From 84931541984119635f492d220baf1c2f76d4d9db Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Wed, 13 Dec 2023 16:04:21 +0100
Subject: [PATCH] add pvc for structure data
---
components/content/MolstarPdbePlugin.vue | 24 +++++++++++++++----
components/content/StructureDb.vue | 7 +++++-
deploy/df-wiki/templates/deployment.yaml | 6 ++++-
deploy/df-wiki/templates/pvc-structure.yaml | 12 ++++++++++
.../df-wiki-cli/df_wiki_cli/content/main.py | 2 +-
5 files changed, 43 insertions(+), 8 deletions(-)
create mode 100644 deploy/df-wiki/templates/pvc-structure.yaml
diff --git a/components/content/MolstarPdbePlugin.vue b/components/content/MolstarPdbePlugin.vue
index 2cc1e5ca..731bccde 100644
--- a/components/content/MolstarPdbePlugin.vue
+++ b/components/content/MolstarPdbePlugin.vue
@@ -104,9 +104,20 @@ const selectedPaePath = computed(() => {
const paeData = ref([])
watch(selectedPaePath, async (newPaePath) => {
if (newPaePath !== null) {
- const data = await d3.tsv(newPaePath);
- // console.log(data)
- paeData.value = data
+ try {
+ const data = await d3.tsv(newPaePath);
+ console.log(data.length)
+ if (data.length > 500) {
+ paeData.value = []
+ }
+ else {
+ paeData.value = data
+ }
+
+ }
+ catch (error) {
+ console.log(error)
+ }
} else {
paeData.value = []
}
@@ -116,9 +127,11 @@ watch(selectedPaePath, async (newPaePath) => {
const sanitizedPaeData = computed(() => {
return paeData.value.reduce((acc, curr, index) => {
const scoredResidue = index
+ // let newAcc = [...acc]
for (const [alignedResidue, value] of Object.entries(curr)) {
// console.log(value)
acc.push({ alignedResidue: parseInt(alignedResidue), scoredResidue: parseInt(scoredResidue), value: parseFloat(value) })
+ // newAcc = [...newAcc, ...[{ alignedResidue: parseInt(alignedResidue), scoredResidue: parseInt(scoredResidue), value: parseFloat(value) }]]
}
return acc
@@ -188,8 +201,9 @@ watch(selectedPdb, (selectedPdb, prevSelectPdb) => {
custom-data-format="cif"></pdbe-molstar>
</v-sheet>
</v-col>
- <v-col v-if="sanitizedPaeData?.length > 0">
- <PlotFigure defer :options="plotPaeOptions"></PlotFigure>
+ <v-col >
+ <PlotFigure v-if="sanitizedPaeData?.length > 0" defer :options="plotPaeOptions"></PlotFigure>
+ <v-alert type="warning">The PAE is to large</v-alert>
<v-card flat color="transparent">
<v-card-title>Model Confidence</v-card-title>
diff --git a/components/content/StructureDb.vue b/components/content/StructureDb.vue
index 4757a267..bf0ba15a 100644
--- a/components/content/StructureDb.vue
+++ b/components/content/StructureDb.vue
@@ -43,6 +43,11 @@ function pdbNameToCif(pdbPath: string) {
return `${cifPath}.cif`
}
+
+function toSystemName(rawName: string) {
+ return rawName.split(/_|-0/)[0].toLocaleLowerCase()
+
+}
</script>
<template>
<ServerDbTable title="Predicted Structures" db="structure" :sortBy="sortBy" :facets="facets"
@@ -58,7 +63,7 @@ function pdbNameToCif(pdbPath: string) {
<td :colspan="columns.length">
<v-card flat color="transparent">
<v-card-text>
- <MolstarPdbePlugin :data-urls="[`/${item.system.toLowerCase()}/${pdbNameToCif(item.pdb)}`]">
+ <MolstarPdbePlugin :data-urls="[`/${toSystemName(item.system)}/${pdbNameToCif(item.pdb)}`]">
</MolstarPdbePlugin>
</v-card-text>
</v-card>
diff --git a/deploy/df-wiki/templates/deployment.yaml b/deploy/df-wiki/templates/deployment.yaml
index 6ac7bd19..10e0c872 100644
--- a/deploy/df-wiki/templates/deployment.yaml
+++ b/deploy/df-wiki/templates/deployment.yaml
@@ -54,6 +54,8 @@ spec:
name: tmp
- name: nginx-config
mountPath: /etc/nginx/conf.d/
+ - name: structure-data-pvc
+ mountPath: /structure-data
{{- with .Values.nodeSelector }}
@@ -74,4 +76,6 @@ spec:
- name: nginx-config
configMap:
name: nginx-config
-
+ - name: structure-data-pvc
+ persistentVolumeClaim:
+ claimName: structure-data-pvc
diff --git a/deploy/df-wiki/templates/pvc-structure.yaml b/deploy/df-wiki/templates/pvc-structure.yaml
new file mode 100644
index 00000000..ec9612a0
--- /dev/null
+++ b/deploy/df-wiki/templates/pvc-structure.yaml
@@ -0,0 +1,12 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+ name: structure-data-pvc
+spec:
+ accessModes:
+ - ReadWriteMany
+ resources:
+ requests:
+ storage: 40Gi
+ storageClassName: isilon
+ volumeMode: Filesystem
\ No newline at end of file
diff --git a/packages/df-wiki-cli/df_wiki_cli/content/main.py b/packages/df-wiki-cli/df_wiki_cli/content/main.py
index d01337bc..32333d16 100644
--- a/packages/df-wiki-cli/df_wiki_cli/content/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/content/main.py
@@ -105,7 +105,7 @@ def structure(
for f in dir.iterdir():
console.print(f"[green] {f.name}")
# get the system name
- system = re.split("_|\.", f.name)[0].lower()
+ system = re.split("_|\.|-0", f.name)[0].lower()
console.print(system)
systemDir = output / system
--
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