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Fix URL generation in run_import.py #424

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merged 1 commit into from
Mar 10, 2025

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This PR address the bug if incorrect data object URL construction.

Results of testing this change:

"data_object_set": [
        {
            "id": "nmdc:dobj-11-9wta9120",
            "type": "nmdc:DataObject",
            "name": "52710.1.424012.TACACGCT-TACACGCT.fastq.gz",
            "file_size_bytes": 121,
            "md5_checksum": "f947d0ae037a73d46294f51c73d06eec",
            "data_object_type": "Metagenome Raw Reads",
            "was_generated_by": "nmdc:omprc-12-hgksne68",
            "url": "https://data.microbiomedata.org/data/nmdc:omprc-12-hgksne68/nmdc:omprc-12-hgksne68/52710.1.424012.TACACGCT-TACACGCT.fastq.gz",
            "description": "Metagenome Raw Reads for nmdc:omprc-12-hgksne68"
        },
        {
            "id": "nmdc:dobj-11-9yhz5945",
            "type": "nmdc:DataObject",
            "name": "nmdc_wfrqc-11-raq6mq89.1_filterStats.txt",
            "file_size_bytes": 311,
            "md5_checksum": "a1f8a5bdd2b117181f1b0235ce7ef5b4",
            "data_object_type": "QC Statistics",
            "was_generated_by": "nmdc:wfrqc-11-raq6mq89.1",
            "url": "https://data.microbiomedata.org/data/nmdc:omprc-12-hgksne68/nmdc:wfrqc-11-raq6mq89.1/nmdc_wfrqc-11-raq6mq89.1_filterStats.txt",
            "description": "Reads QC summary for nmdc:omprc-12-hgksne68"
        },
        {
            "id": "nmdc:dobj-11-cpgm0t36",
            "type": "nmdc:DataObject",
            "name": "nmdc_wfrqc-11-raq6mq89.1_filtered.fastq.gz",
            "file_size_bytes": 121,
            "md5_checksum": "f947d0ae037a73d46294f51c73d06eec",
            "data_object_type": "Filtered Sequencing Reads",
            "was_generated_by": "nmdc:wfrqc-11-raq6mq89.1",
            "url": "https://data.microbiomedata.org/data/nmdc:omprc-12-hgksne68/nmdc:wfrqc-11-raq6mq89.1/nmdc_wfrqc-11-raq6mq89.1_filtered.fastq.gz",
            "description": "Reads QC for nmdc:omprc-12-hgksne68"
        },
        {
            "id": "nmdc:dobj-11-42n4nm48",
            "type": "nmdc:DataObject",
            "name": "nmdc_wfmgas-11-7t8c4c68.1_pairedMapped_sorted.sam.gz",
            "file_size_bytes": 121,
            "md5_checksum": "f947d0ae037a73d46294f51c73d06eec",
            "data_object_type": "Assembly Coverage BAM",
            "was_generated_by": "nmdc:wfmgas-11-7t8c4c68.1",
            "url": "https://data.microbiomedata.org/data/nmdc:omprc-12-hgksne68/nmdc:wfmgas-11-7t8c4c68.1/nmdc_wfmgas-11-7t8c4c68.1_pairedMapped_sorted.sam.gz",
            "description": "Sorted Bam for nmdc:omprc-12-hgksne68"
        },
        {
            "id": "nmdc:dobj-11-z2a1cp87",
            "type": "nmdc:DataObject",
            "name": "nmdc_wfmgas-11-7t8c4c68.1_metaAsm.info",
            "file_size_bytes": 374,
            "md5_checksum": "f2a340c2e37593742818b71fccbe2ce2",
            "data_object_type": "Assembly Info File",
            "was_generated_by": "nmdc:wfmgas-11-7t8c4c68.1",
            "url": "https://data.microbiomedata.org/data/nmdc:omprc-12-hgksne68/nmdc:wfmgas-11-7t8c4c68.1/nmdc_wfmgas-11-7t8c4c68.1_metaAsm.info",
            "description": "Assembly info file for nmdc:omprc-12-hgksne68"
        },
        {
            "id": "nmdc:dobj-11-fjy50189",
            "type": "nmdc:DataObject",
            "name": "nmdc_wfmgas-11-7t8c4c68.1_contigs.fna",
            "file_size_bytes": 568,
            "md5_checksum": "324bb17273f3e00f61e62e017291fd8e",
            "data_object_type": "Assembly Contigs",
            "was_generated_by": "nmdc:wfmgas-11-7t8c4c68.1",
            "url": "https://data.microbiomedata.org/data/nmdc:omprc-12-hgksne68/nmdc:wfmgas-11-7t8c4c68.1/nmdc_wfmgas-11-7t8c4c68.1_contigs.fna",
            "description": "Assembly contigs for nmdc:omprc-12-hgksne68"
        },
        {
            "id": "nmdc:dobj-11-gsetjw05",
            "type": "nmdc:DataObject",
            "name": "nmdc_wfmgas-11-7t8c4c68.1_covstats.txt",
            "file_size_bytes": 828,
            "md5_checksum": "e0a11758eb4c30682838f4422bcfa27a",
            "data_object_type": "Assembly Coverage Stats",
            "was_generated_by": "nmdc:wfmgas-11-7t8c4c68.1",
            "url": "https://data.microbiomedata.org/data/nmdc:omprc-12-hgksne68/nmdc:wfmgas-11-7t8c4c68.1/nmdc_wfmgas-11-7t8c4c68.1_covstats.txt",
            "description": "Coverage Stats for nmdc:omprc-12-hgksne68"
        }
    ]

@mbthornton-lbl mbthornton-lbl requested a review from aclum March 10, 2025 23:00
@mbthornton-lbl mbthornton-lbl linked an issue Mar 10, 2025 that may be closed by this pull request
@mbthornton-lbl mbthornton-lbl merged commit 150b8d6 into main Mar 10, 2025
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Incorrect URLs for data objects
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