From 2633b7d301f60d56c165aa26568809454f616631 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Thu, 20 May 2021 21:59:31 +0200
Subject: [PATCH] fix picture_path
---
gga_init.py | 18 +++++++++---------
speciesData.py | 1 -
templates/gspecies_compose.yml.j2 | 2 +-
3 files changed, 10 insertions(+), 11 deletions(-)
diff --git a/gga_init.py b/gga_init.py
index 1025efa..b87f3f6 100755
--- a/gga_init.py
+++ b/gga_init.py
@@ -38,7 +38,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
"""
- def make_directory_tree(self, picture_path):
+ def make_directory_tree(self):
"""
Generate the directory tree for an organism
@@ -77,18 +77,18 @@ class DeploySpeciesStack(speciesData.SpeciesData):
self.config.pop(constants.CONF_TRIPAL_BANNER_PATH, None)
# Copy the organism picture for tripal
- if picture_path is not None:
- if os.path.isfile(picture_path):
- picture_path_basename = os.path.basename(picture_path)
+ if self.picture_path is not None:
+ if os.path.isfile(self.picture_path):
+ picture_path_basename = os.path.basename(self.picture_path)
picture_path_filename, picture_path_extension = os.path.splitext(picture_path_basename)
if picture_path_extension == ".png" or picture_path_extension == ".jpg":
picture_dest_name = "species%s" % picture_path_extension
picture_dest_path = os.path.join(self.species_dir, picture_dest_name)
- shutil.copy(picture_path, picture_dest_path)
+ shutil.copy(self.picture_path, picture_dest_path)
else:
- logging.error("Specified organism picture has wrong extension (must be '.png' or '.jpg'): {0}".format(picture_path))
+ logging.error("Specified organism picture has wrong extension (must be '.png' or '.jpg'): {0}".format(self.picture_path))
else:
- logging.error("Specified organism picture not found {0} for {1}".format(picture_path, self.genus_uppercase + " " + self.species))
+ logging.error("Specified organism picture not found {0} for {1}".format(self.picture_path, self.genus_uppercase + " " + self.species))
# Create nginx dirs and write/re-write nginx conf
make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
@@ -423,8 +423,8 @@ if __name__ == "__main__":
logging.info("gga_init.py called for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)
# Make/update directory tree
- picture_path = sp_picture_dict[deploy_stack_for_current_organism.genus_species]
- deploy_stack_for_current_organism.make_directory_tree(picture_path)
+ deploy_stack_for_current_organism.picture_path = sp_picture_dict[deploy_stack_for_current_organism.genus_species]
+ deploy_stack_for_current_organism.make_directory_tree()
logging.info("Successfully generated the directory tree for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)
# Make compose files
diff --git a/speciesData.py b/speciesData.py
index 9020e2c..b0d6190 100755
--- a/speciesData.py
+++ b/speciesData.py
@@ -69,7 +69,6 @@ class SpeciesData:
self.date = datetime.today().strftime("%Y-%m-%d")
self.origin = parameters_dictionary_description[constants.ORG_PARAM_DESC_ORIGIN]
self.performed = parameters_dictionary_data[constants.ORG_PARAM_DATA_PERFORMED_BY]
- self.picture_path = parameters_dictionary_description[constants.ORG_PARAM_DESC_PICTURE_PATH]
if parameters_dictionary_data[constants.ORG_PARAM_DATA_GENOME_VERSION] == "":
self.genome_version = "1.0"
diff --git a/templates/gspecies_compose.yml.j2 b/templates/gspecies_compose.yml.j2
index b8c9e1b..1b1e8f8 100644
--- a/templates/gspecies_compose.yml.j2
+++ b/templates/gspecies_compose.yml.j2
@@ -42,7 +42,7 @@ services:
- ./banner.png:/var/www/html/banner.png:ro
{% endif %}
#- /groups/XXX/:/groups/XXX/:ro # We do this when we have symlinks in src_data pointing to /groups/XXX/...
- {% if 'picture_path' is defined and 'picture_path' != '' %}
+ {% if 'picture_path' is defined %}
{% if 'png' in picture_path %}
- ./species.png:/var/www/html/species.png:ro
{% endif %}
--
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