From 1b13e75caf667c131cffbe27ed2148ad6b8a0f5d Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Mon, 31 May 2021 00:26:21 +0200
Subject: [PATCH] fix time_sleep and chado_species_name. Change common_name for
org
---
gga_run_workflow_phaeo_jbrowse.py | 10 ++++------
runWorkflowPhaeo.py | 6 ++----
2 files changed, 6 insertions(+), 10 deletions(-)
diff --git a/gga_run_workflow_phaeo_jbrowse.py b/gga_run_workflow_phaeo_jbrowse.py
index 0591da6..d3e47e1 100644
--- a/gga_run_workflow_phaeo_jbrowse.py
+++ b/gga_run_workflow_phaeo_jbrowse.py
@@ -7,7 +7,6 @@ import os
import logging
import sys
import json
-import time
from bioblend.galaxy.objects import GalaxyInstance
import utilities
@@ -66,11 +65,11 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
self.abbreviation = self.genus_uppercase[0] + ". " + self.chado_species_name
- self.common = self.name
+ self.common = self.genus_uppercase + " " + self.chado_species_name
if not self.common_name is None and self.common_name != "":
# common_name only is not sufficient as may not be unique between the different strains of the species and
- # galaxy will throw error "Found a preexisting organism with the same attributes in the database"
- self.common = self.common_name + "(" + self.name + ")"
+ # galaxy will throw error "OrgWorkflowParam"
+ self.common = self.common + " (" + self.common_name + ")"
self.genome_analysis_name = "genome v{0} of {1}".format(self.genome_version, self.full_name)
self.genome_analysis_programversion = "genome v{0}".format(self.genome_version)
@@ -159,14 +158,13 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
"genus": self.genus_uppercase,
"species": self.chado_species_name,
"common": self.common},
- time_sleep=30
+ time_sleep=10
)
organism_dict = json.loads(add_organism_tool_dataset)
org_id = str(organism_dict["organism_id"]) # id needs to be a str to be recognized by chado tools
# Synchronize newly added organism in Tripal
logging.info("Synchronizing organism %s in Tripal" % self.full_name)
- time.sleep(60)
utilities_bioblend.run_tool(
instance=self.instance,
tool_id=constants_phaeo.ORGANISM_SYNC_TOOL_ID,
diff --git a/runWorkflowPhaeo.py b/runWorkflowPhaeo.py
index 2f6503f..615df0a 100644
--- a/runWorkflowPhaeo.py
+++ b/runWorkflowPhaeo.py
@@ -3,7 +3,6 @@
import logging
import json
-import time
import utilities_bioblend
import speciesData
@@ -15,7 +14,7 @@ class OrgWorkflowParam:
def __init__(self, genus_uppercase, chado_species_name, full_name, species_folder_name,
org_id, history_id, instance):
self.genus_uppercase = genus_uppercase
- self.chado_species_name = chado_species_name,
+ self.chado_species_name = chado_species_name
self.full_name = full_name
self.species_folder_name = species_folder_name
self.org_id = org_id
@@ -79,7 +78,7 @@ class RunWorkflow(speciesData.SpeciesData):
"programversion": programversion,
"sourcename": sourcename,
"date_executed": constants_phaeo.ADD_ANALYSIS_TOOL_PARAM_DATE},
- time_sleep = 30
+ time_sleep = 10
)
analysis_dict = json.loads(add_analysis_tool_dataset)
analysis_id = str(analysis_dict["analysis_id"])
@@ -88,7 +87,6 @@ class RunWorkflow(speciesData.SpeciesData):
def sync_analysis(self, analysis_id):
- time.sleep(60)
utilities_bioblend.run_tool(
instance=self.instance,
tool_id=constants_phaeo.ANALYSIS_SYNC_TOOL_ID,
--
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