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Commit b33c4b5e authored by Arthur Le Bars's avatar Arthur Le Bars
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Added interpro and blast workflows and methods

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1 merge request!1Release 1.0
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gga_init.py
+ 12
− 1
View file @ b33c4b5e
...@@ -181,7 +181,6 @@ class DeploySpeciesStack(speciesData.SpeciesData): ...@@ -181,7 +181,6 @@ class DeploySpeciesStack(speciesData.SpeciesData):
:return: :return:
""" """
# Proceed to the traefik and authelia directories
os.chdir(self.main_dir) os.chdir(self.main_dir)
# Create directory tree # Create directory tree
...@@ -229,6 +228,18 @@ class DeploySpeciesStack(speciesData.SpeciesData): ...@@ -229,6 +228,18 @@ class DeploySpeciesStack(speciesData.SpeciesData):
os.chdir(self.main_dir) os.chdir(self.main_dir)
def make_orthology_compose_files(self):
"""
:return:
"""
os.chdir(self.main_dir)
self.make_dirs["./orthology", "./orthology/src_data", "./orthology/src_data/genomes",
"./orthology/src_data/gff", "./orthology/src_data/newicks", "./orthology/src_data/proteomes"]
def create_mounts(self, working_dir): def create_mounts(self, working_dir):
""" """
Create the folders (volumes) required by a container (to see required volumes, check their compose file) Create the folders (volumes) required by a container (to see required volumes, check their compose file)
......
run_workflow_phaeoexplorer.py
+ 118
− 8
View file @ b33c4b5e
...@@ -337,12 +337,20 @@ class RunWorkflow(speciesData.SpeciesData): ...@@ -337,12 +337,20 @@ class RunWorkflow(speciesData.SpeciesData):
elif "gff" in e["name"]: elif "gff" in e["name"]:
self.datasets["gff_file"] = e["ldda_id"] self.datasets["gff_file"] = e["ldda_id"]
logging.debug("\t" + e["name"] + ": " + e["ldda_id"]) logging.debug("\t" + e["name"] + ": " + e["ldda_id"])
elif e["name"].endswith(".xml") and e["name"].startswith("Interpro"):
self.datasets["interproscan_file"] = e["ldda_id"]
logging.debug("\t" + e["name"] + ": " + e["ldda_id"])
elif e["name"].endswith(".xml") and "diamond" in e["name"]:
self.datasets["blast_diamond_file"] = e["ldda_id"]
logging.debug("\t" + e["name"] + ": " + e["ldda_id"])
logging.info("Uploading datasets into history %s" % self.history_id) logging.info("Uploading datasets into history %s" % self.history_id)
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["genome_file"]) self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["genome_file"])
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["gff_file"]) self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["gff_file"])
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["transcripts_file"]) self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["transcripts_file"])
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["proteins_file"]) self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["proteins_file"])
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["interproscan_file"])
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["blast_diamond_file"])
_datasets = self.instance.datasets.get_datasets() _datasets = self.instance.datasets.get_datasets()
with open(os.path.join(self.main_dir, "datasets_ids.json"), "w") as datasets_ids_outfile: with open(os.path.join(self.main_dir, "datasets_ids.json"), "w") as datasets_ids_outfile:
...@@ -370,13 +378,14 @@ class RunWorkflow(speciesData.SpeciesData): ...@@ -370,13 +378,14 @@ class RunWorkflow(speciesData.SpeciesData):
history_datasets_li = self.instance.datasets.get_datasets() history_datasets_li = self.instance.datasets.get_datasets()
genome_dataset_hda_id, gff_dataset_hda_id, transcripts_dataset_hda_id, proteins_datasets_hda_id = None, None, None, None genome_dataset_hda_id, gff_dataset_hda_id, transcripts_dataset_hda_id, proteins_datasets_hda_id = None, None, None, None
interproscan_dataset_hda_id, blast_diamond_dataset_hda_id = None, None
genome_dataset_hda_id = history_datasets_li[3]["id"] genome_dataset_hda_id = history_datasets_li[3]["id"]
gff_dataset_hda_id = history_datasets_li[2]["id"] gff_dataset_hda_id = history_datasets_li[2]["id"]
transcripts_dataset_hda_id = history_datasets_li[1]["id"] transcripts_dataset_hda_id = history_datasets_li[1]["id"]
proteins_datasets_hda_id = history_datasets_li[0]["id"] proteins_datasets_hda_id = history_datasets_li[0]["id"]
for dataset_dict in history_datasets_li[0:3]: for dataset_dict in history_datasets_li[0:5]:
# Datasets imports should be the last jobs in history if the function calls are in correct order # Datasets imports should be the last jobs in history if the function calls are in correct order
# If not, add the function call "get_datasets_hda_ids()" just after "import_datasets_into_history()" # If not, add the function call "get_datasets_hda_ids()" just after "import_datasets_into_history()"
if dataset_dict["name"].endswith("proteins.fa"): if dataset_dict["name"].endswith("proteins.fa"):
...@@ -388,13 +397,20 @@ class RunWorkflow(speciesData.SpeciesData): ...@@ -388,13 +397,20 @@ class RunWorkflow(speciesData.SpeciesData):
elif dataset_dict["name"].endswith(".gff"): elif dataset_dict["name"].endswith(".gff"):
gff_dataset_hda_id = dataset_dict["id"] gff_dataset_hda_id = dataset_dict["id"]
logging.debug("gff dataset hda ID: %s" % gff_dataset_hda_id) logging.debug("gff dataset hda ID: %s" % gff_dataset_hda_id)
elif dataset_dict["name"].endwsith(".xml") and dataset["name"].startswith("Interpro"):
interproscan_dataset_hda_id = dataset_dict["id"]
logging.debug("InterproScan dataset hda ID: %s" % gff_dataset_hda_id)
elif dataset_dict["name"].endswith(".xml") and "diamond" in dataset_dict["name"]:
blast_diamond_dataset_hda_id = dataset_dict["id"]
logging.debug("Blast Diamond dataset hda ID: %s" % gff_dataset_hda_id)
else: else:
genome_dataset_hda_id = dataset_dict["id"] genome_dataset_hda_id = dataset_dict["id"]
logging.debug("Genome dataset hda id: %s" % genome_dataset_hda_id) logging.debug("Genome dataset hda id: %s" % genome_dataset_hda_id)
# Return a dict made of the hda ids # Return a dict made of the hda ids
return{"genome_hda_id": genome_dataset_hda_id, "transcripts_hda_id": transcripts_dataset_hda_id, return{"genome_hda_id": genome_dataset_hda_id, "transcripts_hda_id": transcripts_dataset_hda_id,
"proteins_hda_id": proteins_datasets_hda_id, "gff_hda_id": gff_dataset_hda_id} "proteins_hda_id": proteins_datasets_hda_id, "gff_hda_id": gff_dataset_hda_id,
"interproscan_hda_id": interproscan_dataset_hda_id, "blast_diamond_hda_id": blast_diamond_dataset_hda_id}
def get_organism_and_analyses_ids(self): def get_organism_and_analyses_ids(self):
""" """
...@@ -442,7 +458,7 @@ class RunWorkflow(speciesData.SpeciesData): ...@@ -442,7 +458,7 @@ class RunWorkflow(speciesData.SpeciesData):
ogs_analysis_output = json.loads(ogs_analysis_json_output)[0] ogs_analysis_output = json.loads(ogs_analysis_json_output)[0]
self.ogs_analysis_id = str(ogs_analysis_output["analysis_id"]) self.ogs_analysis_id = str(ogs_analysis_output["analysis_id"])
except IndexError: except IndexError:
logging.debug("no matching OGS analysis exists in the instance's chado database") logging.debug("No matching OGS analysis exists in the instance's chado database")
# Get the ID for the genome analysis in chado # Get the ID for the genome analysis in chado
genome_analysis = self.instance.tools.run_tool( genome_analysis = self.instance.tools.run_tool(
...@@ -457,7 +473,32 @@ class RunWorkflow(speciesData.SpeciesData): ...@@ -457,7 +473,32 @@ class RunWorkflow(speciesData.SpeciesData):
except IndexError: except IndexError:
logging.debug("no matching genome analysis exists in the instance's chado database") logging.debug("no matching genome analysis exists in the instance's chado database")
return {"org_id": self.org_id, "genome_analysis_id": self.genome_analysis_id, "ogs_analysis_id": self.ogs_analysis_id} interpro_analysis = self.instance.tools.run_tool(
tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_get_analyses/analysis_get_analyses/2.3.3",
history_id=self.history_id,
tool_inputs={"name": "InterproScan on OGS%s" % self.ogs_version})
interpro_analysis_job_out = interpro_analysis["outputs"][0]["id"]
interpro_analysis_json_output = self.instance.datasets.download_dataset(dataset_id=interpro_analysis_job_out)
try:
interpro_analysis_output = json.loads(interpro_analysis_json_output)[0]
self.interpro_analysis_id = str(interpro_analysis_output["analysis_id"])
except IndexError:
logging.debug("No matching InterproScan analysis exists in the instance's chado database")
blast_diamond_analysis = self.instance.tools.run_tool(
tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_get_analyses/analysis_get_analyses/2.3.3",
history_id=self.history_id,
tool_inputs={"name": "Diamond on OGS%s" % self.ogs_version})
blast_diamond_analysis_job_out = blast_diamond_analysis["outputs"][0]["id"]
blast_diamond_analysis_json_output = self.instance.datasets.download_dataset(dataset_id=blast_diamond_analysis_job_out)
try:
blast_diamond_analysis_output = json.loads(blast_diamond_analysis_json_output)[0]
self.blast_diamond_analysis_id = str(blast_diamond_analysis_output["analysis_id"])
except IndexError:
logging.debug("No matching InterproScan analysis exists in the instance's chado database")
return {"org_id": self.org_id, "genome_analysis_id": self.genome_analysis_id, "ogs_analysis_id": self.ogs_analysis_id,
"interpro_analysis_id": self.interpro_analysis_id, "blast_diamond_analysis_id": self.blast_diamond_analysis_id}
if __name__ == "__main__": if __name__ == "__main__":
...@@ -572,7 +613,7 @@ if __name__ == "__main__": ...@@ -572,7 +613,7 @@ if __name__ == "__main__":
# Import datasets into history and retrieve their hda IDs # Import datasets into history and retrieve their hda IDs
run_workflow_for_current_organism.import_datasets_into_history() run_workflow_for_current_organism.import_datasets_into_history()
run_workflow_for_current_organism.get_datasets_hda_ids() hda_ids = run_workflow_for_current_organism.get_datasets_hda_ids()
# Explicit workflow parameter names # Explicit workflow parameter names
GENOME_FASTA_FILE = "0" GENOME_FASTA_FILE = "0"
...@@ -656,8 +697,6 @@ if __name__ == "__main__": ...@@ -656,8 +697,6 @@ if __name__ == "__main__":
run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "hda", "id": hda_ids["genome_hda_id"]} run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "hda", "id": hda_ids["genome_hda_id"]}
run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "hda", "id": hda_ids["gff_hda_id"]} run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "hda", "id": hda_ids["gff_hda_id"]}
# run_workflow_for_current_organism.replace_placeholders_workflow(workflow_str=json.dumps(workflow))
# Run the jbrowse creation workflow # Run the jbrowse creation workflow
run_workflow_for_current_organism.run_workflow(workflow_path=workflow, run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
workflow_parameters=workflow_parameters, workflow_parameters=workflow_parameters,
...@@ -672,13 +711,84 @@ if __name__ == "__main__": ...@@ -672,13 +711,84 @@ if __name__ == "__main__":
run_workflow_for_current_organism.set_get_history() run_workflow_for_current_organism.set_get_history()
# run_workflow_for_current_organism.get_species_history_id() # run_workflow_for_current_organism.get_species_history_id()
# Prepare the instance+history for the current organism (add organism and analyses in Chado)
# (although it should pose no problem as the "Chado add" refuses to duplicate an analysis/organism anyway)
if args.setup:
run_workflow_for_current_organism.prepare_history()
# Get the attributes of the instance and project data files # Get the attributes of the instance and project data files
run_workflow_for_current_organism.get_instance_attributes() run_workflow_for_current_organism.get_instance_attributes()
run_workflow_for_current_organism.get_organism_and_analyses_ids() run_workflow_for_current_organism.get_organism_and_analyses_ids()
# Import datasets into history and retrieve their hda IDs # Import datasets into history and retrieve their hda IDs
run_workflow_for_current_organism.import_datasets_into_history() run_workflow_for_current_organism.import_datasets_into_history()
run_workflow_for_current_organism.get_datasets_hda_ids() hda_ids = run_workflow_for_current_organism.get_datasets_hda_ids()
INTERPRO_FILE = "0"
LOAD_INTERPRO_IN_CHADO = "1"
SYNC_INTERPRO_ANALYSIS_INTO_TRIPAL = "2"
SYNC_FEATURES_INTO_TRIPAL = "3"
POPULATE_MAT_VIEWS = "4"
INDEX_TRIPAL_DATA = "5"
workflow_parameters = {}
workflow_parameters[INTERPRO_FILE] = {}
workflow_parameters[LOAD_INTERPRO_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
"analysis_id": run_workflow_for_current_organism.interpro_analysis_id}
workflow_parameters[SYNC_INTERPRO_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.interpro_analysis_id}
run_workflow_for_current_organism.datamap = {}
run_workflow_for_current_organism.datamap[INTERPRO_FILE] = {"src": "hda", "id": hda_ids["interproscan_hda_id"]}
# Run Interproscan workflow
run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
workflow_parameters=workflow_parameters,
datamap=run_workflow_for_current_organism.datamap,
workflow_name="Interproscan")
elif "Blast" in str(workflow):
logging.info("Executing workflow 'Blast_Diamond")
run_workflow_for_current_organism.connect_to_instance()
run_workflow_for_current_organism.set_get_history()
# run_workflow_for_current_organism.get_species_history_id()
# Prepare the instance+history for the current organism (add organism and analyses in Chado)
# (although it should pose no problem as the "Chado add" refuses to duplicate an analysis/organism anyway)
if args.setup:
run_workflow_for_current_organism.prepare_history()
# Get the attributes of the instance and project data files
run_workflow_for_current_organism.get_instance_attributes()
run_workflow_for_current_organism.get_organism_and_analyses_ids()
# Import datasets into history and retrieve their hda IDs
run_workflow_for_current_organism.import_datasets_into_history()
hda_ids = run_workflow_for_current_organism.get_datasets_hda_ids()
BLAST_FILE = "0"
LOAD_BLAST_IN_CHADO = "1"
SYNC_BLAST_ANALYSIS_INTO_TRIPAL = "2"
SYNC_FEATURES_INTO_TRIPAL = "3"
POPULATE_MAT_VIEWS = "4"
INDEX_TRIPAL_DATA = "5"
workflow_parameters = {}
workflow_parameters[INTERPRO_FILE] = {}
workflow_parameters[LOAD_BLAST_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
"analysis_id": run_workflow_for_current_organism.blast_diamond_analysis_id}
workflow_parameters[SYNC_BLAST_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.blast_diamond_analysis_id}
run_workflow_for_current_organism.datamap = {}
run_workflow_for_current_organism.datamap[INTERPRO_FILE] = {"src": "hda", "id": hda_ids["interproscan_hda_id"]}
# Run Interproscan workflow
run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
workflow_parameters=workflow_parameters,
datamap=run_workflow_for_current_organism.datamap,
workflow_name="Interproscan")
else: else:
......
templates/orthology_compose_template.yml.j2 0 → 100644
+ 149
− 0
View file @ b33c4b5e
# ./docker_data is created and filled with persistent data that should be backuped
version: '3.7'
services:
tripal:
image: quay.io/galaxy-genome-annotation/tripal:v2.x
depends_on:
- tripal-db
volumes:
- ./docker_data/galaxy/:/export/:ro
- ./src_data/:/data/:ro
environment:
DB_HOST: tripal-db.orthology
BASE_URL_PATH: /sp/orthology
UPLOAD_LIMIT: 20M
MEMORY_LIMIT: 512M
TRIPAL_GIT_CLONE_MODULES: "https://github.com/abretaud/tripal_rest_api.git[@c6f9021ea5d4c6d7c67c5bd363a7dd9359228bbc] https://github.com/abretaud/tripal_linkout.git[@91e08a11b788f005631cc0fafa4d68b1d2ce3ceb] https://github.com/abretaud/tripal_phylotree.git[@4cad769c9deaa5cd2933e1ae29be6aea8c8c0cc2]"
TRIPAL_DOWNLOAD_MODULES: ""
TRIPAL_ENABLE_MODULES: "tripal_rest_api tripal_phylotree tripal_linkout"
SITE_NAME: "Orthology"
ENABLE_JBROWSE: 0
ENABLE_APOLLO: 0
ENABLE_BLAST: 0
ENABLE_DOWNLOAD: 0
ENABLE_WIKI: 0
ENABLE_GO: 0
ENABLE_ORTHOLOGY: 1
# Must match the SITE_NAME in the gcv part
GCV_SITE_NAME: "example"
# Use this to point to the external adress of your main tripal host
MAIN_TRIPAL_URL: "http://{{ hostname }}"
#THEME: "{{ tripal_theme_name }}" # Use this to use another theme
#THEME_GIT_CLONE: "{{ tripal_theme_git_clone }}" # Use this to install another theme
ADMIN_PASSWORD: {{ tripal_password }} # You need to define it and update it in galaxy config below
networks:
- traefikbig
- orthology
deploy:
labels:
- "traefik.http.routers.orthology-tripal.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/orthology`))"
- "traefik.http.routers.orthology-tripal.tls=true"
- "traefik.http.routers.orthology-tripal.entryPoints=webs"
- "traefik.http.routers.orthology-tripal.middlewares=sp-auth,sp-trailslash,sp-prefix,tripal-addprefix"
- "traefik.http.services.orthology-tripal.loadbalancer.server.port=80"
restart_policy:
condition: on-failure
delay: 5s
max_attempts: 3
window: 120s
tripal-db:
image: quay.io/galaxy-genome-annotation/chado:1.31-jenkins21-pg9.5
environment:
- POSTGRES_PASSWORD=postgres
# The default chado image would try to install the schema on first run,
# we just want the tools to be available.
- INSTALL_CHADO_SCHEMA=0
- INSTALL_YEAST_DATA=0
volumes:
- ./docker_data/tripal_db/:/var/lib/postgresql/data/
networks:
- orthology
gcv:
image: quay.io/abretaud/lis-gcv
depends_on:
- tripal-db
environment:
DB_HOST: tripal-db.orthology
HOST: {{ hostname }}
SITE_NAME: example
SITE_FULL_NAME: example
DEBUG: "false"
GCV_URL: http://{{ hostname }}/sp/orthology/gcv
SERVICES_URL: http://{{ hostname }}/sp/orthology/gcv_api/services
TRIPAL_URL: http://{{ hostname }}/sp/orthology/
USE_GENE_UNAME: "true"
networks:
- traefikbig
- orthology
deploy:
labels:
- "traefik.http.routers.orthology-gcv.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/orthology/gcv`))"
- "traefik.http.routers.orthology-gcv.tls=true"
- "traefik.http.routers.orthology-gcv.entryPoints=webs"
- "traefik.http.routers.orthology-gcv.service=orthology-gcv"
- "traefik.http.routers.orthology-gcv.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix"
- "traefik.http.services.orthology-gcv.loadbalancer.server.port=80"
- "traefik.http.routers.orthology-gcv-api.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/orthology/gcv_api`))"
- "traefik.http.routers.orthology-gcv-api.tls=true"
- "traefik.http.routers.orthology-gcv-api.entryPoints=webs"
- "traefik.http.routers.orthology-gcv-api.service=orthology-gcv-api"
- "traefik.http.routers.orthology-gcv-api.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix"
- "traefik.http.services.orthology-gcv-api.loadbalancer.server.port=8000"
restart_policy:
condition: on-failure
delay: 5s
max_attempts: 3
window: 120s
galaxy:
image: quay.io/galaxy-genome-annotation/docker-galaxy-annotation:gmod
volumes:
- ../galaxy_data_libs_SI.py:/opt/setup_data_libraries.py
- ./docker_data/galaxy/:/export/
- ./src_data/:/project_data/:ro
#- /groups/XXX/:/groups/XXX/:ro # We do this when we have symlinks in src_data pointing to /groups/XXX/...
environment:
NONUSE: nodejs,proftp,reports,condor
GALAXY_LOGGING: full
GALAXY_CONFIG_BRAND: "Orthology"
GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE: "True"
GALAXY_CONFIG_USE_REMOTE_USER: "True"
GALAXY_CONFIG_REMOTE_USER_MAILDOMAIN: "bipaa"
GALAXY_CONFIG_ADMIN_USERS: "admin@galaxy.org,gogepp@bipaa" # admin@galaxy.org is the default (leave it), gogepp@bipaa is a shared ldap user we use to connect
ENABLE_FIX_PERMS: 0
PROXY_PREFIX: /sp/orthology/galaxy
GALAXY_TRIPAL_URL: http://tripal.orthology/tripal/
GALAXY_TRIPAL_PASSWORD: {{ tripal_password }} # See tripal config above
GALAXY_CHADO_DBHOST: tripal-db.orthology
GALAXY_CHADO_DBSCHEMA: chado
GALAXY_AUTO_UPDATE_DB: 1
GALAXY_AUTO_UPDATE_CONDA: 1
GALAXY_AUTO_UPDATE_TOOLS: "/galaxy-central/tools_1.yaml"
GALAXY_SHARED_DIR: ""
BLAT_ENABLED: 1
networks:
- traefikbig
- orthology
deploy:
labels:
- "traefik.http.routers.orthology-galaxy.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/orthology/galaxy`))"
- "traefik.http.routers.orthology-galaxy.tls=true"
- "traefik.http.routers.orthology-galaxy.entryPoints=webs"
- "traefik.http.routers.orthology-galaxy.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix"
- "traefik.http.services.orthology-galaxy.loadbalancer.server.port=80"
restart_policy:
condition: on-failure
delay: 5s
max_attempts: 3
window: 120s
networks:
traefikbig:
external: true
orthology:
driver: overlay
name: orthology
workflows/Blast_Diamond.ga 0 → 100644
+ 244
− 0
View file @ b33c4b5e
{
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
"name": "Blast_Diamond",
"steps": {
"0": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [],
"label": null,
"name": "Input dataset",
"outputs": [],
"position": {
"left": 200,
"top": 200
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
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