committed Aug 29, 2024
1 parent 5e52c0a commit b676542
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1 change: 1 addition & 0 deletions tests/dataframe_tests/test_data/midrc/original_test_data/DataImportOrder.txt
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Expand Up @@ -8,3 +8,4 @@ ct_series_file
dx_series_file
mr_series_file
rf_series_file
annotation_file
174 changes: 174 additions & 0 deletions tests/dataframe_tests/test_data/midrc/original_test_data/annotation_file.json
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@@ -0,0 +1,174 @@
[
{
"cases": [
{
"submitter_id": "case_protesting_solely"
}
],
"core_metadata_collections": [],
"cr_series_files": [],
"ct_series_files": [
{
"submitter_id": "ct_series_file_exiling_fineness's"
}
],
"datasets": [],
"dx_series_files": [],
"imaging_studies": [
{
"submitter_id": "imaging_study_traffic's_Kaohsiung"
}
],
"mg_series_files": [],
"mr_series_files": [],
"nm_series_files": [],
"pt_series_files": [],
"rf_series_files": [],
"us_series_files": [],
"xa_series_files": [],
"type": "annotation_file",
"submitter_id": "A_Kp7X9r_1.2.827.1.3",
"annotation_name": "midrc_mdai_chestxr",
"data_category": "annotation_file",
"data_format": "JSON",
"data_type": "MIDRC Annotation",
"file_name": "annotation_file_773863174424.json",
"file_size": 702,
"md5sum": "5d33e550c40249120481045352342345",
"annotation_method": "Clinically_derived",
"case_ids": [
"Rimbaud's_sweltering",
"boobs_Yaroslavl"
],
"object_id": "dg.MD1R/0fc28986-0bb2-b12c-ad4c-a32a5d0201f9"
},
{
"cases": [
{
"submitter_id": "case_protesting_solely"
}
],
"core_metadata_collections": [],
"cr_series_files": [],
"ct_series_files": [
{
"submitter_id": "ct_series_file_exiling_fineness's"
}
],
"datasets": [],
"dx_series_files": [],
"imaging_studies": [
{
"submitter_id": "imaging_study_traffic's_Kaohsiung"
}
],
"mg_series_files": [],
"mr_series_files": [],
"nm_series_files": [],
"pt_series_files": [],
"rf_series_files": [],
"us_series_files": [],
"xa_series_files": [],
"type": "annotation_file",
"submitter_id": "A_Kp7X9r_1.2.827.1.2",
"annotation_name": "midrc_bpr_regions",
"data_category": "annotation_file",
"data_format": "JSON",
"data_type": "Other Annotation",
"file_name": "annotation_file_773863174425.json",
"file_size": 702,
"md5sum": "5d33e550c40249120481045352342543",
"annotation_method": "Retrospective_auto",
"case_ids": [
"Rimbaud's_sweltering",
"boobs_Yaroslavl"
],
"object_id": "dg.MD1R/0fc28986-0bb2-c12e-ad4c-a32a5d0201f9"
},
{
"cases": [
{
"submitter_id": "case_blessedly_heuristics"
}
],
"core_metadata_collections": [],
"cr_series_files": [],
"ct_series_files": [
{
"submitter_id": "ct_series_file_oiliest_distributions"
}
],
"datasets": [],
"dx_series_files": [],
"imaging_studies": [
{
"submitter_id": "imaging_study_sriracha_unsolicited"
}
],
"mg_series_files": [],
"mr_series_files": [],
"nm_series_files": [],
"pt_series_files": [],
"rf_series_files": [],
"us_series_files": [],
"xa_series_files": [],
"type": "annotation_file",
"submitter_id": "A_Kp7X9r_1.2.827.4.3",
"annotation_name": "midrc_lung_segs",
"data_category": "annotation_file",
"data_format": "JSON",
"data_type": "MIDRC Annotation",
"file_name": "annotation_file_773863174424.json",
"file_size": 702,
"md5sum": "5d33e550c40249120481045352342456",
"annotation_method": "Retrospective_expert",
"case_ids": [
"accusatives_Deon's",
"Purim's_Gary"
],
"object_id": "dg.MD1R/0fc28986-0bb2-d12f-ad4c-a32a5d0201f9"
},
{
"cases": [
{
"submitter_id": "case_blessedly_heuristics"
}
],
"core_metadata_collections": [],
"cr_series_files": [],
"ct_series_files": [
{
"submitter_id": "ct_series_file_oiliest_distributions"
}
],
"datasets": [],
"dx_series_files": [],
"imaging_studies": [
{
"submitter_id": "imaging_study_sriracha_unsolicited"
}
],
"mg_series_files": [],
"mr_series_files": [],
"nm_series_files": [],
"pt_series_files": [],
"rf_series_files": [],
"us_series_files": [],
"xa_series_files": [],
"type": "annotation_file",
"submitter_id": "A_Kp7X9r_1.2.827.6.7",
"annotation_name": "mRALE_Mastermind_Challenge",
"data_category": "annotation_file",
"data_format": "JSON",
"data_type": "Other Annotation",
"file_name": "annotation_file_773863174425.json",
"file_size": 702,
"md5sum": "5d33e550c40249120481045352342765",
"annotation_method": "Retrospective_general",
"case_ids": [
"accusatives_Deon's",
"Purim's_Gary"
],
"object_id": "dg.MD1R/0fc28986-0bb2-a12b-ad4c-a32a5d0201f9"
}
]
39 changes: 39 additions & 0 deletions tests/dataframe_tests/test_dataframe_injection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,45 @@ def test_flatten_nested_list(translator):
"edge_imagingstudyrelatedtocase", "edge_projectmemberofprogram",
])], indirect=True)
def test_nested_props_injection(translator):
"""
Tset to ensure that the nested dataframe has structure like below
data = [
{
"_data_file_id":"cfd912e8-f9e1-40cc-abd3-6dcb3a16e0b6",
"file_annotations":[
{
"annotation_method":"Retrospective_auto",
"annotation_name":"midrc_bpr_regions",
"_annotation_file_id":"0c7e701e-cb27-4cbf-a996-eaa9142b633f"
},
{
"annotation_method":"Clinically_derived",
"annotation_name":"midrc_mdai_chestxr",
"_annotation_file_id":
"f7648cd4-19cc-4e49-8100-f99b15e28e56"
}
]
},
{
"_data_file_id":"effe5932-2c26-4919-8544-0d4cb62d20f9",
"file_annotations":[
{
"annotation_method":"Retrospective_expert",
"annotation_name":"midrc_lung_segs",
"_annotation_file_id":"82bcca4b-cebc-4062-a614-7ef0072d152f"
},
{
"annotation_method":"Retrospective_general",
"annotation_name":"mRALE_Mastermind_Challenge",
"_annotation_file_id":"8c8558f4-aa4f-487f-b00a-ee4f14b871f6"
}
]
}
]
:param translator:
:return:
"""
[collected_leaf_df, final_df] = get_dataframes_from_names(
get_spark_session(translator.sc),
"midrc",
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