BiomarkerBenchmark_GSE63885
Status: Complete
Testing Directory . . .
Results: PASS
Testing Configuration File . . .
✅ config.yaml contains all necessary configurations.
✅ Title is less than 300 characters
✅ description.md contains a description.
Results: PASS
Running Install . . .
Executing install.sh: Success
Results: PASS
Testing file paths:
✅ test_data.tsv exists.
✅ test_metadata.tsv exists.
✅ download.sh exists.
✅ install.sh exists.
✅ parse.sh exists.
✅ cleanup.sh exists.
✅ description.md exists.
✅ config.yaml exists.
Running user code . . .
Executing download.sh: Success
Executing parse.sh: Success
✅ data.tsv.gz was created and zipped correctly.
✅ metadata.tsv.gz was created and zipped correctly.
Results: PASS
Testing Key Files:
✅ test_data.tsv contains enough unique samples to test
✅ test_data.tsv contains enough test cases (8; min: 8)
✅ test_metadata.tsv contains enough unique samples to test
✅ test_metadata.tsv contains enough test cases (10; min: 8)
Results: PASS
First 5 columns and 5 rows of data.tsv.gz:
| Sample | ENSG00000000003 | ENSG00000000005 | ENSG00000000419 | ENSG00000000457 |
|---|---|---|---|---|
| GSM1559299 | 1.58190624764706 | -0.15402261125 | 2.48422321444444 | 0.4192952234375 |
| GSM1559300 | 2.13530725882353 | -0.04666310125 | 3.01121228 | 0.2587855653125 |
| GSM1559301 | 2.08582202823529 | -0.21383749125 | 2.52594365 | 0.459416181875 |
| GSM1559302 | 2.26551759352941 | -0.08622420625 | 2.42361450666667 | 0.4584177853125 |
Columns: 20025 Rows: 93
“data.tsv.gz” Test Cases (from rows in test file). . .
✅ First column of file is titled “Sample”
✅ Row 1: Success
✅ Row 2: Success
✅ Row 3: Success
✅ Row 4: Success
✅ Row 5: Success
✅ Row 6: Success
✅ Row 7: Success
✅ Row 8: Success
Results: PASS
First 3 columns and 5 rows of metadata.tsv.gz:
| Sample | Variable | Value |
|---|---|---|
| GSM1559299 | adjuwant_chemotherapy | platinum/cyclophosphamide |
| GSM1559299 | brca1_mutation | no mutation |
| GSM1559299 | clinical_status_at_last_follow-up_awd_-_alive_with_disease;dod-_dead_from_disease;ned-_no_evidence_of_disease | DOD |
| GSM1559299 | clinical_status_post_1st_line_chemotherapy_cr_-_complete_response;pr-_partial_response;sd-_stable_disease;p-_progression | P |
Columns: 3 Rows: 931
“metadata.tsv.gz” Test Cases (from rows in test file). . .
✅ First column of file is titled “Sample”
✅ Row 1: Success
✅ Row 2: Success
✅ Row 3: Success
✅ Row 4: Success
✅ Row 5: Success
✅ Row 6: Success
✅ Row 7: Success
✅ Row 8: Success
✅ Row 9: Success
✅ Row 10: Success
Results: PASS
Comparing samples in both files . . .
✅ Samples are the same in both “data.tsv.gz” & “metadata.tsv.gz”