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[FDS-2238, FDS-2236] Automate CLI test plan #1528

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merged 25 commits into from
Nov 14, 2024
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e8fb516
added new configs for CLI tests
andrewelamb Oct 30, 2024
2c2da77
added new manifests for testing CLI commands
andrewelamb Oct 30, 2024
d9a7bae
automate manual CLI tests
andrewelamb Oct 30, 2024
40837ab
ran black
andrewelamb Oct 30, 2024
d1cbc04
temp commit
andrewelamb Nov 4, 2024
d6e99f3
Merge branch 'develop' into FDS-2238-automate-cli-tests
andrewelamb Nov 4, 2024
dd00932
Merge branch 'develop' into FDS-2238-automate-cli-tests
andrewelamb Nov 7, 2024
318171e
manual test files now being saved in manifests folder
andrewelamb Nov 7, 2024
4e1d5b1
manual test files now being saved in manifests folder
andrewelamb Nov 7, 2024
07e0c75
remove lines to delete json files that were under git control
andrewelamb Nov 7, 2024
de4ed61
ran black
andrewelamb Nov 7, 2024
5a19b12
add try finally blocks to remove created files
andrewelamb Nov 7, 2024
1cd1b5a
ran black
andrewelamb Nov 7, 2024
26e8a99
add lines to remove created json files
andrewelamb Nov 7, 2024
35d440b
add lines to remove created json files
andrewelamb Nov 7, 2024
6c3d0ce
add code in finally blocks to reset config to default values, when te…
andrewelamb Nov 8, 2024
34bd8de
complete submit manifest command test
andrewelamb Nov 8, 2024
fbc1298
ran black
andrewelamb Nov 8, 2024
3099be3
Merge branch 'develop' into FDS-2238-automate-cli-tests
andrewelamb Nov 12, 2024
ec896e6
add todos for removing config resets
andrewelamb Nov 13, 2024
8655b8d
temp reduce tests
andrewelamb Nov 13, 2024
4050e71
restore tests
andrewelamb Nov 13, 2024
a610955
uncomment tests
andrewelamb Nov 13, 2024
819aeb4
redid how files are deleted, manual tests values are set
andrewelamb Nov 13, 2024
b275c68
ran black
andrewelamb Nov 13, 2024
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3 changes: 3 additions & 0 deletions tests/data/mock_manifests/CLI_tests/CLI_biospecimen.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
Sample ID,Patient ID,Tissue Status,Component,Id,entityId
123,123,Malignant,Biospecimen,3e413bde-0571-458c-ad93-d56c2b25fadd,syn61260197
456,456,Healthy,Biospecimen,fc314afe-5714-4b58-8c95-3dfd78dc827d,syn61260197
11 changes: 11 additions & 0 deletions tests/data/mock_manifests/CLI_tests/CLI_patient_invalid.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
Patient ID,Sex,Year of Birth,Diagnosis,Component,Cancer Type,Family History
1,Female,,Healthy,Patient,Random,Random
2,Female,,Healthy,Patient,Breast,"Colorectal,Breast"
3,Female,,Healthy,Patient,Breast,"Colorectal,Breast"
4,Female,,Healthy,Patient,Breast,"Colorectal,Breast"
5,Female,,Healthy,Patient,Breast,"Colorectal,Breast"
6,Female,,Healthy,Patient,Breast,"Colorectal,Breast"
7,Female,,Healthy,Patient,Breast,"Colorectal,Breast"
8,Female,,Healthy,Patient,Breast,"Colorectal,Breast"
9,Female,,Healthy,Patient,Breast,"Colorectal,Breast"
10,Female,,Healthy,Patient,Breast,"Colorectal,Breast"
8 changes: 8 additions & 0 deletions tests/data/test_configs/CLI_test_config.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
# This config is used to change the fileview for certain CLI tests
asset_store:
synapse:
config: "../../../.synapseConfig"
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master_fileview_id: 'syn63923487'

google_sheets:
service_acct_creds: "../../../schematic_service_account_creds.json"
12 changes: 12 additions & 0 deletions tests/data/test_configs/CLI_test_config2.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
# This config is used to change the fileview for certain CLI tests
asset_store:
synapse:
config: "../../../.synapseConfig"
master_fileview_id: 'syn51707141'

manifest:
data_type:
- "MockComponent"

google_sheets:
service_acct_creds: "../../../schematic_service_account_creds.json"
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