A Repo for testing a random sample of drs ids to see if they resolve.
Launch the
Open the drs-test.R script. This script takes an NCPI manifest file and gets the DRS ids for 10 randomly selected files and prints the output from the command drs get. Click R to run the whole script and generate and output file called drs-test.sh that contains one drs get command per line.
Open the Terminal and iniate and activate the base Conda environment. You may need to close and reopen the terminal.
Then install the DRS client by running the following command.
pip install ga4gh-drs-client
Then, change the modifications on the drs-test.sh and run it.
chmod u+x drs-test.sh
bash drs-test.sh
The output for drs get https://drs.hmpdacc.org 1L3EGziLLV5a1 should look like:
2022-07-08 22:36:56,995 DEBUG command-line arguments: {'url': 'https://drs.hmpdacc.org', 'object_id': '1L3EGziLLV5a1', 'authtoken': 'omitted', 'download': False, 'expand': False, 'logfile': None, 'max_threads': 1, 'output_dir': '/home/jovyan', 'output_metadata': None, 'silent': False, 'suppress_ssl_verify': False, 'validate_checksum': False, 'verbosity': None}
2022-07-08 22:36:56,995 INFO issuing request to DRS Object endpoint
2022-07-08 22:36:56,995 DEBUG URL: https://drs.hmpdacc.org/ga4gh/drs/v1/objects/1L3EGziLLV5a1
2022-07-08 22:36:56,995 DEBUG Headers: {}
2022-07-08 22:36:56,995 DEBUG Request params: {'expand': False}
{
"id": "1L3EGziLLV5a1",
"created_time": "2020-07-28T20:04:26.000Z",
"drs_id": "1L3EGziLLV5a1",
"checksums": [
{
"checksum": "67d38c1df44e3d9fb3ff5667f961a918",
"type": "md5"
},
{
"checksum": "477ab934afec889bd5dd72404403ab13fa37583ae96315cc6a20970f0f677ecd",
"type": "sha-256"
}
],
"self_uri": "drs://drs.hmpdacc.org/1L3EGziLLV5a1",
"size": 78136036,
"name": "HMP2_J43802_M_ST_T0_B0_0120_ZMGT937-06_C93B2ANXX_L004_R1.fastq.bz2",
"access_methods": [
{
"access_id": "9691359252-1",
"access_url": {
"url": "https://hmpdcc.s3.amazonaws.com/ihmp/t2d/microbiome/wms/raw/HMP2_J43802_M_ST_T0_B0_0120_ZMGT937-06_C93B2ANXX_L004_R1.fastq.bz2"
},
"type": "s3",
"region": "us-east-1"
}
]
}
2022-07-08 15:56:01,746 INFO object/bundle download not requested
2022-07-08 15:56:01,746 INFO exiting with exit code: 0