From efd7697f1d16c656d3e63e639ed18d7670caa363 Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti
Date: Mon, 2 Dec 2024 14:44:22 -0500
Subject: [PATCH 1/6] add citation.cff and version to website
---
CITATION.cff | 9 ++++++
site/bun.lockb | Bin 214369 -> 214697 bytes
site/package.json | 3 +-
site/src/components/Header.astro | 14 +++++++++-
site/src/layouts/meta.js | 8 ++++++
site/src/pages/loci/index.astro | 46 ++++++++++++++++++++++++++-----
6 files changed, 71 insertions(+), 9 deletions(-)
create mode 100644 CITATION.cff
create mode 100644 site/src/layouts/meta.js
diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 00000000..72109bee
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,9 @@
+title: STRchive
+version: 1.2.0
+date-released: "2024-12-07"
+url: https://github.com/dashnowlab/STRchive
+authors:
+ - family-names: Dashnow
+ given-names: Harriet
+ orcid: https://orcid.org/0000-0001-8433-6270
+cff-version: 1.2.0
diff --git a/site/bun.lockb b/site/bun.lockb
index d29e28d5abcbe248fc45348bfc6180d09cb396b3..89232d466e01b2a49457f9075ec9584da90959c3 100755
GIT binary patch
delta 11818
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diff --git a/site/package.json b/site/package.json
index 46307f7f..aacc7502 100755
--- a/site/package.json
+++ b/site/package.json
@@ -35,6 +35,7 @@
"prettier": "^3.3.3",
"prettier-plugin-astro": "^0.14.1",
"prettier-plugin-css-order": "^2.1.2",
- "vite-plugin-svgr": "^4.2.0"
+ "vite-plugin-svgr": "^4.2.0",
+ "yaml": "^2.6.1"
}
}
diff --git a/site/src/components/Header.astro b/site/src/components/Header.astro
index f129bdf8..707a55c0 100644
--- a/site/src/components/Header.astro
+++ b/site/src/components/Header.astro
@@ -2,6 +2,7 @@
import { FaGithub } from "react-icons/fa6";
import Logo from "@/assets/logo.svg?react";
import Link from "@/components/Link";
+import { version } from "@/layouts/meta";
const path = Astro.url.pathname;
@@ -16,10 +17,13 @@ const links = [
-
+
GitHub
@@ -64,9 +62,7 @@ import Layout from "@/layouts/Layout.astro";
-
- GitHub
+ GitHub
diff --git a/site/src/pages/loci/index.astro b/site/src/pages/loci/index.astro
index bca69694..bd0275f0 100755
--- a/site/src/pages/loci/index.astro
+++ b/site/src/pages/loci/index.astro
@@ -9,7 +9,7 @@ import Link from "@/components/Link";
import PlotlyChart from "@/components/PlotlyChart";
import TableOfContents from "@/components/TableOfContents";
import Layout from "@/layouts/Layout.astro";
-import { version } from "@/layouts/meta";
+import { repo, version } from "@/layouts/meta";
import Table from "@/loci/Table";
import hg19bed from "../../../../data/hg19.STRchive-disease-loci.bed?url";
import hg19defs from "../../../../data/hg19.STRchive-disease-loci.TRGT.bed?url";
@@ -55,10 +55,7 @@ const bedDownloads = downloads.slice(3);
Downloads
-
+
Full Dataset
From b798853d838a43527614cc8f0ee20a8ae5cfa3cd Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti
Date: Mon, 2 Dec 2024 15:07:13 -0500
Subject: [PATCH 4/6] fix identifier links
---
site/src/data/identifiers.js | 34 ++++++++++++++++++++--------------
site/src/pages/loci/[id].astro | 4 ++--
2 files changed, 22 insertions(+), 16 deletions(-)
diff --git a/site/src/data/identifiers.js b/site/src/data/identifiers.js
index bc15d2c3..31c5caa6 100644
--- a/site/src/data/identifiers.js
+++ b/site/src/data/identifiers.js
@@ -112,17 +112,23 @@ export const getIdentifiers = (d) =>
},
],
},
- ].map(({ identifiers, ...rest }) => ({
- ...rest,
- identifiers: identifiers
- /** for each reference type */
- .map(({ key, link, ...rest }) => ({
- ...rest,
- /** link text */
- label: d[key],
- /** link target, with id inserted */
- link: link.replace("$ID", d[key]),
- }))
- /** remove types with no identifiers */
- .filter(({ label }) => label?.length),
- }));
+ ]
+ .map(({ identifiers, ...rest }) => ({
+ ...rest,
+ identifiers: identifiers
+ /** for each reference type */
+ .map(({ key, link, ...rest }) => ({
+ ...rest,
+ links:
+ d[key]?.map((id) => ({
+ /** link text */
+ label: id,
+ /** link target, with id inserted */
+ link: link.replace("$ID", id),
+ })) || [],
+ }))
+ /** remove identifiers with no links */
+ .filter(({ links }) => links?.length),
+ }))
+ /** remove types with no identifiers */
+ .filter(({ identifiers }) => identifiers.length);
diff --git a/site/src/pages/loci/[id].astro b/site/src/pages/loci/[id].astro
index 3c790f8f..969a580b 100644
--- a/site/src/pages/loci/[id].astro
+++ b/site/src/pages/loci/[id].astro
@@ -112,13 +112,13 @@ const additionalLiterature =
{name}
- {identifiers.map(({ name, label, link, tooltip, info }) => (
+ {identifiers.map(({ name, links, tooltip, info }) => (
<>
{name}
- {label.map((label) => (
+ {links.map(({ label, link }) => (
{label}
))}
From 613abfcbae8e4bc003cc0abb80106bec632ef510 Mon Sep 17 00:00:00 2001
From: "Laurel (they/he)" <85411760+laurelhiatt@users.noreply.github.com>
Date: Mon, 2 Dec 2024 13:27:20 -0700
Subject: [PATCH 5/6] update webstr URLs
---
site/src/data/identifiers.js | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/site/src/data/identifiers.js b/site/src/data/identifiers.js
index 31c5caa6..bd0571e8 100644
--- a/site/src/data/identifiers.js
+++ b/site/src/data/identifiers.js
@@ -97,7 +97,7 @@ export const getIdentifiers = (d) =>
{
key: "webstr_hg38",
name: "WebSTR hg38",
- link: "https://webstr.ucsd.edu/search?genome=hg38&query=$ID",
+ link: "https://webstr.ucsd.edu/locus?repeat_id=$ID&genome=hg38",
tooltip:
"Genome-wide STR data across populations, with details on variation, expression, constraint, and imputation metrics",
info: "https://webstr.ucsd.edu",
@@ -105,7 +105,7 @@ export const getIdentifiers = (d) =>
{
key: "webstr_hg19",
name: "WebSTR hg19",
- link: "https://webstr.ucsd.edu/search?genome=hg19&query=$ID",
+ link: "https://webstr.ucsd.edu/locus?repeat_id=$ID",
tooltip:
"Genome-wide STR data across populations, with details on variation, expression, constraint, and imputation metrics",
info: "https://webstr.ucsd.edu",
From 0bf2af2299b288873a4ce3e132d8621f05a6e1aa Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti
Date: Mon, 2 Dec 2024 16:06:48 -0500
Subject: [PATCH 6/6] lint
---
site/src/components/Header.astro | 6 +-----
site/src/data/identifiers.js | 2 +-
2 files changed, 2 insertions(+), 6 deletions(-)
diff --git a/site/src/components/Header.astro b/site/src/components/Header.astro
index 64efdcbe..1c070062 100644
--- a/site/src/components/Header.astro
+++ b/site/src/components/Header.astro
@@ -42,11 +42,7 @@ const links = [
-
+
diff --git a/site/src/data/identifiers.js b/site/src/data/identifiers.js
index bd0571e8..a44de07f 100644
--- a/site/src/data/identifiers.js
+++ b/site/src/data/identifiers.js
@@ -97,7 +97,7 @@ export const getIdentifiers = (d) =>
{
key: "webstr_hg38",
name: "WebSTR hg38",
- link: "https://webstr.ucsd.edu/locus?repeat_id=$ID&genome=hg38",
+ link: "https://webstr.ucsd.edu/locus?genome=hg38&repeat_id=$ID",
tooltip:
"Genome-wide STR data across populations, with details on variation, expression, constraint, and imputation metrics",
info: "https://webstr.ucsd.edu",