replaced cnag.crg.eu with cnag.eu

CNAG-Biomedical-Informatics · Dec 8, 2023 · 6dc81b3 · 6dc81b3
1 parent ee8932a
commit 6dc81b3
Show file tree

Hide file tree

Showing 33 changed files with 34 additions and 48 deletions.
diff --git a/convertPheno_client/src/code/apis.js b/convertPheno_client/src/code/apis.js
@@ -12,19 +12,6 @@
 
 import axiosInstance from "./axiosInstance";
 
-// ist this function actually still used?
-export async function fileUpload(token, urlprefix, data) {
-  return fetch(`${urlprefix}api/submission/upload`, {
-    method: "POST",
-    body: data,
-    headers: {
-      Accept: "application/json",
-      connection: "keep-alive",
-      Authorization: token,
-    },
-  });
-}
-
 export async function fileConversion(token, urlprefix, data) {
   try {
     const res = await axiosInstance.post(`${urlprefix}api/submission/convert`, data, {

diff --git a/convertPheno_server/docker-compose.yml b/convertPheno_server/docker-compose.yml
@@ -5,7 +5,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/get_public_kc_key.sh b/convertPheno_server/get_public_kc_key.sh
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 # CERTS_URL="https://client/auth/realms/$KC_REALM/protocol/openid-connect/certs"
@@ -24,4 +24,3 @@ if [ -z "$KEY" ]; then
     exit 1
 fi
 echo KC_PUBLIC_KEY=$KEY
-
diff --git a/convertPheno_server/makefile b/convertPheno_server/makefile
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/apis/captcha.py b/convertPheno_server/server/apis/captcha.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/apis/clinical.py b/convertPheno_server/server/apis/clinical.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/apis/jobs.py b/convertPheno_server/server/apis/jobs.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/apis/submission.py b/convertPheno_server/server/apis/submission.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/apis/test.py b/convertPheno_server/server/apis/test.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/app.py b/convertPheno_server/server/app.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/config/config.py b/convertPheno_server/server/config/config.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 from os import environ

diff --git a/convertPheno_server/server/config/config_test.py b/convertPheno_server/server/config/config_test.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/config/general_config.py b/convertPheno_server/server/config/general_config.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/config/gunicorn_conf.py b/convertPheno_server/server/config/gunicorn_conf.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/model.py b/convertPheno_server/server/model.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/security.py b/convertPheno_server/server/security.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/utils/convert_pheno.py b/convertPheno_server/server/utils/convert_pheno.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 """

diff --git a/convertPheno_server/server/utils/db_helpers.py b/convertPheno_server/server/utils/db_helpers.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 import json

diff --git a/convertPheno_server/server/utils/error_handler.py b/convertPheno_server/server/utils/error_handler.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/server/utils/jsonschema_helpers.py b/convertPheno_server/server/utils/jsonschema_helpers.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/tests/conftest.py b/convertPheno_server/tests/conftest.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/tests/helpers/utils.py b/convertPheno_server/tests/helpers/utils.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/tests/test_auth.py b/convertPheno_server/tests/test_auth.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/tests/test_clinical.py b/convertPheno_server/tests/test_clinical.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/tests/test_download.py b/convertPheno_server/tests/test_download.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/tests/test_health.py b/convertPheno_server/tests/test_health.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/tests/test_jobs.py b/convertPheno_server/tests/test_jobs.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_server/tests/test_submission.py b/convertPheno_server/tests/test_submission.py
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/docs/about.md b/docs/about.md
@@ -1,4 +1,4 @@
-**Convert-Pheno-UI** has been developed at [CNAG](https://cnag.crg.eu), Barcelona, Spain.
+**Convert-Pheno-UI** has been developed at [CNAG](https://cnag.eu), Barcelona, Spain.
 
 ## Developers
 
@@ -20,7 +20,7 @@
 
     * Group Leader: [Ivo G. Gut](https://scholar.google.com/citations?user=YKdDEVYAAAAJ)
     * Design: [Sofia Chaves](https://scholar.google.com/citations?user=Q0wogt8AAAAJ)
-    * Developmental support: [Davide Piscia](https://github.com/dpiscia) and his [team](https://www.cnag.crg.eu/teams/bioinformatics-unit/data-platforms-and-tools-development)
+    * Developmental support: [Davide Piscia](https://github.com/dpiscia) and his [team](https://www.cnag.eu/teams/bioinformatics-unit/data-platforms-and-tools-development)
 
 === "External"
 

diff --git a/docs/makefile b/docs/makefile
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Jun/21/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/get_public_kc_key.sh b/get_public_kc_key.sh
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 

diff --git a/makefile b/makefile
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license
 
@@ -67,7 +67,7 @@ kc-ip:
 db-ip:
 	db_ip=$(docker inspect -f '{{range .NetworkSettings.Networks}}{{.IPAddress}}{{end}}' convert-pheno-api-db)
 	echo $${db_ip}
-	
+
 mkcert:
 	/usr/local/bin/mkcert -cert-file ./nginx_mountpoint/certs/convertpheno.local.dev.pem -key-file ./nginx_mountpoint/certs/convertpheno.local.dev-key.pem convertpheno.local.dev
 

diff --git a/nginx_mountpoint/replace_env_vars.sh b/nginx_mountpoint/replace_env_vars.sh
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.eu)
 #
 #   License: GPL-3.0 license