Merge branch 'dev' into system-distribution-plot

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 

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