From f579a28aad55074eacb48073d9799da965d32063 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Tue, 20 Apr 2021 18:14:45 +0200
Subject: [PATCH] fix typo, renamed files in 'files' dir, fix for jbrowee menu
url
---
...lia_users_template.yml => authelia_users.yml} | 0
...nx_apollo_template.conf => nginx_apollo.conf} | 0
...ownload_template.conf => nginx_download.conf} | 0
gga_init.py | 16 ++++++++++------
run_workflow_phaeoexplorer.py | 2 +-
5 files changed, 11 insertions(+), 7 deletions(-)
rename files/{authelia_users_template.yml => authelia_users.yml} (100%)
rename files/{nginx_apollo_template.conf => nginx_apollo.conf} (100%)
rename files/{nginx_download_template.conf => nginx_download.conf} (100%)
diff --git a/files/authelia_users_template.yml b/files/authelia_users.yml
similarity index 100%
rename from files/authelia_users_template.yml
rename to files/authelia_users.yml
diff --git a/files/nginx_apollo_template.conf b/files/nginx_apollo.conf
similarity index 100%
rename from files/nginx_apollo_template.conf
rename to files/nginx_apollo.conf
diff --git a/files/nginx_download_template.conf b/files/nginx_download.conf
similarity index 100%
rename from files/nginx_download_template.conf
rename to files/nginx_download.conf
diff --git a/gga_init.py b/gga_init.py
index dbe4745..46e104a 100755
--- a/gga_init.py
+++ b/gga_init.py
@@ -79,11 +79,15 @@ class DeploySpeciesStack(speciesData.SpeciesData):
# Create nginx dirs and write/re-write nginx conf
make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
try:
- with open(os.path.abspath("./nginx/conf/default.conf"), 'w') as conf:
- conf.write("server {\n\tlisten 80;\n\tserver_name ~.;\n\tlocation /download/ {\n\t\talias /project_data/; \n\t\tautoindex on;\n\t}\n}") # The species nginx conf
- except OSError as exc:
- logging.critical("Cannot write NginX conf file")
- sys.exit(exc)
+ shutil.copy(os.path.join(self.script_dir, "files/nginx_download.conf"), os.path.abspath("./nginx/conf/default.conf"))
+ except Exception as exc:
+ logging.critical("Could not copy nginx configuration file for %s" % self.full_name)
+ logging.critical(exc)
+ # with open(os.path.abspath("./nginx/conf/default.conf"), 'w') as conf:
+ # conf.write("server {\n\tlisten 80;\n\tserver_name ~.;\n\tlocation /download/ {\n\t\talias /project_data/; \n\t\tautoindex on;\n\t}\n}") # The species nginx conf
+ # except OSError as exc:
+ # logging.critical("Cannot write NginX conf file")
+ # sys.exit(exc)
# Return to main directory
os.chdir(self.main_dir)
@@ -128,7 +132,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
gspecies_compose_file.write(gspecies_compose_output)
- galaxy_nginx_conf_template = env.get_template("galaxy_nginx_conf.j2")
+ 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)
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index fe77cef..49f3a2a 100755
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -493,7 +493,7 @@ class RunWorkflow(speciesData.SpeciesData):
# as runtime values, using runtime parameters makes the tool throw an internal critical error ("replace not found" error)
# Scratchgmod test: need "http" (or "https"), the hostname (+ port)
if "menu_url" not in self.config.keys():
- jbrowse_menu_url = "https://{hostname}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(hostname=self.config["hostname"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}")
+ jbrowse_menu_url = "https://{hostname}/sp/{genus_sp}/feature/{Genus}/{species}/mRNA/{id}".format(hostname=self.config["hostname"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}")
else:
jbrowse_menu_url = self.config["menu_url"]
if workflow_name == "Jbrowse":
--
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