From 39a9162b688a32e709ce73063c8f08aff17324cb Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Tue, 18 May 2021 17:32:20 +0200
Subject: [PATCH] Fix tripal page organism picture
---
constants.py | 2 ++
gga_init.py | 34 +++++++++++++++++++++++++++++-----
speciesData.py | 2 +-
3 files changed, 32 insertions(+), 6 deletions(-)
diff --git a/constants.py b/constants.py
index 9fa3876..8e2fcfc 100644
--- a/constants.py
+++ b/constants.py
@@ -7,6 +7,7 @@ ORG_PARAM_DESC_SEX = "sex"
ORG_PARAM_DESC_STRAIN = "strain"
ORG_PARAM_DESC_COMMON_NAME = "common_name"
ORG_PARAM_DESC_ORIGIN = "origin"
+ORG_PARAM_DESC_PICTURE_PATH = "tripal_species_picture"
ORG_PARAM_DESC_MAIN_SPECIES = "main_species"
ORG_PARAM_DATA = "data"
ORG_PARAM_DATA_GENOME_PATH = "genome_path"
@@ -23,6 +24,7 @@ ORG_PARAM_DATA_PERFORMED_BY = "performed_by"
ORG_PARAM_SERVICES = "services"
ORG_PARAM_SERVICES_BLAST = "blast"
+
# Constants used in the config yaml file
CONF_ALL_HOSTNAME = "hostname"
CONF_ALL_HTTP_PORT = "http_port"
diff --git a/gga_init.py b/gga_init.py
index 1ae0ce4..4be3f70 100755
--- a/gga_init.py
+++ b/gga_init.py
@@ -76,6 +76,21 @@ class DeploySpeciesStack(speciesData.SpeciesData):
logging.debug("Using default banner for Tripal pages")
self.config.pop(constants.CONF_TRIPAL_BANNER_PATH, None)
+ # Copy the organism picture for tripal if one was specified in the input species
+ if self.tripal_species_picture is not None:
+ if self.tripal_species_picture.endswith("png"):
+ species_picture_dest_path = os.path.join(self.species_dir, os.path.abspath("species.png"))
+ try:
+ os.symlink(os.path.abspath(self.tripal_species_picture, species_picture_dest_path))
+ except FileNotFoundError:
+ logging.info("Specified organism picture ({0}) not found for {1}".format(self.tripal_species_picture, self.genus_upper + " " + self.species))
+ elif self.tripal_species_picture.endswith("jpg"):
+ species_picture_dest_path = os.path.join(self.species_dir, os.path.abspath("species.jpg"))
+ try:
+ os.symlink(os.path.abspath(self.tripal_species_picture, species_picture_dest_path))
+ except FileNotFoundError:
+ logging.info("Specified organism picture ({0}) not found for {1}".format(self.tripal_species_picture, self.genus_upper + " " + self.species))
+
# Create nginx dirs and write/re-write nginx conf
make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
try:
@@ -111,11 +126,20 @@ class DeploySpeciesStack(speciesData.SpeciesData):
# We need a dict holding all key (variables) - values that needs to be replaced in the template as our rendering dict
# To do so we need both input file vars and config vars
# Create input file vars dict
- input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species,
- "genus_species": self.genus_species, "genus_species_strain_sex": self.species_folder_name,
- "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species.lower(), self.sex),
- "strain": self.strain, "sex": self.sex, "Genus_species": self.genus_species[0].upper() + self.genus_species[1:],
- "blast": self.blast}
+
+ input_vars = {}
+ if self.tripal_species_picture is not None:
+ input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species,
+ "genus_species": self.genus_species, "genus_species_strain_sex": self.species_folder_name,
+ "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species.lower(), self.sex),
+ "strain": self.strain, "sex": self.sex, "Genus_species": self.genus_species[0].upper() + self.genus_species[1:],
+ "blast": self.blast, "tripal_species_picture": self.tripal_species_picture}
+ else:
+ input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species,
+ "genus_species": self.genus_species, "genus_species_strain_sex": self.species_folder_name,
+ "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species.lower(), self.sex),
+ "strain": self.strain, "sex": self.sex, "Genus_species": self.genus_species[0].upper() + self.genus_species[1:],
+ "blast": self.blast}
if (len(self.config.keys()) == 0):
logging.error("Empty config dictionary")
# Merge the two dicts
diff --git a/speciesData.py b/speciesData.py
index 517ebe7..87c2015 100755
--- a/speciesData.py
+++ b/speciesData.py
@@ -91,7 +91,7 @@ class SpeciesData:
if constants.ORG_PARAM_DESC_PICTURE_PATH in parameters_dictionary_description.keys():
self.tripal_species_picture = parameters_dictionary_services[constants.ORG_PARAM_DESC_PICTURE_PATH]
else:
- self.tripal_species_picture = ""
+ self.tripal_species_picture = None
self.genus_lowercase = self.genus[0].lower() + self.genus[1:]
self.genus_uppercase = self.genus[0].upper() + self.genus[1:]
--
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