Merge branch 'dev' into matrix-pdock

.gitlab-ci.yml

@@ -360,12 +360,13 @@ update-meilisearch-index:prod:
   stage: get-meili-key
   variables:
     MEILI_HOST: "http://localhost:7700"
+    MEILI_HOST_NO_PROTOCOLE: "localhost:7700"
   script:
     - > 
       df-wiki-cli 
       meilisearch 
       --key "${MEILI_MASTER_KEY}" 
-      --host ${MEILI_HOST} 
+      --host "${MEILI_HOST}"
       get-env-var
       --output build.env
   artifacts:
@@ -378,6 +379,7 @@ set-meili-env:dev:
   extends: .set-meili-env
   variables:
     MEILI_HOST: "https://${MEILI_HOST_DEV}"
+    MEILI_HOST_NO_PROTOCOLE: ${MEILI_HOST_DEV}
   rules:
     - if: $CI_COMMIT_BRANCH != "main"  
 
@@ -385,6 +387,8 @@ set-meili-env:prod:
   extends: .set-meili-env
   variables:
     MEILI_HOST: "https://${MEILI_HOST_PROD}"
+    MEILI_HOST_NO_PROTOCOLE: ${MEILI_HOST_PROD}
+
   rules:
     - if: $CI_COMMIT_BRANCH == "main"  
 
@@ -416,7 +420,6 @@ sync-zotero:
     - *docker-login
   script:
     - echo $MEILI_HOST
-    - echo $MEILI_API_KEY
     - >
       docker buildx build --pull -t "$CI_REGISTRY_IMAGE/$IMAGE_NAME:$CI_COMMIT_SHORT_SHA" 
       --build-arg "BASE_URL=$BASE_URL" 
@@ -450,7 +453,7 @@ build:prod:wiki:
     # - get-pfam
   variables:
     BASE_URL: /wiki/
-    HOST_URL: https://${HOST_PROD}
+    HOST_URL: "https://${HOST_PROD}"
 
   rules:
     - if: $CI_COMMIT_BRANCH == "main"  
@@ -517,7 +520,7 @@ deploy:prod:
   variables:
     NODE_ENV: "production"
     KUBE_NAMESPACE: "defense-finder-prod"
-    PUBLIC_URL: "${HOST_PROD}"
+    PUBLIC_URL: "https://${HOST_PROD}"
     CI_DEBUG_TRACE: "false"
     ENV: "production"
   environment:
@@ -601,7 +604,7 @@ create-structures-archives:prod:
   variables:
     NODE_ENV: "production"
     KUBE_NAMESPACE: "defense-finder-prod"
-    PUBLIC_URL: "${HOST_PROD}"
+    PUBLIC_URL: "https://${HOST_PROD}"
     CI_DEBUG_TRACE: "false"
     ENV: "production"
   environment:

components/content/RefseqDb.vue

@@ -18,7 +18,12 @@ const itemValue = ref("id");
 const { width } = useDisplay();
 const dbName = ref("refseq")
 const taxonomyFacet = ref<Record<string, any> | undefined>(undefined)
-
+const cellPlotMargin = ref({
+    marginLeft: 150,
+    marginBottom: 200,
+    marginTop: 0,
+    marginRight: 50
+})
 
 
 onBeforeMount(async () => {
@@ -150,7 +155,7 @@ const availableTaxo: Ref<string[]> = ref([
     "Superkingdom"
 ]);
 
-const scaleTypes = ref<string[]>(['linear', 'sqrt', 'log', 'symlog'])
+const scaleTypes = ref<string[]>(['linear', 'sqrt', 'symlog'])
 const selectedTaxoRank = ref<"species" | "genus" | "family" | "order" | "class" | "phylum" | "Superkingdom">("Superkingdom");
 
 const headers = ref([
@@ -190,7 +195,18 @@ const computedWidth = computed(() => {
     return Math.max(currentWidth, 550);
 });
 
+const cellPlotComputedDimension = computed(() => {
+    const { marginLeft, marginBottom, marginRight, marginTop } = toValue(cellPlotMargin)
+    const toValWidth = toValue(width)
+    const widthFixCell = countSystem.value * 50 + marginLeft + marginRight
+    const heigthFix = countClade.value * 50 + marginTop + marginBottom
+    if (widthFixCell > toValWidth) {
+        return { width: toValWidth - marginLeft - marginRight, height: undefined }
+    } else {
+        return { width: widthFixCell, height: heigthFix }
+    }
 
+})
 
 const allHits: Ref<Record<string, any> | undefined> = ref(undefined)
 
@@ -364,17 +380,33 @@ const sortedCellDomain = computed(() => {
     }
 })
 const binPlotOptions = computed(() => {
+    const { marginLeft, marginBottom } = toValue(cellPlotMargin)
+    const { height } = toValue(cellPlotComputedDimension)
+
     return {
-        marginLeft: 150,
-        marginBottom: 200,
+        marginLeft,
+        marginBottom,
         padding: 0,
         grid: true,
-        aspectRatio: true,
+        aspectRatio: height ? undefined : 1,
         x: { tickRotate: 90, label: "Systems", domain: toValue(sortedCellDomain) },
         color: { scheme: "plasma", legend: true, label: `Proportion per ${selectedTaxoRank.value}`, domain: [0, 100] },
     }
 })
 
+const countSystem = computed(() => {
+    const toValueAllHits = toValue(allHits)
+    const data = toValueAllHits?.hits ?? []
+    const setSystem = new Set(data.map(d => d.type))
+    return setSystem.size
+})
+
+const countClade = computed(() => {
+    const toValueAllHits = toValue(allHits)
+    const data = toValueAllHits?.hits ?? []
+    const setSystem = new Set(data.map(d => d[selectedTaxoRank.value]))
+    return setSystem.size
+})
 
 const binPlotGroup = computed(() => {
     return Plot.group(
@@ -423,9 +455,13 @@ const binPlotDataOptions = computed(() => {
     const toValBinPlotGroup = toValue(binPlotGroup)
     const data = toValueAllHits?.hits ?? []
     const plotCellMark = Plot.cell(data, toValBinPlotGroup)
+    const { width, height } = toValue(cellPlotComputedDimension)
+
+    const dim = height ? { width, height } : { width }
+
     return toValueAllHits?.hits?.length > 0 ? {
         ...binPlotOptions.value,
-        width: width.value,
+        ...dim,
         title: `Proportion of genomes with defense system X per ${selectedTaxoRank.value} taxonomic rank`,
         color: {
             ...binPlotOptions.value.color,

deploy/df-wiki/values.yaml

@@ -35,6 +35,7 @@ securityContext:
   runAsNonRoot: true
   runAsUser: 101
   runAsGroup: 101
+  allowPrivilegeEscalation: false
   # capabilities:
   #   drop:
   #   - ALL

deploy/meilisearch/Chart.yaml

@@ -25,6 +25,6 @@ appVersion: "1.16.0"
 
 dependencies:
   - name: meilisearch
-    version: 0.3.0
+    version: 0.5.0
     repository: "https://meilisearch.github.io/meilisearch-kubernetes"
 

docker-compose.yml

@@ -7,7 +7,7 @@ services:
       args:
         BASE_URL: /wiki
         MEILI_HOST: http://localhost:7700
-        MEILI_API_KEY: f9cc073016cbb392365aae86517878cb3f3408bb85c1fafd06e27f73ccb35e3d
+        MEILI_API_KEY: f5f5f1bc48e6379fc2509f5bf0aed1fce96c1bbf86e0a194c605b258d7cfe890
         HOST_URL: http://localhost:8082
     container_name: nuxt
     environment:
@@ -31,7 +31,7 @@ services:
       - main
 
   meilisearch:
-    image: getmeili/meilisearch:v1.5
+    image: getmeili/meilisearch:v1.7
     # command:
     #   - meilisearch
     #   - --http-addr 

packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py

@@ -137,7 +137,9 @@ def get_env_var(
     keys = client.get_keys()
 
     api_key = [res.key for res in keys.results if res.name == "Default Search API Key"]
+    print(ctx.obj.host)
     if len(api_key) == 1:
         with open(output, "a") as outfile:
-            outfile.write(f"MEILI_HOST={ctx.obj.host}\n")
-            outfile.write(f"MEILI_API_KEY={api_key[0]}\n")
+            print(ctx.obj.host)
+            outfile.write(f'MEILI_HOST="{ctx.obj.host}"\n')
+            outfile.write(f'MEILI_API_KEY="{api_key[0]}"\n')

scripts/fill-local-meilisearch.sh

+#!/bin/bash 
+# REFSEQ
+df-wiki-cli meilisearch delete-all-documents refseq
+df-wiki-cli meilisearch update --file ../data/refseq_res.csv --document refseq
+
+
+# REF SEQ TAXO
+df-wiki-cli content refseq-group-per-assembly --input ../data/refseq_res.csv --output /tmp/refseqtaxo.csv
+df-wiki-cli meilisearch delete-all-documents refseqtaxo
+df-wiki-cli meilisearch update --file /tmp/refseqtaxo.csv --document refseqtaxo
+
+# REFSEQ TAXO TYPE
+
+df-wiki-cli content refseq-group-per-assembly-and-type --input ../data/refseq_res.csv --output /tmp/refseqtaxotype.csv
+df-wiki-cli meilisearch delete-all-documents refseqtaxotype
+df-wiki-cli meilisearch  update --file /tmp/refseqtaxotype.csv --document refseqtaxotype
+
+
+# SANITIZED REFSEQ
+df-wiki-cli content refseq-sanitized-hits --input ../data/refseq_res.csv --output /tmp/refseq-sanitized.csv
+
+df-wiki-cli meilisearch delete-all-documents refseqsanitized
+df-wiki-cli meilisearch update --file /tmp/refseq-sanitized.csv --document refseqsanitized 
+
+# systems
+df-wiki-cli content systems --dir ../content/3.defense-systems/ --pfam ../public/pfam-a-hmm.csv --output /tmp/list-systems.json
+df-wiki-cli meilisearch update --file /tmp/list-systems.json --document systems
+
+# STRUCTURE 
+df-wiki-cli meilisearch update --file ../data/all_predictions_statistics_clean.csv --document structure
+
+# ARTICLES
+# df-wiki-cli meilisearch delete-all-documents article
+# df-wiki-cli meilisearch