From b2ce2b86c843460c85e5bdb1932ca20d5aa340a1 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Fri, 14 May 2021 22:02:34 +0200
Subject: [PATCH] Get input yml keys from constants
---
examples/citrus_sinensis.yml | 4 +--
templates/organisms.yml.j2 | 48 ++++++++++++++++++------------------
utilities.py | 35 +++++++++++++++++++++++++-
3 files changed, 59 insertions(+), 28 deletions(-)
diff --git a/examples/citrus_sinensis.yml b/examples/citrus_sinensis.yml
index 14fe1dc..ce35202 100644
--- a/examples/citrus_sinensis.yml
+++ b/examples/citrus_sinensis.yml
@@ -33,6 +33,4 @@
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: "False"
- wiki: "False"
- apollo: "False"
\ No newline at end of file
+ blast: "False"
\ No newline at end of file
diff --git a/templates/organisms.yml.j2 b/templates/organisms.yml.j2
index 915bbed..4739153 100644
--- a/templates/organisms.yml.j2
+++ b/templates/organisms.yml.j2
@@ -1,25 +1,25 @@
-- name: {{ name }}
- description:
- genus: {{ genus }}
- species: {{ species }}
- sex: {{ sex }}
- strain: {{ strain }}
- common_name: {{ common_name }}
- origin: {{ origin }}
- {% if main_species is defined and main_species is sameas true %}
- main_species: yes
+- {{ org_param_name }}: {{ org_param_name_value }}
+ {{ org_param_desc }}:
+ {{ org_param_desc_genus }}: {{ org_param_desc_genus_value }}
+ {{ org_param_desc_species }}: {{ org_param_desc_species_value }}
+ {{ org_param_desc_sex }}: {{ org_param_desc_sex_value }}
+ {{ org_param_desc_strain }}: {{ org_param_desc_strain_value }}
+ {{ org_param_desc_common_name }}: {{ org_param_desc_common_name_value }}
+ {{ org_param_desc_origin }}: {{ org_param_desc_origin_value }}
+ {% if org_param_desc_main_species_value is defined and org_param_desc_main_species_value is same as true %}
+ {{ org_param_desc_main_species }}: yes
{% endif %}
- data:
- genome_path: {{ genome_path }}
- transcripts_path: {{ transcripts_path }}
- proteins_path: {{ proteins_path }}
- gff_path: {{ gff_path }}
- interpro_path: {{ interpro_path }}
- orthofinder_path: {{ orthofinder_path }}
- blastp_path: {{ blastp_path }}
- blastx_path: {{ blastx_path }}
- genome_version: {{ genome_version }}
- ogs_version: {{ ogs_version }}
- performed_by: {{ performed_by }}
- services:
- blast: {{ blast }}
\ No newline at end of file
+ {{ org_param_data }}:
+ {{ org_param_data_genome_path }}: {{ org_param_data_genome_path_value }}
+ {{ org_param_data_transcripts_path }}: {{ org_param_data_transcripts_path_value }}
+ {{ org_param_data_proteins_path }}: {{ org_param_data_proteins_path_value }}
+ {{ org_param_data_gff_path }}: {{ org_param_data_gff_path_value }}
+ {{ org_param_data_interpro_path }}: {{ org_param_data_interpro_path_value }}
+ {{ org_param_data_orthofinder_path }}: {{ org_param_data_orthofinder_path_value }}
+ {{ org_param_data_blastp_path }}: {{ org_param_data_blastp_path_value }}
+ {{ org_param_data_blastx_path }}: {{ org_param_data_blastx_path_value }}
+ {{ org_param_data_genome_version }}: {{ org_param_data_genome_version_value }}
+ {{ 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
diff --git a/utilities.py b/utilities.py
index 139d083..b23ec21 100755
--- a/utilities.py
+++ b/utilities.py
@@ -187,4 +187,37 @@ def run_tool_and_get_single_output_dataset_id(instance, tool_id, history_id, too
output_dict = run_tool(instance, tool_id, history_id, tool_inputs)
single_output_dataset_id = output_dict["outputs"][0]["id"]
- return single_output_dataset_id
\ No newline at end of file
+ return single_output_dataset_id
+
+def create_org_param_dict_from_constants():
+ """
+ Create a dictionary of variables containing the keys needed to render the organisms.yml.j2 (NOT the values)
+ Created from the constants
+ """
+
+ org_param_dict={}
+ org_param_dict[constants.ORG_PARAM_NAME] = constants.ORG_PARAM_NAME
+ org_param_dict[constants.ORG_PARAM_DESC] = constants.ORG_PARAM_DESC
+ org_param_dict[constants.ORG_PARAM_DESC_GENUS] = constants.ORG_PARAM_DESC_GENUS
+ org_param_dict[constants.ORG_PARAM_DESC_SPECIES] = constants.ORG_PARAM_DESC_SPECIES
+ org_param_dict[constants.ORG_PARAM_DESC_SEX] = constants.ORG_PARAM_DESC_SEX
+ org_param_dict[constants.ORG_PARAM_DESC_STRAIN] = constants.ORG_PARAM_DESC_STRAIN
+ org_param_dict[constants.ORG_PARAM_DESC_COMMON_NAME] = constants.ORG_PARAM_DESC_COMMON_NAME
+ org_param_dict[constants.ORG_PARAM_DESC_ORIGIN] = constants.ORG_PARAM_DESC_ORIGIN
+ org_param_dict[constants.ORG_PARAM_DESC_MAIN_SPECIES] = constants.ORG_PARAM_DESC_MAIN_SPECIES
+ org_param_dict[constants.ORG_PARAM_DATA] = constants.ORG_PARAM_DATA
+ org_param_dict[constants.ORG_PARAM_DATA_GENOME_PATH] = constants.ORG_PARAM_DATA_GENOME_PATH
+ org_param_dict[constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH] = constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH
+ org_param_dict[constants.ORG_PARAM_DATA_PROTEINS_PATH] = constants.ORG_PARAM_DATA_PROTEINS_PATH
+ org_param_dict[constants.ORG_PARAM_DATA_GFF_PATH] = constants.ORG_PARAM_DATA_GFF_PATH
+ org_param_dict[constants.ORG_PARAM_DATA_INTERPRO_PATH] = constants.ORG_PARAM_DATA_INTERPRO_PATH
+ org_param_dict[constants.ORG_PARAM_DATA_ORTHOFINDER_PATH] = constants.ORG_PARAM_DATA_ORTHOFINDER_PATH
+ org_param_dict[constants.ORG_PARAM_DATA_BLASTP_PATH] = constants.ORG_PARAM_DATA_BLASTP_PATH
+ org_param_dict[constants.ORG_PARAM_DATA_BLASTX_PATH] = constants.ORG_PARAM_DATA_BLASTX_PATH
+ org_param_dict[constants.ORG_PARAM_DATA_GENOME_VERSION] = constants.ORG_PARAM_DATA_GENOME_VERSION
+ org_param_dict[constants.ORG_PARAM_DATA_OGS_VERSION] = constants.ORG_PARAM_DATA_GENOME_VERSION
+ org_param_dict[constants.ORG_PARAM_DATA_PERFORMED_BY] = constants.ORG_PARAM_DATA_PERFORMED_BY
+ org_param_dict[constants.ORG_PARAM_SERVICES] = constants.ORG_PARAM_SERVICES
+ org_param_dict[constants.ORG_PARAM_SERVICES_BLAST] = constants.ORG_PARAM_SERVICES_BLAST
+
+ return org_param_dict
\ No newline at end of file
--
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