From ec3f5a5590fa1bbd1cff4f6e181c5914e4fb46e1 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Tue, 20 Apr 2021 16:53:12 +0200
Subject: [PATCH] galaxy_nginx.conf jinja2 template writing, moved
configuration files from 'templates' to 'files' for clarity
---
.../authelia_users_template.yml | 0
.../nginx_apollo_template.conf | 0
.../nginx_download_template.conf | 0
gga_init.py | 34 +++++--------------
templates/galaxy_nginx.conf.j2 | 19 +++++++++++
5 files changed, 28 insertions(+), 25 deletions(-)
rename {templates => files}/authelia_users_template.yml (100%)
rename templates/nginx_apollo.conf => files/nginx_apollo_template.conf (100%)
rename templates/nginx_download.conf => files/nginx_download_template.conf (100%)
create mode 100644 templates/galaxy_nginx.conf.j2
diff --git a/templates/authelia_users_template.yml b/files/authelia_users_template.yml
similarity index 100%
rename from templates/authelia_users_template.yml
rename to files/authelia_users_template.yml
diff --git a/templates/nginx_apollo.conf b/files/nginx_apollo_template.conf
similarity index 100%
rename from templates/nginx_apollo.conf
rename to files/nginx_apollo_template.conf
diff --git a/templates/nginx_download.conf b/files/nginx_download_template.conf
similarity index 100%
rename from templates/nginx_download.conf
rename to files/nginx_download_template.conf
diff --git a/gga_init.py b/gga_init.py
index 86e4c11..dbe4745 100755
--- a/gga_init.py
+++ b/gga_init.py
@@ -76,30 +76,6 @@ class DeploySpeciesStack(speciesData.SpeciesData):
logging.debug("Using default banner for Tripal pages")
self.config.pop("banner_path", None)
-
- # Write galaxy_nginx.conf
- try:
- with open(os.path.abspath(os.path.join(self.main_dir, "galaxy_nginx.conf")), "w") as galaxy_nginx_conf:
- galaxy_nginx_conf.truncate(0)
- galaxy_nginx_conf.write("uwsgi_param QUERY_STRING $query_string;")
- galaxy_nginx_conf.write("uwsgi_param REQUEST_METHOD $request_method;")
- galaxy_nginx_conf.write("uwsgi_param CONTENT_TYPE $content_type;")
- galaxy_nginx_conf.write("uwsgi_param CONTENT_LENGTH $content_length;")
- galaxy_nginx_conf.write("uwsgi_param REQUEST_URI $request_uri;")
- galaxy_nginx_conf.write("uwsgi_param PATH_INFO $document_uri;")
- galaxy_nginx_conf.write("uwsgi_param DOCUMENT_ROOT $document_root;")
- galaxy_nginx_conf.write("uwsgi_param SERVER_PROTOCOL $server_protocol;")
- galaxy_nginx_conf.write("uwsgi_param REQUEST_SCHEME $scheme;")
- galaxy_nginx_conf.write("uwsgi_param HTTPS $https if_not_empty;")
- galaxy_nginx_conf.write("uwsgi_param REMOTE_ADDR $remote_addr;")
- galaxy_nginx_conf.write("uwsgi_param REMOTE_PORT $remote_port;")
- galaxy_nginx_conf.write("uwsgi_param SERVER_PORT $server_port;")
- galaxy_nginx_conf.write("uwsgi_param SERVER_NAME $server_name;")
- galaxy_nginx_conf.write("uwsgi_param HTTP_REMOTE_USER gga;")
- except OSError as exc:
- logging.critical("Cannot write galaxy NginX conf file (%s)" % os.path.abspath(self.script_dir))
- sys.exit(exc)
-
# Create nginx dirs and write/re-write nginx conf
make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
try:
@@ -151,6 +127,14 @@ class DeploySpeciesStack(speciesData.SpeciesData):
gspecies_compose_file.truncate(0)
gspecies_compose_file.write(gspecies_compose_output)
+
+ galaxy_nginx_conf_template = env.get_template("galaxy_nginx_conf.j2")
+ galaxy_nginx_conf_output = galaxy_nginx_conf_template.render(render_vars)
+ with open(os.path.join(self.main_dir, "galaxy_nginx.conf"), "w") as galaxy_nginx_conf_file:
+ logging.debug("Writing the galaxy_nginx.conf file for %s" % self.genus_species)
+ galaxy_nginx_conf_file.truncate(0)
+ galaxy_nginx_conf_file.write(galaxy_nginx_conf_output)
+
# Create the volumes (directory) of the species docker-compose file
create_mounts(working_dir=".", main_dir=self.main_dir)
@@ -248,7 +232,7 @@ def make_traefik_compose_files(config, main_dir):
sys.exit()
# Path to the authelia users in the repo
- authelia_users_path = script_dir + "/templates/authelia_users_template.yml"
+ authelia_users_path = script_dir + "/files/authelia_users_template.yml"
# Copy authelia "users" file
if not os.path.isfile("./traefik/authelia/users.yml"):
shutil.copy(authelia_users_path, "./traefik/authelia/users.yml")
diff --git a/templates/galaxy_nginx.conf.j2 b/templates/galaxy_nginx.conf.j2
new file mode 100644
index 0000000..5d05b1f
--- /dev/null
+++ b/templates/galaxy_nginx.conf.j2
@@ -0,0 +1,19 @@
+#jinja2: lstrip_blocks: “Trueâ€, trim_blocks: "True"
+uwsgi_param QUERY_STRING $query_string;
+uwsgi_param REQUEST_METHOD $request_method;
+uwsgi_param CONTENT_TYPE $content_type;
+uwsgi_param CONTENT_LENGTH $content_length;
+
+uwsgi_param REQUEST_URI $request_uri;
+uwsgi_param PATH_INFO $document_uri;
+uwsgi_param DOCUMENT_ROOT $document_root;
+uwsgi_param SERVER_PROTOCOL $server_protocol;
+uwsgi_param REQUEST_SCHEME $scheme;
+uwsgi_param HTTPS $https if_not_empty;
+
+uwsgi_param REMOTE_ADDR $remote_addr;
+uwsgi_param REMOTE_PORT $remote_port;
+uwsgi_param SERVER_PORT $server_port;
+uwsgi_param SERVER_NAME $server_name;
+
+uwsgi_param HTTP_REMOTE_USER {% if https_port is defined %}$http_remote_user if_not_empty;{% elif galaxy_defaut_admin_user is defined %}{{ galaxy_defaut_admin_user }};{% else %}$http_remote_user if_not_empty;{% endif %}
--
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