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Incorrect URLs for data objects #423

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aclum opened this issue Mar 10, 2025 · 0 comments · Fixed by #424
Closed

Incorrect URLs for data objects #423

aclum opened this issue Mar 10, 2025 · 0 comments · Fixed by #424
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bug Something isn't working import priority-high

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@aclum
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aclum commented Mar 10, 2025

URLs are malconstructed for data objects from the bioscales import, this ticket is to fix the code. There will be a separate ticket for data cleanup.

Observed URL:
"url": "https://data.microbiomedata.org/data/nmdc:omprc-11-kpsyyn56//global/cfs/cdirs/m3408/ficus/pipeline_products/nmdc:omprc-11-kpsyyn56/nmdc:wfrqc-11-pbtmz555.1/nmdc_wfrqc-11-pbtmz555.1_filterStats.txt",
expected URL

https://data.microbiomedata.org/data/nmdc:omprc-11-kpsyyn56/nmdc:wfrqc-11-pbtmz555.1/nmdc_wfrqc-11-pbtmz555.1_filterStats.txt
{
"_id": {
"$oid": "67c2146ffe24de19b770cebc"
},
"id": "nmdc:wfrqc-11-pbtmz555.1",
"name": "Read QC for nmdc:wfrqc-11-pbtmz555.1",
"type": "nmdc:ReadQcAnalysis",
"has_input": [
"nmdc:dobj-11-rcxkyd57"
],
"has_output": [
"nmdc:dobj-11-248zen55",
"nmdc:dobj-11-8pwy7n32"
],
"git_url": "https://github.com/microbiomedata/ReadsQC",
"version": "v1.0.14",
"execution_resource": "JGI",
"started_at_time": "2025-02-28T19:54:21.249431+00:00",
"ended_at_time": "2025-02-28T19:54:21.249438+00:00",
"was_informed_by": "nmdc:omprc-11-kpsyyn56",
"do_output": [
{
"_id": {
"$oid": "67c2146ffe24de19b770ceb7"
},
"id": "nmdc:dobj-11-248zen55",
"type": "nmdc:DataObject",
"name": "nmdc_wfrqc-11-pbtmz555.1_filterStats.txt",
"file_size_bytes": 33,
"md5_checksum": "a6fecbf593d3177a328750461c8e1ee7",
"data_object_type": "QC Statistics",
"was_generated_by": "nmdc:wfrqc-11-pbtmz555.1",
"url": "https://data.microbiomedata.org/data/nmdc:omprc-11-kpsyyn56//global/cfs/cdirs/m3408/ficus/pipeline_products/nmdc:omprc-11-kpsyyn56/nmdc:wfrqc-11-pbtmz555.1/nmdc_wfrqc-11-pbtmz555.1_filterStats.txt",
"description": "Reads QC summary for nmdc:omprc-11-kpsyyn56"
},
{
"_id": {
"$oid": "67c2146ffe24de19b770ceb8"
},
"id": "nmdc:dobj-11-8pwy7n32",
"type": "nmdc:DataObject",
"name": "nmdc_wfrqc-11-pbtmz555.1_filtered.fastq.gz",
"file_size_bytes": 33,
"md5_checksum": "f4e0b508fbcc4db8022cdbcd6879c286",
"data_object_type": "Filtered Sequencing Reads",
"was_generated_by": "nmdc:wfrqc-11-pbtmz555.1",
"url": "https://data.microbiomedata.org/data/nmdc:omprc-11-kpsyyn56//global/cfs/cdirs/m3408/ficus/pipeline_products/nmdc:omprc-11-kpsyyn56/nmdc:wfrqc-11-pbtmz555.1/nmdc_wfrqc-11-pbtmz555.1_filtered.fastq.gz",
"description": "Reads QC for nmdc:omprc-11-kpsyyn56"
}

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