Release_2.0 next

General

• Move constants to file constants.py
• Set default config file in scripts.
• Update description of scripts in main.
• Update README.md

Input config file

• Change config root to dict and update parse_config().
• Change some config parameters name (galaxy_persist_data, tripal_banner_path, jbrowse_menu_url), update example config file and compose templates.
• Remove apollo config variables (webapollo_user, webapollo_password) in config file and in gspecies compose template, because apollo service not deployed here.

Utilities.py

• Factorize parse_input() et parse_config().
• Get input yml keys from constants (update organisms.yml.j2 and add create_org_param_dict_from_constants())

gspecies_compose.yml

• set ENABLE_WIKI and ENABLE_APOLLO to 0 in gspecies compose template
• fix ENABLE_BLAST value in gspecies compose template

gga_get_data.py

• Remove useless variable datasets_to_get

gga_init.py

• replace subprocess.call() with subprocess.run(). Factorize run_command() and run_docker_stack_deploy()
• fix banner copy

utilities.py

@@ -158,7 +158,8 @@ def get_unique_species_dict_list(sp_dict_list):
 
     for sp in sp_dict_list:
         gspecies = get_gspecies_string_from_sp_dict(sp)
-        if gspecies not in unique_species_dict.keys() or sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_MAIN_SPECIES] == True :
+        if gspecies not in unique_species_dict.keys() or ( constants.ORG_PARAM_DESC_MAIN_SPECIES in sp[constants.ORG_PARAM_DESC].keys() and
+                                                           sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_MAIN_SPECIES] == True ) :
             unique_species_dict[gspecies] = sp
         else:
             continue
@@ -196,28 +197,28 @@ def create_org_param_dict_from_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
+    org_param_dict["org_param_name"] = constants.ORG_PARAM_NAME
+    org_param_dict["org_param_desc"] = constants.ORG_PARAM_DESC
+    org_param_dict["org_param_desc_genus"] = constants.ORG_PARAM_DESC_GENUS
+    org_param_dict["org_param_desc_species"] = constants.ORG_PARAM_DESC_SPECIES
+    org_param_dict["org_param_desc_sex"] = constants.ORG_PARAM_DESC_SEX
+    org_param_dict["org_param_desc_strain"] = constants.ORG_PARAM_DESC_STRAIN
+    org_param_dict["org_param_desc_common_name"] = constants.ORG_PARAM_DESC_COMMON_NAME
+    org_param_dict["org_param_desc_origin"] = constants.ORG_PARAM_DESC_ORIGIN
+    org_param_dict["org_param_desc_main_species"] = constants.ORG_PARAM_DESC_MAIN_SPECIES
+    org_param_dict["org_param_data"] = constants.ORG_PARAM_DATA
+    org_param_dict["org_param_data_genome_path"] = constants.ORG_PARAM_DATA_GENOME_PATH
+    org_param_dict["org_param_data_transcripts_path"] = constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH
+    org_param_dict["org_param_data_proteins_path"] = constants.ORG_PARAM_DATA_PROTEINS_PATH
+    org_param_dict["org_param_data_gff_path"] = constants.ORG_PARAM_DATA_GFF_PATH
+    org_param_dict["org_param_data_interpro_path"] = constants.ORG_PARAM_DATA_INTERPRO_PATH
+    org_param_dict["org_param_data_orthofinder_path"] = constants.ORG_PARAM_DATA_ORTHOFINDER_PATH
+    org_param_dict["org_param_data_blastp_path"] = constants.ORG_PARAM_DATA_BLASTP_PATH
+    org_param_dict["org_param_data_blastx_path"] = constants.ORG_PARAM_DATA_BLASTX_PATH
+    org_param_dict["org_param_data_genome_version"] = constants.ORG_PARAM_DATA_GENOME_VERSION
+    org_param_dict["org_param_data_ogs_version"] = constants.ORG_PARAM_DATA_OGS_VERSION
+    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
 
     return org_param_dict
\ No newline at end of file