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Fix gh workflow #1

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Merged
bedroesb merged 9 commits into from
Sep 18, 2025
Merged

Fix gh workflow #1

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9f38fbb
update paths in workflow file
kdp-cloud Sep 17, 2025
d56ec44
Do sparse-checkout for the test data
kdp-cloud Sep 17, 2025
479af37
Change checkout version
kdp-cloud Sep 17, 2025
2b4c4c2
Correct repo format
kdp-cloud Sep 17, 2025
8bf5651
update cache dependency path
kdp-cloud Sep 17, 2025
32311fb
one more try...
kdp-cloud Sep 17, 2025
873a627
one more try...
kdp-cloud Sep 17, 2025
ff1b0a5
Add MARS repo as submodule for test data
kdp-cloud Sep 18, 2025
a952888
Remove ls
kdp-cloud Sep 18, 2025
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10 changes: 5 additions & 5 deletions .github/workflows/test-mars.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ name: Test MARS
on:
push:
paths:
- "mars-cli/**"
- "mars_lib/**"
pull_request:
paths:
- "mars-cli/**"
- "mars_lib/**"
branches:
- main
workflow_dispatch:
Expand All @@ -17,11 +17,11 @@ jobs:
os: [ubuntu-latest, windows-latest]
python-version: ["3.9", "3.13"]
runs-on: ${{ matrix.os }}
env:
working-directory: ./mars-cli

steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v5
with:
submodules: 'recursive'
- name: Set up Python
uses: actions/setup-python@v5
with:
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3 changes: 3 additions & 0 deletions .gitmodules
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
[submodule "MARS"]
path = MARS
url = https://github.com/elixir-europe/MARS.git
1 change: 1 addition & 0 deletions MARS
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Submodule MARS added at ed9752
2 changes: 1 addition & 1 deletion tests/test_biosample_external_references.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ def test_load_json_file():


def test_handle_input_dict():
input = "../test-data/ISA-BH2023-ALL/isa-bh2023-all.json"
input = "MARS/test-data/ISA-BH2023-ALL/isa-bh2023-all.json"
assert handle_input_dict(input)

not_a_json = "./tests/fixtures/bad_json.json"
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2 changes: 1 addition & 1 deletion tests/test_ftp_upload.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ def test_upload_success():
uploader = FTPUploader("webin2.ebi.ac.uk", creds["username"], creds["password"])
uploader.upload(
[
Path("../test-data/ENA_TEST2.R1.fastq.gz"),
Path("MARS/test-data/ENA_TEST2.R1.fastq.gz"),
Path("./tests/fixtures/not_a_json_file.txt"),
]
)
68 changes: 34 additions & 34 deletions tests/test_isa_json.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,13 +27,13 @@
def test_load_isa_json():
# Should test the validation process of the ISA JSON file where root level = investigation.
valid_isa_json01 = load_isa_json(
"../test-data/ISA-BH2023-ALL/isa-bh2023-all.json", True
"MARS/test-data/ISA-BH2023-ALL/isa-bh2023-all.json", True
)
assert len(valid_isa_json01.investigation.studies) == 1
assert valid_isa_json01.investigation.studies[0].identifier == "BH2023"

# Should test the validation process of the ISA JSON file where root has 'investigation' as key.
valid_isa_json02 = load_isa_json("../test-data/biosamples-input-isa.json", False)
valid_isa_json02 = load_isa_json("MARS/test-data/biosamples-input-isa.json", False)
assert len(valid_isa_json02.investigation.studies) == 1
assert valid_isa_json02.investigation.studies[0].title == "Arabidopsis thaliana"

Expand All @@ -43,7 +43,7 @@ def test_load_isa_json():

def test_reduce_isa_json_for_target_repo():
good_isa_json = load_isa_json(
"../test-data/ISA-BH2023-ALL/isa-bh2023-all.json", True
"MARS/test-data/ISA-BH2023-ALL/isa-bh2023-all.json", True
)

filtered_isa_json = reduce_isa_json_for_target_repo(
Expand All @@ -60,7 +60,7 @@ def test_reduce_isa_json_for_target_repo():

def test_reduce_isa_json_for_biosamples():
good_isa_json = load_isa_json(
"../test-data/ISA-BH2023-ALL/isa-bh2023-all.json", True
"MARS/test-data/ISA-BH2023-ALL/isa-bh2023-all.json", True
)

filtered_isa_json = reduce_isa_json_for_target_repo(
Expand Down Expand Up @@ -180,7 +180,7 @@ def test_person_phone_nr_validator():

def test_update_study_materials_no_accession_categories():
# This file has no characteristics for accessions
json_path = "../test-data/biosamples-original-isa-no-accesion-char.json"
json_path = "MARS/test-data/biosamples-original-isa-no-accesion-char.json"
with open(json_path) as json_file:
json_data = json.load(json_file)

Expand Down Expand Up @@ -214,7 +214,7 @@ def test_update_study_materials_no_accession_categories():

def test_update_study_materials_with_accession_categories():
# This file has no characteristics for accessions
json_path = "../test-data/biosamples-original-isa.json"
json_path = "MARS/test-data/biosamples-original-isa.json"
with open(json_path) as json_file:
json_data = json.load(json_file)

Expand Down Expand Up @@ -308,45 +308,45 @@ def test_filename_validation():

def test_map_data_files_to_repositories():
isa_json = load_isa_json(
file_path="../test-data/ISA-BH2024-ALL/isa-bh2024-all.json",
file_path="MARS/test-data/ISA-BH2024-ALL/isa-bh2024-all.json",
investigation_is_root=True,
)
exact_match_files = [
"../test-data/ISA-BH2024-ALL/cnv-seq-data-0.fastq",
"../test-data/ISA-BH2024-ALL/cnv-seq-data-1.fastq",
"../test-data/ISA-BH2024-ALL/cnv-seq-data-2.fastq",
"../test-data/ISA-BH2024-ALL/cnv-seq-data-3.fastq",
"../test-data/ISA-BH2024-ALL/metpro-analysis.txt",
"../test-data/ISA-BH2024-ALL/ms-data-metpro--1.mzml",
"../test-data/ISA-BH2024-ALL/ms-data-metpro--2.mzml",
"../test-data/ISA-BH2024-ALL/ms-data-metpro--3.mzml",
"../test-data/ISA-BH2024-ALL/ms-data-metpro--4.mzml",
"../test-data/ISA-BH2024-ALL/rna-seq-data-0.fastq",
"../test-data/ISA-BH2024-ALL/rna-seq-data-1.fastq",
"../test-data/ISA-BH2024-ALL/rna-seq-data-2.fastq",
"../test-data/ISA-BH2024-ALL/rna-seq-data-3.fastq",
"MARS/test-data/ISA-BH2024-ALL/cnv-seq-data-0.fastq",
"MARS/test-data/ISA-BH2024-ALL/cnv-seq-data-1.fastq",
"MARS/test-data/ISA-BH2024-ALL/cnv-seq-data-2.fastq",
"MARS/test-data/ISA-BH2024-ALL/cnv-seq-data-3.fastq",
"MARS/test-data/ISA-BH2024-ALL/metpro-analysis.txt",
"MARS/test-data/ISA-BH2024-ALL/ms-data-metpro--1.mzml",
"MARS/test-data/ISA-BH2024-ALL/ms-data-metpro--2.mzml",
"MARS/test-data/ISA-BH2024-ALL/ms-data-metpro--3.mzml",
"MARS/test-data/ISA-BH2024-ALL/ms-data-metpro--4.mzml",
"MARS/test-data/ISA-BH2024-ALL/rna-seq-data-0.fastq",
"MARS/test-data/ISA-BH2024-ALL/rna-seq-data-1.fastq",
"MARS/test-data/ISA-BH2024-ALL/rna-seq-data-2.fastq",
"MARS/test-data/ISA-BH2024-ALL/rna-seq-data-3.fastq",
]

check_map = dict(
{
"metabolights": [
"../test-data/ISA-BH2024-ALL/metpro-analysis.txt",
"../test-data/ISA-BH2024-ALL/ms-data-metpro--1.mzml",
"../test-data/ISA-BH2024-ALL/ms-data-metpro--2.mzml",
"../test-data/ISA-BH2024-ALL/ms-data-metpro--3.mzml",
"../test-data/ISA-BH2024-ALL/ms-data-metpro--4.mzml",
"MARS/test-data/ISA-BH2024-ALL/metpro-analysis.txt",
"MARS/test-data/ISA-BH2024-ALL/ms-data-metpro--1.mzml",
"MARS/test-data/ISA-BH2024-ALL/ms-data-metpro--2.mzml",
"MARS/test-data/ISA-BH2024-ALL/ms-data-metpro--3.mzml",
"MARS/test-data/ISA-BH2024-ALL/ms-data-metpro--4.mzml",
],
"arrayexpress": [
"../test-data/ISA-BH2024-ALL/rna-seq-data-0.fastq",
"../test-data/ISA-BH2024-ALL/rna-seq-data-1.fastq",
"../test-data/ISA-BH2024-ALL/rna-seq-data-2.fastq",
"../test-data/ISA-BH2024-ALL/rna-seq-data-3.fastq",
"MARS/test-data/ISA-BH2024-ALL/rna-seq-data-0.fastq",
"MARS/test-data/ISA-BH2024-ALL/rna-seq-data-1.fastq",
"MARS/test-data/ISA-BH2024-ALL/rna-seq-data-2.fastq",
"MARS/test-data/ISA-BH2024-ALL/rna-seq-data-3.fastq",
],
"eva": [
"../test-data/ISA-BH2024-ALL/cnv-seq-data-0.fastq",
"../test-data/ISA-BH2024-ALL/cnv-seq-data-1.fastq",
"../test-data/ISA-BH2024-ALL/cnv-seq-data-2.fastq",
"../test-data/ISA-BH2024-ALL/cnv-seq-data-3.fastq",
"MARS/test-data/ISA-BH2024-ALL/cnv-seq-data-0.fastq",
"MARS/test-data/ISA-BH2024-ALL/cnv-seq-data-1.fastq",
"MARS/test-data/ISA-BH2024-ALL/cnv-seq-data-2.fastq",
"MARS/test-data/ISA-BH2024-ALL/cnv-seq-data-3.fastq",
],
}
)
Expand All @@ -361,7 +361,7 @@ def test_map_data_files_to_repositories():
map_data_files_to_repositories(not_enough_files, isa_json)

too_many_files = exact_match_files.copy()
one_too_many = "../test-data/ISA-BH2024-ALL/one-too-many.fastq"
one_too_many = "MARS/test-data/ISA-BH2024-ALL/one-too-many.fastq"
too_many_files.append(one_too_many)

result_maps = map_data_files_to_repositories(too_many_files, isa_json)
Expand Down
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