From 2bd127eb87dd77d2ebf44489a7732c820179297a Mon Sep 17 00:00:00 2001 From: Donny Winston Date: Tue, 17 Dec 2024 16:05:24 -0500 Subject: [PATCH] fix: docs links (#847) closes #820 closes #821 --- docs/howto-guides/claim-and-run-jobs.md | 2 +- docs/howto-guides/jobs/gold-translation-etl.md | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/howto-guides/claim-and-run-jobs.md b/docs/howto-guides/claim-and-run-jobs.md index 095cb02d..c0d4a9ff 100644 --- a/docs/howto-guides/claim-and-run-jobs.md +++ b/docs/howto-guides/claim-and-run-jobs.md @@ -3,7 +3,7 @@ The Runtime advertises jobs to be done, where a [Job](https://api.microbiomedata.org/docs#/jobs) is a [Workflow](https://api.microbiomedata.org/docs#/workflows) paired with a chosen input [Object](https://api.microbiomedata.org/docs#/objects). See [Guide - Create Workflow Triggers To -Spawn Jobs](guide-create-triggers.md) to learn how to arrange for jobs of interest to be +Spawn Jobs](create-triggers.md) to learn how to arrange for jobs of interest to be automatically available when relevant new workflow inputs are available. You can list open jobs via [`GET /jobs`](https://api.microbiomedata.org/docs#/jobs/list_jobs_jobs_get). To diff --git a/docs/howto-guides/jobs/gold-translation-etl.md b/docs/howto-guides/jobs/gold-translation-etl.md index 81b2dd3a..91829f65 100644 --- a/docs/howto-guides/jobs/gold-translation-etl.md +++ b/docs/howto-guides/jobs/gold-translation-etl.md @@ -1,6 +1,5 @@ # GOLD Translation ETL - This job takes a `nmdc_merged_data.tsv.zip` file as a data object input. First, start your local runtime stack: @@ -13,7 +12,6 @@ Load and ensure the `translation` repository i ![dagster-workspace-repo-loaded](../../img/dagster-workspace-repo-loaded.png) - Next, navigate to the Jobs page for the `translation` repository: ![dagster-translation-repo-jobs](../../img/dagster-translation-repo-jobs.png) @@ -53,12 +51,13 @@ mongoexport --host="localhost:27018" \ -d nmdc_etl_staging -c gold.biosample_set \ --jsonArray -o gold.biosample_set.json ``` + ``` jq '{biosample_set:.}' gold.biosample_set.json \ > gold.biosample_set.as_nmdcdb.2021-11-18.json ``` -Now, you may [submit this metadata as JSON through the API](../tutorials/tutorial-metadata-in.md). +Now, you may [submit this metadata as JSON through the API](../../tutorials/metadata-in.md) In the tutorial linked to above, GitHub's Gist service is used to host and obtain a URL for the JSON. Here's let's walk through using the NMDC's `www` directory on NERSC to host the file and @@ -70,6 +69,7 @@ a DRS object in the API: scp gold.biosample_set.as_nmdcdb.2021-11-18.json \ dtn01.nersc.gov:/global/cfs/cdirs/m3408/www/meta/ ``` + ``` ssh dtn01.nersc.gov