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Included filter_stat_json into output for shortreads because NMDC-EDGE needs it:
https://github.com/microbiomedata/ReadsQC/blob/ddc0cd9f79cc53aa9cf25b40cf67196b5cd71a29/shortReadsqc.wdl#L68
- [ ] …
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I volunteered to attempt to transfer the endpoint documentation currently implemented as freeform blurbs for "sections" (i.e. tags) in Swagger UI; into endpoint parameter-specific annotations.
Toda…
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While working on https://github.com/microbiomedata/issues/issues/612 I noticed that some depth values for this project are suspiciously high, considering that our units are meters. Are the values actu…
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Test execution of NMDC workflows. Launch workflows and ensure workflow output matches expectations
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Prioritize and start with Soil and Envo
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Here is a single example.
Excerpt from `violations.tsv`:
|source_collection_name|source_field_name|source_document_object_id|source_document_id |target_id |
|---------------…
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15 mags_activity_set
```
{
"_id" : ObjectId("649b0052ec087f6bbab34903"),
"id" : "nmdc:wfmag-11-t8gc3c64.1",
"has_input" : "nmdc:dobj-11-y2f0gn35"
},
…
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Script: https://github.com/microbiomedata/nmdc-runtime/blob/main/nmdc_runtime/site/export/ncbi_xml_utils.py
Details are in the comment linked below.
> change `designated_class ` to `type`, `des…
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In the JGI template, this column is Y/N ... not yes/no.
Options for resolution
- Leave yes/no in NMDC and do a transformation to Y/N
- Change the NMDC slot enumeration to Y/N
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Chris and I met this week and went over the subset of KEGG BRITE that would be useful for NMDC functional search.
The suggestion yesterday was to include 1.2, 1.3, 1.4, 1.5, 1.6
my new suggestion i…
aclum updated
2 weeks ago