From 342fff322c9c5fd25f7496e5419861434228ad9f Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Thu, 20 May 2021 17:56:32 +0200
Subject: [PATCH] Add go summary functionality
---
constants.py | 1 +
examples/citrus_sinensis.yml | 8 ++++----
gga_init.py | 2 +-
speciesData.py | 14 +++++++++-----
templates/gspecies_compose.yml.j2 | 2 +-
templates/organisms.yml.j2 | 3 ++-
utilities.py | 1 +
7 files changed, 19 insertions(+), 12 deletions(-)
diff --git a/constants.py b/constants.py
index 70724c3..2a50710 100644
--- a/constants.py
+++ b/constants.py
@@ -23,6 +23,7 @@ ORG_PARAM_DATA_OGS_VERSION = "ogs_version"
ORG_PARAM_DATA_PERFORMED_BY = "performed_by"
ORG_PARAM_SERVICES = "services"
ORG_PARAM_SERVICES_BLAST = "blast"
+ORG_PARAM_SERVICES_GO = "go"
# Constants used in the config yaml file
diff --git a/examples/citrus_sinensis.yml b/examples/citrus_sinensis.yml
index 63483e4..38087bb 100644
--- a/examples/citrus_sinensis.yml
+++ b/examples/citrus_sinensis.yml
@@ -18,7 +18,7 @@
# Paths to the different datasets to copy and import into the galaxy container (as a shared library)
# Must be absolute paths to the dataset
genome_path: /path/to/repo/examples/src_data/genome/v1.0/Citrus_sinensis-scaffold00001.fasta # Mandatory!
- transcripts_path: /path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.fasta # Mandatory!
+ transcripts_path: /path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.fasta
proteins_path: # Mandatory!
gff_path: /path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.gff3 # Mandatory!
interpro_path: /path/to/repo/examples/src_data/annotation/v1.0/functional_annotation/Citrus_sinensis-orange1.1g015632m.g.iprscan.xml
@@ -33,6 +33,6 @@
ogs_version: 1.0
performed_by:
services:
- # List the optional services to be deploy in the stack
- # By default, only tripal, tripaldb, galaxy, jbrowse and elasticsearch services will be deployed
- blast: 0
\ No newline at end of file
+ # List the optional services/resources to add
+ blast: 0 # "1" to add links to blast form, "some/url" to specify, multiple urls as "Name1=url1&Name2=url2", "0" to disable it. Default: "0"
+ go: 1 # "1" to add links to GO summary, "0" to disable it. Default: "0"
\ No newline at end of file
diff --git a/gga_init.py b/gga_init.py
index 6c2f702..a4fdb01 100755
--- a/gga_init.py
+++ b/gga_init.py
@@ -130,7 +130,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
"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": "{0} {1}".format(self.genus_uppercase, self.species_lower()),
- "blast": self.blast, "picture_path": self.picture_path}
+ "blast": self.blast, "go": self.go, "picture_path": self.picture_path}
if (len(self.config.keys()) == 0):
logging.error("Empty config dictionary")
# Merge the two dicts
diff --git a/speciesData.py b/speciesData.py
index 34c817f..d505da6 100755
--- a/speciesData.py
+++ b/speciesData.py
@@ -47,12 +47,18 @@ class SpeciesData:
else:
return string
+ def set_service_attribute(self, attribute, service, parameters_dictionary):
+ parameters_dictionary_services = parameters_dictionary[constants.ORG_PARAM_SERVICES]
+ if(service in parameters_dictionary_services.keys()):
+ attribute = parameters_dictionary_services[service]
+ else:
+ attribute = "0"
+
def __init__(self, parameters_dictionary):
self.parameters_dictionary = parameters_dictionary
self.name = parameters_dictionary[constants.ORG_PARAM_NAME]
parameters_dictionary_description=parameters_dictionary[constants.ORG_PARAM_DESC]
parameters_dictionary_data = parameters_dictionary[constants.ORG_PARAM_DATA]
- parameters_dictionary_services = parameters_dictionary[constants.ORG_PARAM_SERVICES]
self.species = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_SPECIES])
self.genus = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_GENUS])
@@ -83,10 +89,8 @@ class SpeciesData:
self.blastx_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_BLASTX_PATH]
self.orthofinder_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_ORTHOFINDER_PATH]
- if(constants.ORG_PARAM_SERVICES_BLAST in parameters_dictionary_services.keys()):
- self.blast = parameters_dictionary_services[constants.ORG_PARAM_SERVICES_BLAST]
- else:
- self.blast = "0"
+ self.set_service_attribute(self.blast, constants.ORG_PARAM_SERVICES_BLAST, parameters_dictionary)
+ self.set_service_attribute(self.go, constants.ORG_PARAM_SERVICES_GO, parameters_dictionary)
if constants.ORG_PARAM_DESC_PICTURE_PATH in parameters_dictionary_description.keys():
self.picture_path = parameters_dictionary_description[constants.ORG_PARAM_DESC_PICTURE_PATH]
diff --git a/templates/gspecies_compose.yml.j2 b/templates/gspecies_compose.yml.j2
index 97dbb00..1b1e8f8 100644
--- a/templates/gspecies_compose.yml.j2
+++ b/templates/gspecies_compose.yml.j2
@@ -65,7 +65,7 @@ services:
ENABLE_BLAST: {{ blast }}
ENABLE_DOWNLOAD: 1
ENABLE_WIKI: 0
- ENABLE_GO: 0
+ ENABLE_GO: {{ go }}
ENABLE_ORTHOLOGY: 0
ENABLE_ORTHOLOGY_LINKS: 0
THEME: "{{ tripal_theme_name }}" # Use this to use another theme
diff --git a/templates/organisms.yml.j2 b/templates/organisms.yml.j2
index 9a05ccf..019fce0 100644
--- a/templates/organisms.yml.j2
+++ b/templates/organisms.yml.j2
@@ -23,4 +23,5 @@
{{ org_param_data_ogs_version }}: {{ org_param_data_ogs_version_value }}
{{ org_param_data_performed_by }}: {{ org_param_data_performed_by_value }}
{{ org_param_services }}:
- {{ org_param_services_blast }}: {{ org_param_services_blast_value }}
\ No newline at end of file
+ {{ org_param_services_blast }}: {{ org_param_services_blast_value }}
+ {{ org_param_services_go }}: {{ org_param_services_go_value }}
\ No newline at end of file
diff --git a/utilities.py b/utilities.py
index f08c11b..bcee45e 100755
--- a/utilities.py
+++ b/utilities.py
@@ -236,5 +236,6 @@ def create_org_param_dict_from_constants():
org_param_dict["org_param_data_performed_by"] = constants.ORG_PARAM_DATA_PERFORMED_BY
org_param_dict["org_param_services"] = constants.ORG_PARAM_SERVICES
org_param_dict["org_param_services_blast"] = constants.ORG_PARAM_SERVICES_BLAST
+ org_param_dict["org_param_services_go"] = constants.ORG_PARAM_SERVICES_GO
return org_param_dict
--
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