Data QC: workflow_execution_has_input_data_objects

[mbthornton-lbl]

15 mags_activity_set

{
            "_id" : ObjectId("649b0052ec087f6bbab34903"),
            "id" : "nmdc:wfmag-11-t8gc3c64.1",
            "has_input" : "nmdc:dobj-11-y2f0gn35"
        },
        {
            "_id" : ObjectId("649b0052ec087f6bbab34903"),
            "id" : "nmdc:wfmag-11-t8gc3c64.1",
            "has_input" : "nmdc:dobj-11-achfhn33"
        },
        {
            "_id" : ObjectId("649b0052ec087f6bbab34903"),
            "id" : "nmdc:wfmag-11-t8gc3c64.1",
            "has_input" : "nmdc:dobj-11-vt4jr220"
        },
        {
            "_id" : ObjectId("649b0052ec087f6bbab34907"),
            "id" : "nmdc:wfmag-11-0gwm7d87.1",
            "has_input" : "nmdc:dobj-11-9a9pn310"
        },
        {
            "_id" : ObjectId("649b0052ec087f6bbab34907"),
            "id" : "nmdc:wfmag-11-0gwm7d87.1",
            "has_input" : "nmdc:dobj-11-dpnhb305"
        },
        {
            "_id" : ObjectId("649b0052ec087f6bbab34907"),
            "id" : "nmdc:wfmag-11-0gwm7d87.1",
            "has_input" : "nmdc:dobj-11-1fkqcg08"
        },
        {
            "_id" : ObjectId("649b0052ec087f6bbab34941"),
            "id" : "nmdc:wfmag-11-dchy6q29.1",
            "has_input" : "nmdc:dobj-11-1wzar939"
        },
        {
            "_id" : ObjectId("649b0052ec087f6bbab34941"),
            "id" : "nmdc:wfmag-11-dchy6q29.1",
            "has_input" : "nmdc:dobj-11-fg28a080"
        },
        {
            "_id" : ObjectId("649b0052ec087f6bbab34941"),
            "id" : "nmdc:wfmag-11-dchy6q29.1",
            "has_input" : "nmdc:dobj-11-s4hp2x64"
        },
        {
            "_id" : ObjectId("649b0052ec087f6bbab34942"),
            "id" : "nmdc:wfmag-11-8s9xk838.1",
            "has_input" : "nmdc:dobj-11-kr8ev105"
        },
        {
            "_id" : ObjectId("649b0052ec087f6bbab34942"),
            "id" : "nmdc:wfmag-11-8s9xk838.1",
            "has_input" : "nmdc:dobj-11-gxgpbv06"
        },
        {
            "_id" : ObjectId("649b0052ec087f6bbab34942"),
            "id" : "nmdc:wfmag-11-8s9xk838.1",
            "has_input" : "nmdc:dobj-11-whq9ph06"
        },
        {
            "_id" : ObjectId("649b0054ec087f6bbab34a76"),
            "id" : "nmdc:wfmag-11-29carm07.1",
            "has_input" : "nmdc:dobj-11-t0wzq938"
        },
        {
            "_id" : ObjectId("649b0054ec087f6bbab34a76"),
            "id" : "nmdc:wfmag-11-29carm07.1",
            "has_input" : "nmdc:dobj-11-cvcxxr53"
        },
        {
            "_id" : ObjectId("649b0054ec087f6bbab34a76"),
            "id" : "nmdc:wfmag-11-29carm07.1",
            "has_input" : "nmdc:dobj-11-qkzjq615"
        }

7 metagenome_assembly_set

{
            "_id" : ObjectId("649b005f2ca5ee4adb13a1a0"),
            "id" : "nmdc:wfmgas-11-k8x7bf78.1",
            "has_input" : "nmdc:dobj-11-6appe696"
        },
        {
            "_id" : ObjectId("649b005f2ca5ee4adb13a1df"),
            "id" : "nmdc:wfmgas-11-r8dyz821.1",
            "has_input" : "nmdc:dobj-11-xbb2mp07"
        },
        {
            "_id" : ObjectId("649b005f2ca5ee4adb13a1e2"),
            "id" : "nmdc:wfmgas-11-6pbs6265.1",
            "has_input" : "nmdc:dobj-11-axnsyw61"
        },
        {
            "_id" : ObjectId("649b005f2ca5ee4adb13a29d"),
            "id" : "nmdc:wfmgas-11-yh8n1e65.1",
            "has_input" : "nmdc:dobj-11-nz4neg35"
        },
        {
            "_id" : ObjectId("649b005f2ca5ee4adb13a302"),
            "id" : "nmdc:wfmgas-11-kk38rr46.1",
            "has_input" : "nmdc:dobj-11-aetz2k16"
        },
        {
            "_id" : ObjectId("649b005f2ca5ee4adb13a306"),
            "id" : "nmdc:wfmgas-11-10vezr29.1",
            "has_input" : "nmdc:dobj-11-h673kw16"
        }

5 metagenome_annotation_activity_set

{
            "_id" : ObjectId("649b005bbf2caae0415efba8"),
            "id" : "nmdc:wfmgan-11-c516q834.1",
            "has_input" : "nmdc:dobj-11-dpnhb305"
        },
        {
            "_id" : ObjectId("649b005bbf2caae0415efba9"),
            "id" : "nmdc:wfmgan-11-yzp9eq74.1",
            "has_input" : "nmdc:dobj-11-achfhn33"
        },
        {
            "_id" : ObjectId("649b005bbf2caae0415efbef"),
            "id" : "nmdc:wfmgan-11-fmymf551.1",
            "has_input" : "nmdc:dobj-11-fg28a080"
        },
        {
            "_id" : ObjectId("649b005bbf2caae0415efbf0"),
            "id" : "nmdc:wfmgan-11-3nkefn97.1",
            "has_input" : "nmdc:dobj-11-gxgpbv06"
        },
        {
            "_id" : ObjectId("649b005dbf2caae0415efd26"),
            "id" : "nmdc:wfmgan-11-w1d6gy98.1",
            "has_input" : "nmdc:dobj-11-cvcxxr53"
        }

1 metatranscriptome_activity_set

{
            "_id" : ObjectId("65affcdc07a1abea27b3fa1f"),
            "id" : "nmdc:wfmt-11-y9cf0x90.1",
            "has_input" : "nmdc:dobj-11-xwqq5x15"
        }

6 read_based_taxonomy_analysis_set

        {
            "_id" : ObjectId("649b009bff710ae353f8ccdc"),
            "id" : "nmdc:wfrbt-12-zfccjh43.1",
            "has_input" : "nmdc:dobj-11-6bdffd27"
        },
        {
            "_id" : ObjectId("649b009bff710ae353f8cd18"),
            "id" : "nmdc:wfrbt-12-3qany071.1",
            "has_input" : "nmdc:dobj-11-xbb2mp07"
        },
        {
            "_id" : ObjectId("649b009bff710ae353f8cd1f"),
            "id" : "nmdc:wfrbt-12-5p0p4731.1",
            "has_input" : "nmdc:dobj-11-6appe696"
        },
        {
            "_id" : ObjectId("649b009bff710ae353f8cd25"),
            "id" : "nmdc:wfrbt-12-arwnpf44.1",
            "has_input" : "nmdc:dobj-11-axnsyw61"
        },
        {
            "_id" : ObjectId("649b009cff710ae353f8d16e"),
            "id" : "nmdc:wfrbt-11-dkzdrn42.1",
            "has_input" : "nmdc:dobj-11-nz4neg35"
        },
        {
            "_id" : ObjectId("649b009cff710ae353f8d1cf"),
            "id" : "nmdc:wfrbt-11-z5a29n65.1",
            "has_input" : "nmdc:dobj-11-aetz2k16"
        }

[aclum]

Not a blocker. None of these are for studies we are re-iding, most are from ingesting records from JGI. We can look at this once re-iding is complete.

[aclum]

we should be able to use nmdc_automation/run_process/run_workflows.py to generate records for these.
these were all from GROW and Bioscales which are still on the file systems
/global/cfs/cdirs/m3408/aim2/dev/bioscales_mapping/grow_analysis_projects/ and /global/cfs/cdirs/m3408/aim2/dev/bioscales_mapping/bioscales_analysis_projects/

[eecavanna]

For my own future reference and easy of "copy/pasting," here's a list of the 33 ids in the "has_input" fields above (wrapped in quotes and delimited by commas):

"nmdc:dobj-11-y2f0gn35",
"nmdc:dobj-11-achfhn33",
"nmdc:dobj-11-vt4jr220",
"nmdc:dobj-11-9a9pn310",
"nmdc:dobj-11-dpnhb305",
"nmdc:dobj-11-1fkqcg08",
"nmdc:dobj-11-1wzar939",
"nmdc:dobj-11-fg28a080",
"nmdc:dobj-11-s4hp2x64",
"nmdc:dobj-11-kr8ev105",
"nmdc:dobj-11-gxgpbv06",
"nmdc:dobj-11-whq9ph06",
"nmdc:dobj-11-t0wzq938",
"nmdc:dobj-11-cvcxxr53",
"nmdc:dobj-11-qkzjq615",
"nmdc:dobj-11-6appe696",
"nmdc:dobj-11-xbb2mp07",
"nmdc:dobj-11-axnsyw61",
"nmdc:dobj-11-nz4neg35",
"nmdc:dobj-11-aetz2k16",
"nmdc:dobj-11-h673kw16",
"nmdc:dobj-11-dpnhb305",
"nmdc:dobj-11-achfhn33",
"nmdc:dobj-11-fg28a080",
"nmdc:dobj-11-gxgpbv06",
"nmdc:dobj-11-cvcxxr53",
"nmdc:dobj-11-xwqq5x15",
"nmdc:dobj-11-6bdffd27",
"nmdc:dobj-11-xbb2mp07",
"nmdc:dobj-11-6appe696",
"nmdc:dobj-11-axnsyw61",
"nmdc:dobj-11-nz4neg35",

That list only contains 23 distinct id (the other 10 are repeats). Here's a table showing the number of times each id occurs in the list.

# Occurrences	id
2	nmdc:dobj-11-6appe696
2	nmdc:dobj-11-achfhn33
2	nmdc:dobj-11-aetz2k16
2	nmdc:dobj-11-axnsyw61
2	nmdc:dobj-11-cvcxxr53
2	nmdc:dobj-11-dpnhb305
2	nmdc:dobj-11-fg28a080
2	nmdc:dobj-11-gxgpbv06
2	nmdc:dobj-11-nz4neg35
2	nmdc:dobj-11-xbb2mp07
1	nmdc:dobj-11-1fkqcg08
1	nmdc:dobj-11-1wzar939
1	nmdc:dobj-11-6bdffd27
1	nmdc:dobj-11-9a9pn310
1	nmdc:dobj-11-h673kw16
1	nmdc:dobj-11-kr8ev105
1	nmdc:dobj-11-qkzjq615
1	nmdc:dobj-11-s4hp2x64
1	nmdc:dobj-11-t0wzq938
1	nmdc:dobj-11-vt4jr220
1	nmdc:dobj-11-whq9ph06
1	nmdc:dobj-11-xwqq5x15
1	nmdc:dobj-11-y2f0gn35

Here are all the (23) distinct ids:

"nmdc:dobj-11-6appe696",
"nmdc:dobj-11-achfhn33",
"nmdc:dobj-11-aetz2k16",
"nmdc:dobj-11-axnsyw61",
"nmdc:dobj-11-cvcxxr53",
"nmdc:dobj-11-dpnhb305",
"nmdc:dobj-11-fg28a080",
"nmdc:dobj-11-gxgpbv06",
"nmdc:dobj-11-nz4neg35",
"nmdc:dobj-11-xbb2mp07",
"nmdc:dobj-11-1fkqcg08",
"nmdc:dobj-11-1wzar939",
"nmdc:dobj-11-6bdffd27",
"nmdc:dobj-11-9a9pn310",
"nmdc:dobj-11-h673kw16",
"nmdc:dobj-11-kr8ev105",
"nmdc:dobj-11-qkzjq615",
"nmdc:dobj-11-s4hp2x64",
"nmdc:dobj-11-t0wzq938",
"nmdc:dobj-11-vt4jr220",
"nmdc:dobj-11-whq9ph06",
"nmdc:dobj-11-xwqq5x15",
"nmdc:dobj-11-y2f0gn35",

[eecavanna]

There may be a typo in the issue description.

7 metagenome_assembly_set

There are only 6 JSON objects in that list.

[eecavanna]

Regarding the 1 metatranscriptome_activity_set document listed above:

{
    "_id" : ObjectId("65affcdc07a1abea27b3fa1f"),
    "id" : "nmdc:wfmt-11-y9cf0x90.1",
    "has_input" : "nmdc:dobj-11-xwqq5x15"
}

As of today, October 26, 2024, the database (i.e. any of the schema-described collections) no longer contains a reference to a document whose id is nmdc:dobj-11-xwqq5x15. Also, there is no document whose id is nmdc:wfmt-11-y9cf0x90.1.

Based on those two things, I think this particular violation is obsolete.