BiomarkerBenchmark_GSE2109_Ovary
Status: Complete
Testing Directory . . .
Results: PASS
Testing Configuration File . . .
✅ config.yaml contains all necessary configurations.
✅ Title is less than 100 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 (8; min: 8)
Results: PASS
First 5 columns and 5 rows of data.tsv.gz:
| Sample | ENSG00000000003 | ENSG00000000005 | ENSG00000000419 | ENSG00000000457 |
|---|---|---|---|---|
| GSM38071 | 2.68516924882353 | -0.24817909 | 2.63589104777778 | 0.3856919240625 |
| GSM38088 | 2.03102289647059 | -0.1970764175 | 2.74216320444444 | 0.4001315015625 |
| GSM46815 | 1.70166555235294 | -0.1766490275 | 2.81732544111111 | 0.691595185 |
| GSM46830 | 1.99339338882353 | -0.14836305 | 2.24644423 | 0.317661369375 |
Columns: 20025 Rows: 154
“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 |
|---|---|---|
| GSM38071 | Alcohol_Consumption | Yes |
| GSM38071 | Days_from_Patient_Diagnosis_to_Excision | 11 |
| GSM38071 | Ethnic_Background | Caucasian |
| GSM38071 | Family_History_of_Cancer | Yes |
Columns: 3 Rows: 2211
“metadata.tsv.gz” Test Cases (from rows in test file). . .
✅ First column of file is titled “Sample”
⚠ The value for variable "Primary_Site" for all samples is the same ("Ovary"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "Ethnic_Background" for all samples is the same ("Caucasian"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "Grade" for all samples is the same ("1"). This variable has been removed from metadata.tsv.gz
✅ 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
Comparing samples in both files . . .
✅ Samples are the same in both “data.tsv.gz” & “metadata.tsv.gz”