diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..a3b761c --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,33 @@ +name: Test Collect Metadata Script + +on: + push: + branches: + - main + pull_request: + +jobs: + test: + runs-on: ubuntu-latest + strategy: + matrix: + include: + - series_id: GSE191067 + - series_id: GSE264508 + - series_id: GSE274955 + - series_id: GSE250130 + + steps: + - name: Checkout repository + uses: actions/checkout@v3 + + - name: Set up environment + run: | + sudo apt-get update + sudo apt-get install -y wget perl curl jq + + - name: Run metadata collection tests + run: | + chmod +x ./scripts/* + chmod +x ./tests/test_metadata.sh + ./tests/test_metadata.sh ${matrix.series_id} \ No newline at end of file diff --git a/test_data/GSE191067/GSE191067.accessions.tsv b/test_data/GSE191067/GSE191067.accessions.tsv new file mode 100644 index 0000000..de33c63 --- /dev/null +++ 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a/test_data/GSE191067/GSE191067.parsed.tsv b/test_data/GSE191067/GSE191067.parsed.tsv new file mode 100644 index 0000000..f7ac3de --- /dev/null +++ b/test_data/GSE191067/GSE191067.parsed.tsv @@ -0,0 +1,44 @@ +SRR17249654 Homo sapiens https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17249/SRR17249654/SRR17249654.lite.1 SRA +SRR17249655 Homo sapiens https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17249/SRR17249655/SRR17249655.lite.1 SRA +SRR17249656 Homo sapiens https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17249/SRR17249656/SRR17249656.lite.1 SRA +SRR17249657 Homo sapiens https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17249/SRR17249657/SRR17249657.lite.1 SRA +SRR17249658 Homo sapiens https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17249/SRR17249658/SRR17249658.lite.1 SRA +SRR17249659 Homo sapiens 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+https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17249/SRR17249691/SRR17249691.lite.1 +https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17249/SRR17249692/SRR17249692.lite.1 +https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17249/SRR17249693/SRR17249693.lite.1 +https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17249/SRR17249694/SRR17249694.lite.1 +https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17249/SRR17249695/SRR17249695.lite.1 +https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17249/SRR17249696/SRR17249696.lite.1 +https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17249/SRR17249697/SRR17249697.lite.1 diff --git a/test_data/GSE250130/GSE250130.accessions.tsv b/test_data/GSE250130/GSE250130.accessions.tsv new file mode 100644 index 0000000..5cba66c --- /dev/null +++ b/test_data/GSE250130/GSE250130.accessions.tsv @@ -0,0 +1,28 @@ +GSM7974277 SRS19844433 SRX22870939 SRR27190826 +GSM7974278 SRS19844434 SRX22870940 SRR27190825 +GSM7974279 SRS19844445 SRX22870951 SRR27190814 +GSM7974280 SRS19844454 SRX22870960 SRR27190805 +GSM7974281 SRS19844455 SRX22870961 SRR27190804 +GSM7974282 SRS19844456 SRX22870962 SRR27190803 +GSM7974283 SRS19844457 SRX22870963 SRR27190802 +GSM7974284 SRS19844458 SRX22870964 SRR27190801 +GSM7974285 SRS19844459 SRX22870965 SRR27190800 +GSM7974286 SRS19844460 SRX22870966 SRR27190799 +GSM7974287 SRS19844435 SRX22870941 SRR27190824 +GSM7974288 SRS19844436 SRX22870942 SRR27190823 +GSM7974289 SRS19844437 SRX22870943 SRR27190822 +GSM7974290 SRS19844438 SRX22870944 SRR27190821 +GSM7974291 SRS19844439 SRX22870945 SRR27190820 +GSM7974292 SRS19844440 SRX22870946 SRR27190819 +GSM7974293 SRS19844441 SRX22870947 SRR27190818 +GSM7974294 SRS19844442 SRX22870948 SRR27190817 +GSM7974295 SRS19844443 SRX22870949 SRR27190816 +GSM7974296 SRS19844444 SRX22870950 SRR27190815 +GSM7974297 SRS19844446 SRX22870952 SRR27190813 +GSM7974298 SRS19844447 SRX22870953 SRR27190812 +GSM7974299 SRS19844448 SRX22870954 SRR27190811 +GSM7974300 SRS19844449 SRX22870955 SRR27190810 +GSM7974301 SRS19844450 SRX22870956 SRR27190809 +GSM7974302 SRS19844451 SRX22870957 SRR27190808 +GSM7974303 SRS19844452 SRX22870958 SRR27190807 +GSM7974304 SRS19844453 SRX22870959 SRR27190806 diff --git a/test_data/GSE250130/GSE250130.parsed.tsv b/test_data/GSE250130/GSE250130.parsed.tsv new file mode 100644 index 0000000..188f269 --- /dev/null +++ b/test_data/GSE250130/GSE250130.parsed.tsv @@ -0,0 +1,28 @@ +SRR27190799 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/099/SRR27190799/SRR27190799_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/099/SRR27190799/SRR27190799_2.fastq.gz ENAFQ +SRR27190800 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/000/SRR27190800/SRR27190800_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/000/SRR27190800/SRR27190800_2.fastq.gz ENAFQ +SRR27190801 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/001/SRR27190801/SRR27190801_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/001/SRR27190801/SRR27190801_2.fastq.gz ENAFQ +SRR27190802 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/002/SRR27190802/SRR27190802_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/002/SRR27190802/SRR27190802_2.fastq.gz ENAFQ +SRR27190803 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/003/SRR27190803/SRR27190803_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/003/SRR27190803/SRR27190803_2.fastq.gz ENAFQ +SRR27190804 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/004/SRR27190804/SRR27190804_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/004/SRR27190804/SRR27190804_2.fastq.gz ENAFQ +SRR27190805 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/005/SRR27190805/SRR27190805_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/005/SRR27190805/SRR27190805_2.fastq.gz ENAFQ +SRR27190806 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/006/SRR27190806/SRR27190806_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/006/SRR27190806/SRR27190806_2.fastq.gz ENAFQ +SRR27190807 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/007/SRR27190807/SRR27190807_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/007/SRR27190807/SRR27190807_2.fastq.gz ENAFQ +SRR27190808 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/008/SRR27190808/SRR27190808_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/008/SRR27190808/SRR27190808_2.fastq.gz ENAFQ +SRR27190809 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/009/SRR27190809/SRR27190809_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/009/SRR27190809/SRR27190809_2.fastq.gz ENAFQ +SRR27190810 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/010/SRR27190810/SRR27190810_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/010/SRR27190810/SRR27190810_2.fastq.gz ENAFQ +SRR27190811 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/011/SRR27190811/SRR27190811_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/011/SRR27190811/SRR27190811_2.fastq.gz ENAFQ +SRR27190812 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/012/SRR27190812/SRR27190812_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/012/SRR27190812/SRR27190812_2.fastq.gz ENAFQ +SRR27190813 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/013/SRR27190813/SRR27190813_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/013/SRR27190813/SRR27190813_2.fastq.gz ENAFQ +SRR27190814 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/014/SRR27190814/SRR27190814_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/014/SRR27190814/SRR27190814_2.fastq.gz ENAFQ +SRR27190815 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/015/SRR27190815/SRR27190815_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/015/SRR27190815/SRR27190815_2.fastq.gz ENAFQ +SRR27190816 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/016/SRR27190816/SRR27190816_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/016/SRR27190816/SRR27190816_2.fastq.gz ENAFQ +SRR27190817 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/017/SRR27190817/SRR27190817_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/017/SRR27190817/SRR27190817_2.fastq.gz ENAFQ +SRR27190818 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/018/SRR27190818/SRR27190818_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/018/SRR27190818/SRR27190818_2.fastq.gz ENAFQ +SRR27190819 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/019/SRR27190819/SRR27190819_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/019/SRR27190819/SRR27190819_2.fastq.gz ENAFQ +SRR27190820 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/020/SRR27190820/SRR27190820_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/020/SRR27190820/SRR27190820_2.fastq.gz ENAFQ +SRR27190821 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/021/SRR27190821/SRR27190821_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/021/SRR27190821/SRR27190821_2.fastq.gz ENAFQ +SRR27190822 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/022/SRR27190822/SRR27190822_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/022/SRR27190822/SRR27190822_2.fastq.gz ENAFQ +SRR27190823 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/023/SRR27190823/SRR27190823_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/023/SRR27190823/SRR27190823_2.fastq.gz ENAFQ +SRR27190824 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/024/SRR27190824/SRR27190824_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/024/SRR27190824/SRR27190824_2.fastq.gz ENAFQ +SRR27190825 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/025/SRR27190825/SRR27190825_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/025/SRR27190825/SRR27190825_2.fastq.gz ENAFQ +SRR27190826 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/026/SRR27190826/SRR27190826_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/026/SRR27190826/SRR27190826_2.fastq.gz ENAFQ diff --git a/test_data/GSE250130/GSE250130.run.list b/test_data/GSE250130/GSE250130.run.list new file mode 100644 index 0000000..94aad8d --- /dev/null +++ b/test_data/GSE250130/GSE250130.run.list @@ -0,0 +1,28 @@ +SRR27190799 +SRR27190800 +SRR27190801 +SRR27190802 +SRR27190803 +SRR27190804 +SRR27190805 +SRR27190806 +SRR27190807 +SRR27190808 +SRR27190809 +SRR27190810 +SRR27190811 +SRR27190812 +SRR27190813 +SRR27190814 +SRR27190815 +SRR27190816 +SRR27190817 +SRR27190818 +SRR27190819 +SRR27190820 +SRR27190821 +SRR27190822 +SRR27190823 +SRR27190824 +SRR27190825 +SRR27190826 diff --git a/test_data/GSE250130/GSE250130.sample.list b/test_data/GSE250130/GSE250130.sample.list new file mode 100644 index 0000000..2a53be0 --- /dev/null +++ b/test_data/GSE250130/GSE250130.sample.list @@ -0,0 +1,28 @@ +GSM7974277 +GSM7974278 +GSM7974279 +GSM7974280 +GSM7974281 +GSM7974282 +GSM7974283 +GSM7974284 +GSM7974285 +GSM7974286 +GSM7974287 +GSM7974288 +GSM7974289 +GSM7974290 +GSM7974291 +GSM7974292 +GSM7974293 +GSM7974294 +GSM7974295 +GSM7974296 +GSM7974297 +GSM7974298 +GSM7974299 +GSM7974300 +GSM7974301 +GSM7974302 +GSM7974303 +GSM7974304 diff --git a/test_data/GSE250130/GSE250130.sample_x_run.tsv b/test_data/GSE250130/GSE250130.sample_x_run.tsv new file mode 100644 index 0000000..ba6ec14 --- /dev/null +++ b/test_data/GSE250130/GSE250130.sample_x_run.tsv @@ -0,0 +1,28 @@ +GSM7974277 SRR27190826 +GSM7974278 SRR27190825 +GSM7974279 SRR27190814 +GSM7974280 SRR27190805 +GSM7974281 SRR27190804 +GSM7974282 SRR27190803 +GSM7974283 SRR27190802 +GSM7974284 SRR27190801 +GSM7974285 SRR27190800 +GSM7974286 SRR27190799 +GSM7974287 SRR27190824 +GSM7974288 SRR27190823 +GSM7974289 SRR27190822 +GSM7974290 SRR27190821 +GSM7974291 SRR27190820 +GSM7974292 SRR27190819 +GSM7974293 SRR27190818 +GSM7974294 SRR27190817 +GSM7974295 SRR27190816 +GSM7974296 SRR27190815 +GSM7974297 SRR27190813 +GSM7974298 SRR27190812 +GSM7974299 SRR27190811 +GSM7974300 SRR27190810 +GSM7974301 SRR27190809 +GSM7974302 SRR27190808 +GSM7974303 SRR27190807 +GSM7974304 SRR27190806 diff --git a/test_data/GSE250130/GSE250130.urls.list b/test_data/GSE250130/GSE250130.urls.list new file mode 100644 index 0000000..2667a6d --- /dev/null +++ b/test_data/GSE250130/GSE250130.urls.list @@ -0,0 +1,56 @@ +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/099/SRR27190799/SRR27190799_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/099/SRR27190799/SRR27190799_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/000/SRR27190800/SRR27190800_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/000/SRR27190800/SRR27190800_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/001/SRR27190801/SRR27190801_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/001/SRR27190801/SRR27190801_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/002/SRR27190802/SRR27190802_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/002/SRR27190802/SRR27190802_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/003/SRR27190803/SRR27190803_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/003/SRR27190803/SRR27190803_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/004/SRR27190804/SRR27190804_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/004/SRR27190804/SRR27190804_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/005/SRR27190805/SRR27190805_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/005/SRR27190805/SRR27190805_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/006/SRR27190806/SRR27190806_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/006/SRR27190806/SRR27190806_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/007/SRR27190807/SRR27190807_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/007/SRR27190807/SRR27190807_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/008/SRR27190808/SRR27190808_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/008/SRR27190808/SRR27190808_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/009/SRR27190809/SRR27190809_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/009/SRR27190809/SRR27190809_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/010/SRR27190810/SRR27190810_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/010/SRR27190810/SRR27190810_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/011/SRR27190811/SRR27190811_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/011/SRR27190811/SRR27190811_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/012/SRR27190812/SRR27190812_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/012/SRR27190812/SRR27190812_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/013/SRR27190813/SRR27190813_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/013/SRR27190813/SRR27190813_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/014/SRR27190814/SRR27190814_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/014/SRR27190814/SRR27190814_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/015/SRR27190815/SRR27190815_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/015/SRR27190815/SRR27190815_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/016/SRR27190816/SRR27190816_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/016/SRR27190816/SRR27190816_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/017/SRR27190817/SRR27190817_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/017/SRR27190817/SRR27190817_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/018/SRR27190818/SRR27190818_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/018/SRR27190818/SRR27190818_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/019/SRR27190819/SRR27190819_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/019/SRR27190819/SRR27190819_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/020/SRR27190820/SRR27190820_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/020/SRR27190820/SRR27190820_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/021/SRR27190821/SRR27190821_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/021/SRR27190821/SRR27190821_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/022/SRR27190822/SRR27190822_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/022/SRR27190822/SRR27190822_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/023/SRR27190823/SRR27190823_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/023/SRR27190823/SRR27190823_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/024/SRR27190824/SRR27190824_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/024/SRR27190824/SRR27190824_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/025/SRR27190825/SRR27190825_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/025/SRR27190825/SRR27190825_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/026/SRR27190826/SRR27190826_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR271/026/SRR27190826/SRR27190826_2.fastq.gz diff --git a/test_data/GSE264508/GSE264508.accessions.tsv b/test_data/GSE264508/GSE264508.accessions.tsv new file mode 100644 index 0000000..14c6407 --- /dev/null +++ b/test_data/GSE264508/GSE264508.accessions.tsv @@ -0,0 +1,18 @@ +GSM8219160 SRS21085587 SRX24324207 SRR28758707 +GSM8219161 SRS21085570 SRX24324190 SRR28758748,SRR28758749,SRR28758750,SRR28758751 +GSM8219162 SRS21085571 SRX24324191 SRR28758747 +GSM8219163 SRS21085572 SRX24324192 SRR28758746 +GSM8219164 SRS21085573 SRX24324193 SRR28758742,SRR28758743,SRR28758744,SRR28758745 +GSM8219165 SRS21085577 SRX24324197 SRR28758729 +GSM8219166 SRS21085574 SRX24324194 SRR28758738,SRR28758739,SRR28758740,SRR28758741 +GSM8219167 SRS21085575 SRX24324195 SRR28758734,SRR28758735,SRR28758736,SRR28758737 +GSM8219168 SRS21085576 SRX24324196 SRR28758730,SRR28758731,SRR28758732,SRR28758733 +GSM8219169 SRS21085578 SRX24324198 SRR28758728 +GSM8219170 SRS21085579 SRX24324199 SRR28758727 +GSM8219171 SRS21085580 SRX24324200 SRR28758726 +GSM8219172 SRS21085581 SRX24324201 SRR28758725 +GSM8219173 SRS21085582 SRX24324202 SRR28758724 +GSM8219174 SRS21085588 SRX24324208 SRR28758706 +GSM8219175 SRS21085583 SRX24324203 SRR28758720,SRR28758721,SRR28758722,SRR28758723 +GSM8219176 SRS21085584 SRX24324204 SRR28758716,SRR28758717,SRR28758718,SRR28758719 +GSM8219177 SRS21085585 SRX24324205 SRR28758708,SRR28758709,SRR28758710,SRR28758711 diff --git a/test_data/GSE264508/GSE264508.parsed.tsv b/test_data/GSE264508/GSE264508.parsed.tsv new file mode 100644 index 0000000..51e7be7 --- /dev/null +++ b/test_data/GSE264508/GSE264508.parsed.tsv @@ -0,0 +1,42 @@ +SRR28758706 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/006/SRR28758706/SRR28758706_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/006/SRR28758706/SRR28758706_2.fastq.gz ENAFQ +SRR28758707 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/007/SRR28758707/SRR28758707_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/007/SRR28758707/SRR28758707_2.fastq.gz ENAFQ +SRR28758708 Homo sapiens ftp.sra.ebi.ac.uk/vol1/srr/SRR287/008/SRR28758708/SRR28758708.lite SRA +SRR28758709 Homo sapiens ftp.sra.ebi.ac.uk/vol1/srr/SRR287/009/SRR28758709/SRR28758709 SRA +SRR28758710 Homo sapiens ftp.sra.ebi.ac.uk/vol1/srr/SRR287/010/SRR28758710/SRR28758710.lite SRA +SRR28758711 Homo sapiens ftp.sra.ebi.ac.uk/vol1/srr/SRR287/011/SRR28758711/SRR28758711.lite SRA +SRR28758716 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/016/SRR28758716/SRR28758716_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/016/SRR28758716/SRR28758716_2.fastq.gz ENAFQ +SRR28758717 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/017/SRR28758717/SRR28758717_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/017/SRR28758717/SRR28758717_2.fastq.gz ENAFQ +SRR28758718 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/018/SRR28758718/SRR28758718_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/018/SRR28758718/SRR28758718_2.fastq.gz ENAFQ +SRR28758719 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/019/SRR28758719/SRR28758719_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/019/SRR28758719/SRR28758719_2.fastq.gz ENAFQ +SRR28758720 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/020/SRR28758720/SRR28758720_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/020/SRR28758720/SRR28758720_2.fastq.gz ENAFQ +SRR28758721 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/021/SRR28758721/SRR28758721_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/021/SRR28758721/SRR28758721_2.fastq.gz ENAFQ +SRR28758722 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/022/SRR28758722/SRR28758722_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/022/SRR28758722/SRR28758722_2.fastq.gz ENAFQ +SRR28758723 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/023/SRR28758723/SRR28758723_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/023/SRR28758723/SRR28758723_2.fastq.gz ENAFQ +SRR28758724 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/024/SRR28758724/SRR28758724_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/024/SRR28758724/SRR28758724_2.fastq.gz ENAFQ +SRR28758725 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/025/SRR28758725/SRR28758725_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/025/SRR28758725/SRR28758725_2.fastq.gz ENAFQ +SRR28758726 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/026/SRR28758726/SRR28758726_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/026/SRR28758726/SRR28758726_2.fastq.gz ENAFQ +SRR28758727 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/027/SRR28758727/SRR28758727_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/027/SRR28758727/SRR28758727_2.fastq.gz ENAFQ +SRR28758728 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/028/SRR28758728/SRR28758728_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/028/SRR28758728/SRR28758728_2.fastq.gz ENAFQ +SRR28758729 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/029/SRR28758729/SRR28758729_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/029/SRR28758729/SRR28758729_2.fastq.gz ENAFQ +SRR28758730 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/030/SRR28758730/SRR28758730_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/030/SRR28758730/SRR28758730_2.fastq.gz ENAFQ +SRR28758731 Homo sapiens ftp.sra.ebi.ac.uk/vol1/srr/SRR287/031/SRR28758731/SRR28758731.lite SRA +SRR28758732 Homo sapiens ftp.sra.ebi.ac.uk/vol1/srr/SRR287/032/SRR28758732/SRR28758732.lite SRA +SRR28758733 Homo sapiens ftp.sra.ebi.ac.uk/vol1/srr/SRR287/033/SRR28758733/SRR28758733 SRA +SRR28758734 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/034/SRR28758734/SRR28758734_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/034/SRR28758734/SRR28758734_2.fastq.gz ENAFQ +SRR28758735 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/035/SRR28758735/SRR28758735_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/035/SRR28758735/SRR28758735_2.fastq.gz ENAFQ +SRR28758736 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/036/SRR28758736/SRR28758736_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/036/SRR28758736/SRR28758736_2.fastq.gz ENAFQ +SRR28758737 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/037/SRR28758737/SRR28758737_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/037/SRR28758737/SRR28758737_2.fastq.gz ENAFQ +SRR28758738 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/038/SRR28758738/SRR28758738_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/038/SRR28758738/SRR28758738_2.fastq.gz ENAFQ +SRR28758739 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/039/SRR28758739/SRR28758739_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/039/SRR28758739/SRR28758739_2.fastq.gz ENAFQ +SRR28758740 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/040/SRR28758740/SRR28758740_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/040/SRR28758740/SRR28758740_2.fastq.gz ENAFQ +SRR28758741 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/041/SRR28758741/SRR28758741_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/041/SRR28758741/SRR28758741_2.fastq.gz ENAFQ +SRR28758742 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/042/SRR28758742/SRR28758742_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/042/SRR28758742/SRR28758742_2.fastq.gz ENAFQ +SRR28758743 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/043/SRR28758743/SRR28758743_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/043/SRR28758743/SRR28758743_2.fastq.gz ENAFQ +SRR28758744 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/044/SRR28758744/SRR28758744_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/044/SRR28758744/SRR28758744_2.fastq.gz ENAFQ +SRR28758745 Homo sapiens ftp.sra.ebi.ac.uk/vol1/srr/SRR287/045/SRR28758745/SRR28758745.lite SRA +SRR28758746 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/046/SRR28758746/SRR28758746_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/046/SRR28758746/SRR28758746_2.fastq.gz ENAFQ +SRR28758747 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/047/SRR28758747/SRR28758747_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/047/SRR28758747/SRR28758747_2.fastq.gz ENAFQ +SRR28758748 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/048/SRR28758748/SRR28758748_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/048/SRR28758748/SRR28758748_2.fastq.gz ENAFQ +SRR28758749 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/049/SRR28758749/SRR28758749_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/049/SRR28758749/SRR28758749_2.fastq.gz ENAFQ +SRR28758750 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/050/SRR28758750/SRR28758750_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/050/SRR28758750/SRR28758750_2.fastq.gz ENAFQ +SRR28758751 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/051/SRR28758751/SRR28758751_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/051/SRR28758751/SRR28758751_2.fastq.gz ENAFQ diff --git a/test_data/GSE264508/GSE264508.run.list b/test_data/GSE264508/GSE264508.run.list new file mode 100644 index 0000000..b153fef --- /dev/null +++ b/test_data/GSE264508/GSE264508.run.list @@ -0,0 +1,42 @@ +SRR28758706 +SRR28758707 +SRR28758708 +SRR28758709 +SRR28758710 +SRR28758711 +SRR28758716 +SRR28758717 +SRR28758718 +SRR28758719 +SRR28758720 +SRR28758721 +SRR28758722 +SRR28758723 +SRR28758724 +SRR28758725 +SRR28758726 +SRR28758727 +SRR28758728 +SRR28758729 +SRR28758730 +SRR28758731 +SRR28758732 +SRR28758733 +SRR28758734 +SRR28758735 +SRR28758736 +SRR28758737 +SRR28758738 +SRR28758739 +SRR28758740 +SRR28758741 +SRR28758742 +SRR28758743 +SRR28758744 +SRR28758745 +SRR28758746 +SRR28758747 +SRR28758748 +SRR28758749 +SRR28758750 +SRR28758751 diff --git a/test_data/GSE264508/GSE264508.sample.list b/test_data/GSE264508/GSE264508.sample.list new file mode 100644 index 0000000..758cb46 --- /dev/null +++ b/test_data/GSE264508/GSE264508.sample.list @@ -0,0 +1,18 @@ +GSM8219160 +GSM8219161 +GSM8219162 +GSM8219163 +GSM8219164 +GSM8219165 +GSM8219166 +GSM8219167 +GSM8219168 +GSM8219169 +GSM8219170 +GSM8219171 +GSM8219172 +GSM8219173 +GSM8219174 +GSM8219175 +GSM8219176 +GSM8219177 diff --git a/test_data/GSE264508/GSE264508.sample_x_run.tsv b/test_data/GSE264508/GSE264508.sample_x_run.tsv new file mode 100644 index 0000000..2b07044 --- /dev/null +++ b/test_data/GSE264508/GSE264508.sample_x_run.tsv @@ -0,0 +1,18 @@ +GSM8219160 SRR28758707 +GSM8219161 SRR28758748,SRR28758749,SRR28758750,SRR28758751 +GSM8219162 SRR28758747 +GSM8219163 SRR28758746 +GSM8219164 SRR28758742,SRR28758743,SRR28758744,SRR28758745 +GSM8219165 SRR28758729 +GSM8219166 SRR28758738,SRR28758739,SRR28758740,SRR28758741 +GSM8219167 SRR28758734,SRR28758735,SRR28758736,SRR28758737 +GSM8219168 SRR28758730,SRR28758731,SRR28758732,SRR28758733 +GSM8219169 SRR28758728 +GSM8219170 SRR28758727 +GSM8219171 SRR28758726 +GSM8219172 SRR28758725 +GSM8219173 SRR28758724 +GSM8219174 SRR28758706 +GSM8219175 SRR28758720,SRR28758721,SRR28758722,SRR28758723 +GSM8219176 SRR28758716,SRR28758717,SRR28758718,SRR28758719 +GSM8219177 SRR28758708,SRR28758709,SRR28758710,SRR28758711 diff --git a/test_data/GSE264508/GSE264508.urls.list b/test_data/GSE264508/GSE264508.urls.list new file mode 100644 index 0000000..9916afb --- /dev/null +++ b/test_data/GSE264508/GSE264508.urls.list @@ -0,0 +1,76 @@ +ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/006/SRR28758706/SRR28758706_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/006/SRR28758706/SRR28758706_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/007/SRR28758707/SRR28758707_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/007/SRR28758707/SRR28758707_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/srr/SRR287/008/SRR28758708/SRR28758708.lite +ftp.sra.ebi.ac.uk/vol1/srr/SRR287/009/SRR28758709/SRR28758709 +ftp.sra.ebi.ac.uk/vol1/srr/SRR287/010/SRR28758710/SRR28758710.lite +ftp.sra.ebi.ac.uk/vol1/srr/SRR287/011/SRR28758711/SRR28758711.lite +ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/016/SRR28758716/SRR28758716_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/016/SRR28758716/SRR28758716_2.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/017/SRR28758717/SRR28758717_1.fastq.gz +ftp.sra.ebi.ac.uk/vol1/fastq/SRR287/017/SRR28758717/SRR28758717_2.fastq.gz 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b/test_data/GSE274955/GSE274955.accessions.tsv new file mode 100644 index 0000000..eaa7d40 --- /dev/null +++ b/test_data/GSE274955/GSE274955.accessions.tsv @@ -0,0 +1,5 @@ +GSM8462812 SRS22358709 SRX25717812 SRR30256652 +GSM8462813 SRS22358710 SRX25717813 SRR30256651 +GSM8462814 SRS22358713 SRX25717814 SRR30256650 +GSM8462815 SRS22358712 SRX25717815 SRR30256649 +GSM8462816 SRS22358714 SRX25717816 SRR30256648 diff --git a/test_data/GSE274955/GSE274955.parsed.tsv b/test_data/GSE274955/GSE274955.parsed.tsv new file mode 100644 index 0000000..b951d24 --- /dev/null +++ b/test_data/GSE274955/GSE274955.parsed.tsv @@ -0,0 +1,5 @@ +SRR30256648 Homo sapiens https://sra-pub-src-1.s3.amazonaws.com/SRR30256648/s6_bam.bam.1 BAM +SRR30256649 Homo sapiens ftp.sra.ebi.ac.uk/vol1/srr/SRR302/049/SRR30256649/s5_bam.bam BAM +SRR30256650 Homo sapiens ftp.sra.ebi.ac.uk/vol1/srr/SRR302/050/SRR30256650/s4_bam.bam BAM +SRR30256651 Homo sapiens ftp.sra.ebi.ac.uk/vol1/srr/SRR302/051/SRR30256651/s3_bam.bam BAM +SRR30256652 Homo sapiens ftp.sra.ebi.ac.uk/vol1/srr/SRR302/052/SRR30256652/s2_bam.bam BAM diff --git a/test_data/GSE274955/GSE274955.run.list b/test_data/GSE274955/GSE274955.run.list new file mode 100644 index 0000000..10bed13 --- /dev/null +++ b/test_data/GSE274955/GSE274955.run.list @@ -0,0 +1,5 @@ +SRR30256648 +SRR30256649 +SRR30256650 +SRR30256651 +SRR30256652 diff --git a/test_data/GSE274955/GSE274955.sample.list b/test_data/GSE274955/GSE274955.sample.list new file mode 100644 index 0000000..88c6e99 --- /dev/null +++ b/test_data/GSE274955/GSE274955.sample.list @@ -0,0 +1,5 @@ +GSM8462812 +GSM8462813 +GSM8462814 +GSM8462815 +GSM8462816 diff --git a/test_data/GSE274955/GSE274955.sample_x_run.tsv b/test_data/GSE274955/GSE274955.sample_x_run.tsv new file mode 100644 index 0000000..28fe9d6 --- /dev/null +++ b/test_data/GSE274955/GSE274955.sample_x_run.tsv @@ -0,0 +1,5 @@ +GSM8462812 SRR30256652 +GSM8462813 SRR30256651 +GSM8462814 SRR30256650 +GSM8462815 SRR30256649 +GSM8462816 SRR30256648 diff --git a/test_data/GSE274955/GSE274955.urls.list b/test_data/GSE274955/GSE274955.urls.list new file mode 100644 index 0000000..642e985 --- /dev/null +++ b/test_data/GSE274955/GSE274955.urls.list @@ -0,0 +1,5 @@ +https://sra-pub-src-1.s3.amazonaws.com/SRR30256648/s6_bam.bam.1 +ftp.sra.ebi.ac.uk/vol1/srr/SRR302/049/SRR30256649/s5_bam.bam +ftp.sra.ebi.ac.uk/vol1/srr/SRR302/050/SRR30256650/s4_bam.bam +ftp.sra.ebi.ac.uk/vol1/srr/SRR302/051/SRR30256651/s3_bam.bam +ftp.sra.ebi.ac.uk/vol1/srr/SRR302/052/SRR30256652/s2_bam.bam diff --git a/tests/test_metadata.sh b/tests/test_metadata.sh new file mode 100644 index 0000000..491e74d --- /dev/null +++ b/tests/test_metadata.sh @@ -0,0 +1,51 @@ +#!/bin/bash +set -e + +if [ "$#" -lt 1 ]; then + echo "Usage: $0 " + exit 1 +fi + +SERIES=$1 +SAMPLE_LIST=${2:-""} +OUTPUT_DIR="output/$SERIES" + +# Create output directory and copy all scripts +mkdir -p $OUTPUT_DIR +cp ./scripts/* $OUTPUT_DIR +cd $OUTPUT_DIR + +# Load metadata +echo "Loading metadata for $SERIES $SAMPLE_LIST" +./collect_metadata.sh $SERIES $SAMPLE_LIST + +# Test output +for file in test_data/$SERIES/* +do + filename=$(basename $file) + echo "Testing $file" + + # Check if the expected output file is created + if [ ! -f $filename ] + then + echo "❌ERROR: Expected output file $filename not found!" + exit 1 + fi + + # Check if the file is not empty + if [ ! -s $filename ] + then + echo "❌ERROR: Output file $filename is empty!" + exit 1 + fi + + # Compare the actual output with the expected output + if ! diff -q $filename $file + then + echo "❌ERROR: Output file $filename does not match expected output!" + exit 1 + fi +done + +# Print Success +echo "✅$SERIES: All tests passed!"