diff --git a/convertPheno_client/src/code/apis.js b/convertPheno_client/src/code/apis.js index 78aa5220..894f9977 100644 --- 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 index 7ca68bd0..b50f7a2c 100644 --- 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 index 53357803..0fa781ad 100755 --- 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 index 70b46009..4e51f2d2 100644 --- 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 index 650e5491..77b3e8da 100644 --- 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 index 34d3a9f4..8a71fd1d 100644 --- 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 index e2c4a49c..c443bcb2 100644 --- 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 index 5d0cca24..dacad173 100644 --- 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 index fc3db454..7a43f16f 100644 --- 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 index e4a69cfe..2b1fe7d2 100644 --- 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 index 46a8da66..2b5632df 100644 --- 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 index c8e91f65..c94b327f 100644 --- 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 index b70f1152..410a4941 100644 --- 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 index 87db9e25..c206633f 100644 --- 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 index 86267ef1..a46892da 100644 --- 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 index c33c7240..b61127d5 100644 --- 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 index 05e8e10b..f1d80d77 100644 --- 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 index a5f43e28..9a662500 100644 --- 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 index 65d7befc..bad3dd1d 100644 --- 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 index 83f6798c..821f427a 100644 --- 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 index 3b02380e..077c2a83 100644 --- 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 index cae81162..09c44f25 100644 --- 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 index 125141e4..870652fb 100644 --- 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 index abcc1cca..224711c8 100644 --- 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 index 937070a0..a82253e9 100644 --- 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 index 82de65d4..ec9f3fa4 100644 --- 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 index 45c41172..2bddd5b2 100644 --- 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 index 5be70053..8d29694c 100644 --- 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 index ad51e3eb..540d40b0 100644 --- 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 index 5b7aaba1..ae51e343 100644 --- 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 index 4500561b..707ed5fd 100755 --- 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 index 759051c1..b7d29d9a 100644 --- 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 index a41f793c..e567d96e 100755 --- 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