diff --git a/constants_phaeo.py b/constants_phaeo.py
index b37db4840d3ace2f1c78872ef517b1b2e52dd3c2..3bf4b2f4cfd2951a0fcaee2a1c394c760688ad50 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 a892f03b4a0a81d672312f15c61f1dae5329c3b3..3ddfb18a96e415c4b6576e30f7f4b4f37582a7b0 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 b8be831f3b520a2740e25d78e5a1b4c61575b776..85a565bde0b2dc78892f7b38a7e15b89dadca97e 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 4c7f6a6b960f6d94a9c6328f05cb89490b894c6a..741ede2051685e199730be3cfb5ec35352569f9f 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 0000000000000000000000000000000000000000..768f926620d08682560eaf64b9cf8aea80ef7df3
--- /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": {
+ "annotation": "",
+ "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": {
+ "annotation": "",
+ "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": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
+ "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,
+ "right": 905.5,
+ "top": 192,
+ "width": 200,
+ "x": 705.5,
+ "y": 192
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
+ "tool_shed_repository": {
+ "changeset_revision": "ba4d07fbaf47",
+ "name": "chado_feature_load_fasta",
+ "owner": "gga",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"do_update\": \"false\", \"ext_db\": {\"db\": \"\", \"re_db_accession\": \"\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"re_name\": \"\", \"re_uniquename\": \"\", \"relationships\": {\"rel_type\": \"none\", \"__current_case__\": 0}, \"sequence_type\": \"contig\", \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "2.3.4+galaxy0",
+ "type": "tool",
+ "uuid": "1cfa9fc4-e962-4448-8dfc-aa4b428276e9",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "results",
+ "uuid": "c637b026-2e81-462f-bb93-1d0f7da4628f"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "reference_genome|genome": {
+ "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": {
+ "bottom": 594.1999969482422,
+ "height": 205.1999969482422,
+ "left": 690.5,
+ "right": 890.5,
+ "top": 389,
+ "width": 200,
+ "x": 690.5,
+ "y": 389
+ },
+ "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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