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RE2022-334: add docs re adding new collections #696

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Apr 10, 2024
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using engma as example acress the doc
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Tianhao-Gu committed Apr 9, 2024
commit 7da6b1a19bdbad7462ab51f4538b6f910181f3c1
36 changes: 18 additions & 18 deletions docs/genome_to_collection.md
Original file line number Diff line number Diff line change
Expand Up @@ -25,9 +25,9 @@ the Genome objects from the KBase workspace to NERSC. The following command faci

```commandline
# update arguments as needed
workspace_id=69739
kbase_collection=ENIGMA
source_verion=2023.10
workspace_id=69278
kbase_collection=PMI
source_verion=2023.09
env=CI
token_filepath=path/to/token_file.txt # This is a single-line file with the KBase token

Expand Down Expand Up @@ -200,17 +200,12 @@ from the currently activated collection by using the `get_collection` endpoint.
**example return**
```commandline
{
"name": "Plant Microbe Interfaces",
"name": "ENIGMA",
"ver_src": "2023.11",
"desc": "The goal of the Plant-Microbe Interfaces SFA is to gain a deeper understanding of the diversity and functioning of mutually beneficial interactions between plants and microbes in the rhizosphere.",
"icon_url": "https://ci.kbase.us/services/shock-api/node/674c4e6b-851f-4ee2-ad5a-35effeb8cd68/?download_raw",
"attribution": "This collection was contributed by the Plant Microbe Interfaces (PMI) Science Focus Area (SFA). For more details, see [TODO: FAIR Narrative doi], and https://www.kbase.us/research/doktycz-sfa.\n\nKBase will automatically cite any data from this collection used in a Narrative. If you would like to acknowledge the collection, please copy the text below:\n\nThe authors would like to acknowledge the KBase collection, PMI, supported by the Genomic Science Program, U.S. Department of Energy, Office of Science, Biological and Environmental Research at Oak Ridge National Laboratory under contract DE-AC05-00OR22725, for sharing their data at https://ci-europa.kbase.us/collections/PMI.",
"desc": "Ecosystems and Networks Integrated with Genes and Molecular Assemblies",
"icon_url": "https://ci.kbase.us/services/shock-api/node/9af1c606-724a-4a63-ab64-8191a89dd462/?download_raw",
"attribution": "This collection was contributed by the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) Science Focus Area (SFA). For more details, see [FAIR Narrative doi], and https://www.kbase.us/research/adams-sfa.\nKBase will automatically cite any data from this collection used in a Narrative. If you would like to acknowledge the collection, please copy the text below:\nThe authors would like to acknowledge the KBase collection, ENIGMA, supported by Genomic Science Program, U.S. Department of Energy, Office of Science, Biological and Environmental Research under Contract No. [###], for sharing their data at https://ci-europa.kbase.us/collections/GROW",
"data_products": [
{
"product": "biolog",
"version": "2023.11",
"search_view": null
},
{
"product": "genome_attribs",
"version": "2023.11",
Expand All @@ -221,6 +216,11 @@ from the currently activated collection by using the `get_collection` endpoint.
"version": "2023.11",
"search_view": null
},
{
"product": "samples",
"version": "2023.11",
"search_view": "samples_0bd4242"
},
{
"product": "taxa_count",
"version": "2023.11",
Expand All @@ -241,18 +241,18 @@ from the currently activated collection by using the `get_collection` endpoint.
"matcher": "minhash_homology",
"parameters": {
"service_wizard_url": "https://ci.kbase.us/services/service_wizard",
"sketch_database_name": "Collections_CI_PMI2023_11"
"sketch_database_name": "Collections_CI_ENIGMA2023_11"
}
}
],
"default_select": "genome_attribs",
"metadata": null,
"id": "PMI",
"ver_tag": "2023.11_r5",
"ver_num": 14,
"date_create": "2024-01-12T16:17:21.213453+00:00",
"id": "ENIGMA",
"ver_tag": "2023.11_r9",
"ver_num": 13,
"date_create": "2024-01-31T03:22:34.785596+00:00",
"user_create": "tgu2",
"date_active": "2024-01-12T16:17:41.694010+00:00",
"date_active": "2024-01-31T03:22:49.149964+00:00",
"user_active": "tgu2"
}
```
Expand Down
Binary file modified docs/screenshots/get_collection_endpoint.png
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