From d396190fe50385f23cf1c2b54491f93696967fec Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Mon, 31 May 2021 17:08:47 +0200
Subject: [PATCH] Update to wf_v7: sync in wf
---
constants_phaeo.py | 27 +-
gga_run_workflow_phaeo.py | 25 +-
gga_run_workflow_phaeo_blast_interpro.py | 6 +-
gga_run_workflow_phaeo_jbrowse.py | 21 +-
...load_tripal_synchronize_jbrowse_1org_v7.ga | 695 ++++++++++
...load_tripal_synchronize_jbrowse_2org_v7.ga | 1201 +++++++++++++++++
6 files changed, 1946 insertions(+), 29 deletions(-)
create mode 100644 workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v7.ga
create mode 100644 workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v7.ga
diff --git a/constants_phaeo.py b/constants_phaeo.py
index b37db48..3bf4b2f 100644
--- a/constants_phaeo.py
+++ b/constants_phaeo.py
@@ -8,7 +8,7 @@ import constants
WORKFLOWS_PATH = "workflows_phaeoexplorer/"
-WF_LOAD_GFF_JB_1_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v6.ga"
+WF_LOAD_GFF_JB_1_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v7.ga"
WF_LOAD_GFF_JB_1_ORG_INPUT_GENOME = "0"
WF_LOAD_GFF_JB_1_ORG_INPUT_GFF = "1"
WF_LOAD_GFF_JB_1_ORG_INPUT_PROTEINS = "2"
@@ -16,11 +16,14 @@ WF_LOAD_GFF_JB_1_ORG_STEP_LOAD_FASTA = "3"
WF_LOAD_GFF_JB_1_ORG_STEP_JBROWSE = "4"
WF_LOAD_GFF_JB_1_ORG_STEP_LOAD_GFF = "5"
WF_LOAD_GFF_JB_1_ORG_STEP_JB_TO_CONTAINER = "6"
-WF_LOAD_GFF_JB_1_ORG_STEP_FEATURE_SYNC = "7"
-WF_LOAD_GFF_JB_1_ORG_STEP_POPULATE_VIEWS = "8"
-WF_LOAD_GFF_JB_1_ORG_STEP_INDEX = "9"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_FEATURE = "7"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_ORG = "8"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_GENOME_ANALYSIS = "9"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_OGS_ANALYSIS = "10"
+WF_LOAD_GFF_JB_1_ORG_STEP_POPULATE_VIEWS = "11"
+WF_LOAD_GFF_JB_1_ORG_STEP_INDEX = "12"
-WF_LOAD_GFF_JB_2_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v6.ga"
+WF_LOAD_GFF_JB_2_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v7.ga"
WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1 = "0"
WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1 = "1"
WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG1 = "2"
@@ -32,12 +35,18 @@ WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1 = "7"
WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2 = "8"
WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_GFF_ORG1 = "9"
WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER = "10"
-WF_LOAD_GFF_JB_2_ORG_STEP_FEATURE_SYNC_ORG1 = "11"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG1 = "11"
WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_FASTA_ORG2 = "12"
WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_GFF_ORG2 = "13"
-WF_LOAD_GFF_JB_2_ORG_STEP_FEATURE_SYNC_ORG2 = "14"
-WF_LOAD_GFF_JB_2_ORG_STEP_POPULATE_VIEWS = "15"
-WF_LOAD_GFF_JB_2_ORG_STEP_INDEX = "16"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG2 = "14"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_ORG1 = "15"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_ORG2 = "16"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_GENOME_ANALYSIS_ORG1 = "17"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_OGS_ANALYSIS_ORG1 = "18"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_GENOME_ANALYSIS_ORG2 = "19"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_OGS_ANALYSIS_ORG2 = "20"
+WF_LOAD_GFF_JB_2_ORG_STEP_POPULATE_VIEWS = "21"
+WF_LOAD_GFF_JB_2_ORG_STEP_INDEX = "22"
### Galaxy tools
diff --git a/gga_run_workflow_phaeo.py b/gga_run_workflow_phaeo.py
index a892f03..3ddfb18 100644
--- a/gga_run_workflow_phaeo.py
+++ b/gga_run_workflow_phaeo.py
@@ -94,11 +94,17 @@ class RunWorkflow(species_data.SpeciesData):
history_id=self.history_id,
tool_inputs={"analysis_id": analysis_id})
- def add_analysis_and_sync(self, analyses_dict_list, analysis_name, analysis_programversion, analysis_sourcename):
+ def add_analysis_if_needed(self, analyses_dict_list, analysis_name, analysis_programversion, analysis_sourcename):
"""
Add one analysis to Chado database
Required for Chado Load Tripal Synchronize workflow (which should be ran as the first workflow)
Called outside workflow for practical reasons (Chado add doesn't have an input link for analysis or organism)
+
+ :param analyses_dict_list: output dict from get_analyses()
+ :param analysis_name:
+ :param analysis_programversion:
+ :param analysis_sourcename:
+ :return:
"""
analysis_id = None
@@ -115,6 +121,23 @@ class RunWorkflow(species_data.SpeciesData):
sourcename=analysis_sourcename
)
+ return analysis_id
+
+ def add_analysis_and_sync(self, analyses_dict_list, analysis_name, analysis_programversion, analysis_sourcename):
+ """
+ Add one analysis to Chado database
+ Required for Chado Load Tripal Synchronize workflow (which should be ran as the first workflow)
+ Called outside workflow for practical reasons (Chado add doesn't have an input link for analysis or organism)
+
+ :param analyses_dict_list: output dict from get_analyses()
+ :param analysis_name:
+ :param analysis_programversion:
+ :param analysis_sourcename:
+ :return:
+ """
+
+ self.add_analysis_if_needed(analyses_dict_list, analysis_name, analysis_programversion, analysis_sourcename)
+
# Synchronize analysis in Tripal
logging.info("Synchronizing analysis %s in Tripal" % analysis_name)
time.sleep(10)
diff --git a/gga_run_workflow_phaeo_blast_interpro.py b/gga_run_workflow_phaeo_blast_interpro.py
index b8be831..85a565b 100644
--- a/gga_run_workflow_phaeo_blast_interpro.py
+++ b/gga_run_workflow_phaeo_blast_interpro.py
@@ -925,7 +925,7 @@ if __name__ == "__main__":
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_LOAD_GFF] = {
"organism": sp_wf_param.org_id,
"analysis_id": sp_wf_param.ogs_analysis_id}
- workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_FEATURE_SYNC] = {
+ workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_FEATURE] = {
"organism_id": sp_wf_param.org_id}
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_POPULATE_VIEWS] = {}
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_INDEX] = {}
@@ -1025,7 +1025,7 @@ if __name__ == "__main__":
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_GFF_ORG1] = {
"organism": sp_wf_param_org1.org_id,
"analysis_id": sp_wf_param_org1.ogs_analysis_id}
- workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_FEATURE_SYNC_ORG1] = {
+ workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG1] = {
"organism_id": sp_wf_param_org1.org_id}
# workflow_parameters[JBROWSE_CONTAINER] = {"organisms": [{"name": org1_full_name, "unique_id": org1_species_folder_name, }, {"name": org2_full_name, "unique_id": org2_species_folder_name}]}
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER] = {}
@@ -1040,7 +1040,7 @@ if __name__ == "__main__":
"analysis_id": sp_wf_param_org2.ogs_analysis_id}
# workflow_parameters[JRBOWSE_ORG2] = {"jbrowse_menu_url": jbrowse_menu_url_org2}
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2] = {}
- workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_FEATURE_SYNC_ORG2] = {
+ workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG2] = {
"organism_id": sp_wf_param_org2.org_id}
# POPULATE + INDEX DATA
diff --git a/gga_run_workflow_phaeo_jbrowse.py b/gga_run_workflow_phaeo_jbrowse.py
index 4c7f6a6..741ede2 100644
--- a/gga_run_workflow_phaeo_jbrowse.py
+++ b/gga_run_workflow_phaeo_jbrowse.py
@@ -163,14 +163,6 @@ class RunWorkflowJbrowse(gga_run_workflow_phaeo.RunWorkflow):
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)
- utilities_bioblend.run_tool(
- instance=self.instance,
- tool_id=constants_phaeo.ORGANISM_SYNC_TOOL_ID,
- history_id=self.history_id,
- tool_inputs={"organism_id": org_id})
-
return org_id
def import_datasets_into_history(self, config):
@@ -292,13 +284,13 @@ def prepare_history_and_get_wf_param(sp_dict_list, main_dir, config):
analyses_dict_list = run_workflow_for_current_organism.get_analyses()
org_id = run_workflow_for_current_organism.add_organism_and_sync()
- genome_analysis_id = run_workflow_for_current_organism.add_analysis_and_sync(
+ genome_analysis_id = run_workflow_for_current_organism.add_analysis_if_needed(
analyses_dict_list=analyses_dict_list,
analysis_name=run_workflow_for_current_organism.genome_analysis_name,
analysis_programversion=run_workflow_for_current_organism.genome_analysis_programversion,
analysis_sourcename=run_workflow_for_current_organism.genome_analysis_sourcename
)
- ogs_analysis_id = run_workflow_for_current_organism.add_analysis_and_sync(
+ ogs_analysis_id = run_workflow_for_current_organism.add_analysis_if_needed(
analyses_dict_list=analyses_dict_list,
analysis_name=run_workflow_for_current_organism.ogs_analysis_name,
analysis_programversion=run_workflow_for_current_organism.ogs_analysis_programversion,
@@ -414,9 +406,6 @@ if __name__ == "__main__":
# Set the workflow parameters (individual tools runtime parameters in the workflow)
workflow_parameters = {}
# Input files have no parameters (they are set via assigning the hda IDs in the datamap parameter of the bioblend method)
- workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_INPUT_GENOME] = {}
- workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_INPUT_GFF] = {}
- workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_INPUT_PROTEINS] = {}
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_LOAD_FASTA] = {
"organism": org_wf_param.org_id,
"analysis_id": org_wf_param.genome_analysis_id,
@@ -425,7 +414,7 @@ if __name__ == "__main__":
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_LOAD_GFF] = {
"organism": org_wf_param.org_id,
"analysis_id": org_wf_param.ogs_analysis_id}
- workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_FEATURE_SYNC] = {
+ workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_FEATURE] = {
"organism_id": org_wf_param.org_id}
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_POPULATE_VIEWS] = {}
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_INDEX] = {}
@@ -524,7 +513,7 @@ if __name__ == "__main__":
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_GFF_ORG1] = {
"organism": sp_wf_param_org1.org_id,
"analysis_id": sp_wf_param_org1.ogs_analysis_id}
- workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_FEATURE_SYNC_ORG1] = {
+ workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG1] = {
"organism_id": sp_wf_param_org1.org_id}
# workflow_parameters[JBROWSE_CONTAINER] = {"organisms": [{"name": org1_full_name, "unique_id": org1_species_folder_name, }, {"name": org2_full_name, "unique_id": org2_species_folder_name}]}
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER] = {}
@@ -538,7 +527,7 @@ if __name__ == "__main__":
"analysis_id": sp_wf_param_org2.ogs_analysis_id}
# workflow_parameters[JRBOWSE_ORG2] = {"jbrowse_menu_url": jbrowse_menu_url_org2}
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2] = {}
- workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_FEATURE_SYNC_ORG2] = {
+ workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG2] = {
"organism_id": sp_wf_param_org2.org_id}
# POPULATE + INDEX DATA
workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_POPULATE_VIEWS] = {}
diff --git a/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v7.ga b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v7.ga
new file mode 100644
index 0000000..768f926
--- /dev/null
+++ b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v7.ga
@@ -0,0 +1,695 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "chado_load_tripal_synchronize_jbrowse_1org_v7",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "genome"
+ }
+ ],
+ "label": "genome",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "bottom": 256.8000030517578,
+ "height": 61.80000305175781,
+ "left": 375.5,
+ "right": 575.5,
+ "top": 195,
+ "width": 200,
+ "x": 375.5,
+ "y": 195
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "45f3447e-b282-40c7-8bd9-347bd322cd7b",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "77d9ce40-535a-4e53-a628-a9463741d96a"
+ }
+ ]
+ },
+ "1": {
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+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "annotations"
+ }
+ ],
+ "label": "annotations",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "bottom": 341.8000030517578,
+ "height": 61.80000305175781,
+ "left": 384.5,
+ "right": 584.5,
+ "top": 280,
+ "width": 200,
+ "x": 384.5,
+ "y": 280
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "5c2c519c-956a-4998-95a6-9568a816ab95",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "3a224015-480b-4a72-b1e4-e9240a51738a"
+ }
+ ]
+ },
+ "2": {
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+ "content_id": null,
+ "errors": null,
+ "id": 2,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "proteins"
+ }
+ ],
+ "label": "proteins",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "bottom": 429.8000030517578,
+ "height": 61.80000305175781,
+ "left": 395.5,
+ "right": 595.5,
+ "top": 368,
+ "width": 200,
+ "x": 395.5,
+ "y": 368
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "48b7a52a-3c75-42d1-961b-c4ff7aaa1fcb",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "5b39855a-565e-42a2-8727-0ecbb5c15ddd"
+ }
+ ]
+ },
+ "3": {
+ "annotation": "",
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+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "fasta": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "analysis_id"
+ },
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "fasta"
+ },
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "organism"
+ },
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "wait_for"
+ }
+ ],
+ "label": null,
+ "name": "Chado load fasta",
+ "outputs": [
+ {
+ "name": "results",
+ "type": "json"
+ }
+ ],
+ "position": {
+ "bottom": 336,
+ "height": 144,
+ "left": 705.5,
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+ "tool_shed_repository": {
+ "changeset_revision": "ba4d07fbaf47",
+ "name": "chado_feature_load_fasta",
+ "owner": "gga",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
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+ "type": "tool",
+ "uuid": "1cfa9fc4-e962-4448-8dfc-aa4b428276e9",
+ "workflow_outputs": [
+ {
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+ "output_name": "results",
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+ "id": 0,
+ "output_name": "output"
+ },
+ "track_groups_0|data_tracks_0|data_format|annotation": {
+ "id": 1,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "JBrowse",
+ "outputs": [
+ {
+ "name": "output",
+ "type": "html"
+ }
+ ],
+ "position": {
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+ "height": 205.1999969482422,
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+ "top": 389,
+ "width": 200,
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+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0",
+ "tool_shed_repository": {
+ "changeset_revision": "4542035c1075",
+ "name": "jbrowse",
+ "owner": "iuc",
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new file mode 100644
index 0000000..0b79aad
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