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Release v6.2 #761

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Release v6.2 #761

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09f104d
add release v6.2 files and update references
onursumer Feb 5, 2025
3477236
update data
onursumer Feb 5, 2025
d9ab990
add release notes
onursumer Feb 10, 2025
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8 changes: 4 additions & 4 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -20,11 +20,11 @@ that using these commands (requires access to the htan-dcc google project):

```bash
cd data
bq extract --destination_format CSV released.entities_v6_1 gs://htan-release-files/entities_v6_1.csv
bq extract --destination_format CSV released.metadata_v6_1 gs://htan-release-files/metadata_v6_1.csv
bq extract --destination_format CSV released.entities_v6_2 gs://htan-release-files/entities_v6_2.csv
bq extract --destination_format CSV released.metadata_v6_2 gs://htan-release-files/metadata_v6_2.csv
bq extract --destination_format NEWLINE_DELIMITED_JSON released.cds_drs_mapping_V2 gs://htan-release-files/cds_drs_mapping.json
gsutil cp gs://htan-release-files/entities_v6_1.csv entities_v6_1.csv
gsutil cp gs://htan-release-files/metadata_v6_1.csv metadata_v6_1.csv
gsutil cp gs://htan-release-files/entities_v6_2.csv entities_v6_2.csv
gsutil cp gs://htan-release-files/metadata_v6_2.csv metadata_v6_2.csv
gsutil cp gs://htan-release-files/cds_drs_mapping.json cds_drs_mapping.json
```

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2 changes: 1 addition & 1 deletion components/HomePage.tsx
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Expand Up @@ -54,7 +54,7 @@ const HomePage: React.FunctionComponent<IHomePropsProps> = ({
}}
>
<a style={{ color: 'white' }} href="/data-updates">
Data Release V6.1 (Last updated 2024-12-11)
Data Release V6.2 (Last updated 2025-02-10)
</a>
</div>
<Row className="justify-content-md-center">
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77 changes: 77 additions & 0 deletions data/entities_v6_1.csv → data/entities_v6_2.csv
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Expand Up @@ -210,6 +210,79 @@ syn26937866,Release 2.0,,file,v22.6.2.img,,ImagingLevel2,2,syn26942637
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Expand Down Expand Up @@ -170321,6 +170394,10 @@ syn26530850,Release 2.0,,file,v23.10.1.seq,,ScATAC-seqLevel2,,
syn26530901,Release 2.0,,file,v23.10.1.seq,,ScATAC-seqLevel2,,
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4 changes: 2 additions & 2 deletions data/get_syn_data.py
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Expand Up @@ -103,13 +103,13 @@ def generate_json(include_at_risk_populations, include_released_only, do_not_dow
}

if include_released_only:
released_entities_df = pd.read_csv("entities_v6_1.csv")
released_entities_df = pd.read_csv("entities_v6_2.csv")
include_release_ids = set(released_entities_df['entityId'])

# store all metadata synapse ids for downloading submitted metadata directly
portal_metadata = {}

released_metadata_df = pd.read_csv("metadata_v6_1.csv")
released_metadata_df = pd.read_csv("metadata_v6_2.csv")
released_synapse_metadata_ids = set(released_metadata_df['Manifest_Id'])

# iterate over projects; map to HTAN ID, inspect metadata and add to portal JSON dump
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