From 682f375b1c329013c988969d09944237d9d91bfc Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Thu, 11 Mar 2021 17:00:51 +0100
Subject: [PATCH] datasets import and detection depending on organism, version
and history now working correctly
---
misc/banner.png | Bin 429858 -> 429851 bytes
run_workflow_phaeoexplorer.py | 202 ++++++++-------------
speciesData.py | 4 +
templates/gspecies_compose_template.yml.j2 | 4 +-
4 files changed, 80 insertions(+), 130 deletions(-)
diff --git a/misc/banner.png b/misc/banner.png
index 06f7b085b4ede50ea7d91dfde8e30a2a88ff821a..2be0af67b7bd67b76a4f7d13eee392d4bd6f6bf7 100644
GIT binary patch
delta 12682
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diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index f3fd8e7..2857feb 100644
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -447,7 +447,7 @@ class RunWorkflow(speciesData.SpeciesData):
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 IndexErro as exc:
+ except IndexError as exc:
logging.critical("No matching InterproScan analysis exists in the instance's chado database")
sys.exit(exc)
@@ -551,83 +551,89 @@ class RunWorkflow(speciesData.SpeciesData):
instance_source_data_folders = self.instance.libraries.get_folders(library_id=str(library_id))
folders_ids = {}
- current_folder_name = ""
+ folder_name = ""
+
# Loop over the folders in the library and map folders names to their IDs
for i in instance_source_data_folders:
- for k, v in i.items():
- if k == "name":
- folders_ids[v] = 0
- current_folder_name = v
- if k == "id":
- folders_ids[current_folder_name] = v
+ folders_ids[i["name"]] = i["id"]
- 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
- interproscan_dataset_hda_id, blast_diamond_dataset_hda_id = None, None
-
- # Store datasets that are in the history already in a dict
- hda_ids = self.get_datasets_hda_ids()
# Iterating over the folders to find datasets and map datasets to their IDs
logging.debug("Datasets IDs: ")
for k, v in folders_ids.items():
- if k == "/genome":
+ # print(self.full_name)
+ # print(self.species_folder_name)
+ # print(k)
+ # print(v)
+ if k == "/genome/{0}/v{1}".format(self.species_folder_name, self.genome_version):
sub_folder_content = self.instance.folders.show_folder(folder_id=v, contents=True)
- final_sub_folder_content = self.instance.folders.show_folder(folder_id=sub_folder_content["folder_contents"][0]["id"], contents=True)
- for k2, v2 in final_sub_folder_content.items():
+ for k2, v2 in sub_folder_content.items():
for e in v2:
if type(e) == dict:
+ # print(e)
if e["name"].endswith(".fa"):
self.datasets["genome_file"] = e["ldda_id"]
- logging.debug("Genome file:\t" + e["name"] + ": " + e["ldda_id"])
- if k == "/annotation":
+ self.datasets_name["genome_file"] = e["name"]
+ logging.debug("\tGenome file:\t" + e["name"] + ": " + e["ldda_id"])
+ # print("Genome file:\t" + e["name"] + ": " + e["ldda_id"])
+
+ # print(self.species_folder_name)
+ if k == "/annotation/{0}/OGS{1}".format(self.species_folder_name, self.ogs_version):
sub_folder_content = self.instance.folders.show_folder(folder_id=v, contents=True)
- final_sub_folder_content = self.instance.folders.show_folder(folder_id=sub_folder_content["folder_contents"][0]["id"], contents=True)
- for k2, v2 in final_sub_folder_content.items():
+ for k2, v2 in sub_folder_content.items():
for e in v2:
if type(e) == dict:
if "transcripts" in e["name"]:
self.datasets["transcripts_file"] = e["ldda_id"]
- logging.debug("Transcripts file:\t" + e["name"] + ": " + e["ldda_id"])
+ self.datasets_name["transcripts_file"] = e["name"]
+ logging.debug("\tTranscripts file:\t" + e["name"] + ": " + e["ldda_id"])
elif "proteins.fa" in e["name"]:
self.datasets["proteins_file"] = e["ldda_id"]
- logging.debug("Proteins file:\t" + e["name"] + ": " + e["ldda_id"])
+ self.datasets_name["proteins_file"] = e["name"]
+ logging.debug("\tProteins file:\t" + e["name"] + ": " + e["ldda_id"])
elif "gff" in e["name"]:
self.datasets["gff_file"] = e["ldda_id"]
- logging.debug("GFF file:\t" + e["name"] + ": " + e["ldda_id"])
+ self.datasets_name["gff_file"] = e["name"]
+ logging.debug("\tGFF file:\t" + e["name"] + ": " + e["ldda_id"])
elif "Interpro" in e["name"]:
self.datasets["interproscan_file"] = e["ldda_id"]
- logging.debug("Interproscan file:\t" + e["name"] + ": " + e["ldda_id"])
+ self.datasets_name["interproscan_file"] = e["name"]
+ logging.debug("\tInterproscan file:\t" + e["name"] + ": " + e["ldda_id"])
elif "diamond-blastp" in e["name"]:
self.datasets["blast_diamond_file"] = e["ldda_id"]
- logging.debug("Blastp diamond file:\t" + e["name"] + ": " + e["ldda_id"])
+ self.datasets_name["blast_diamond_file"] = e["name"]
+ logging.debug("\tBlastp diamond file:\t" + e["name"] + ": " + e["ldda_id"])
logging.debug("Uploading datasets into history %s" % self.history_id)
# Import each dataset into history if it is not imported
- if hda_ids["genome_hda_id"] is None:
+
+ first_hda_ids = self.get_datasets_hda_ids()
+
+ if first_hda_ids["genome_hda_id"] is None:
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["genome_file"])
- if hda_ids["gff_hda_id"] is None:
+ if first_hda_ids["gff_hda_id"] is None:
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["gff_file"])
- if hda_ids["transcripts_hda_id"] is None:
+ if first_hda_ids["transcripts_hda_id"] is None:
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["transcripts_file"])
- if hda_ids["proteins_hda_id"] is None:
+ if first_hda_ids["proteins_hda_id"] is None:
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["proteins_file"])
- if hda_ids["interproscan_hda_id"] is None:
+ if first_hda_ids["interproscan_hda_id"] is None:
try:
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["interproscan_file"])
except Exception as exc:
- logging.debug("Interproscan file not found in library (history: {0})\n{1}".format(self.history_id, exc))
- if hda_ids["blast_diamond_hda_id"] is None:
+ logging.debug("Interproscan file not found in library (history: {0})".format(self.history_id))
+ if first_hda_ids["blast_diamond_hda_id"] is None:
try:
self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["blast_diamond_file"])
except Exception as exc:
- logging.debug("Blastp file not found in library (history: {0})\n{1}".format(self.history_id, exc))
+ logging.debug("Blastp file not found in library (history: {0})".format(self.history_id))
# _datasets = self.instance.datasets.get_datasets()
# with open(os.path.join(self.main_dir, "datasets_ids.json"), "w") as datasets_ids_outfile:
# datasets_ids_outfile.write(str(_datasets))
- return {"history_id": self.history_id, "library_id": library_id, "datasets": self.datasets}
+ # Return a dict made of the hda ids
+ return self.get_datasets_hda_ids()
def get_datasets_hda_ids(self):
@@ -641,109 +647,46 @@ class RunWorkflow(speciesData.SpeciesData):
:return:
"""
- # Create an object of the galaxy instance
- gio = GalaxyInstance(url=self.instance_url,
- email=self.config["galaxy_default_admin_email"],
- password=self.config["galaxy_default_admin_password"])
-
- prj_lib = gio.libraries.get_previews(name="Project Data")
- library_id = prj_lib[0].id
-
- instance_source_data_folders = self.instance.libraries.get_folders(library_id=str(library_id))
-
- folders_ids = {}
- current_folder_name = ""
- # Loop over the folders in the library and map folders names to their IDs
- for i in instance_source_data_folders:
- for k, v in i.items():
- if k == "name":
- folders_ids[v] = 0
- current_folder_name = v
- if k == "id":
- folders_ids[current_folder_name] = v
-
- 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
- interproscan_dataset_hda_id, blast_diamond_dataset_hda_id = None, None
-
- # Iterating over the folders to find datasets and map datasets to their IDs
- # TODO: Add a required matching of the version (genome/ogs)
- logging.debug("Datasets IDs: ")
- for k, v in folders_ids.items():
- if k == "/genome":
- sub_folder_content = self.instance.folders.show_folder(folder_id=v, contents=True)
- final_sub_folder_content = self.instance.folders.show_folder(folder_id=sub_folder_content["folder_contents"][0]["id"], contents=True)
- for k2, v2 in final_sub_folder_content.items():
- for e in v2:
- if type(e) == dict:
- if e["name"].endswith(".fa"):
- self.datasets["genome_file"] = e["ldda_id"]
- self.datasets_name["genome_file"] = e["name"]
- logging.debug("Genome file:\t" + e["name"] + ": " + e["ldda_id"])
- if k == "/annotation":
- sub_folder_content = self.instance.folders.show_folder(folder_id=v, contents=True)
- final_sub_folder_content = self.instance.folders.show_folder(folder_id=sub_folder_content["folder_contents"][0]["id"], contents=True)
- for k2, v2 in final_sub_folder_content.items():
- for e in v2:
- if type(e) == dict:
- if "transcripts" in e["name"]:
- self.datasets["transcripts_file"] = e["ldda_id"]
- self.datasets_name["transcripts_file"] = e["name"]
- logging.debug("Transcripts file:\t" + e["name"] + ": " + e["ldda_id"])
- elif "proteins.fa" in e["name"]:
- self.datasets["proteins_file"] = e["ldda_id"]
- self.datasets_name["proteins_file"] = e["name"]
- logging.debug("Proteins file:\t" + e["name"] + ": " + e["ldda_id"])
- elif "gff" in e["name"]:
- self.datasets["gff_file"] = e["ldda_id"]
- self.datasets_name["gff_file"] = e["name"]
- logging.debug("GFF file:\t" + e["name"] + ": " + e["ldda_id"])
- elif "Interpro" in e["name"]:
- self.datasets["interproscan_file"] = e["ldda_id"]
- self.datasets_name["interproscan_file"] = e["name"]
- logging.debug("Interproscan file:\t" + e["name"] + ": " + e["ldda_id"])
- elif "diamond-blastp" in e["name"]:
- self.datasets["blast_diamond_file"] = e["ldda_id"]
- self.datasets_name["blast_diamond_file"] = e["name"]
- logging.debug("Blastp diamond file:\t" + e["name"] + ": " + e["ldda_id"])
-
# List of all datasets in the instance (including outputs from jobs)
# "limit" and "offset" options *may* be used to restrict search to specific datasets but since
# there is no way to know which imported datasets are the correct ones depending on history content
# it's not currently used
history_datasets_li = self.instance.datasets.get_datasets()
+ print(history_datasets_li)
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
- # Match files imported in history names vs library datasets names to assign their respective hda_id
+ # Match files imported in history names vs library datasets names to assign their respective hda_id
for dataset_dict in history_datasets_li:
- if dataset_dict["name"] == self.datasets_name["genome_file"]:
- genome_dataset_hda_id = dataset_dict["id"]
- logging.debug("Genome dataset hda id: %s" % genome_dataset_hda_id)
- elif dataset_dict["name"] == self.datasets_name["proteins_file"]:
- proteins_datasets_hda_id = dataset_dict["id"]
- logging.debug("Proteins dataset hda ID: %s" % proteins_datasets_hda_id)
- elif dataset_dict["name"] == self.datasets_name["transcripts_file"]:
- transcripts_dataset_hda_id = dataset_dict["id"]
- logging.debug("Transcripts dataset hda ID: %s" % transcripts_dataset_hda_id)
- elif dataset_dict["name"] == self.datasets_name["gff_file"]:
- gff_dataset_hda_id = dataset_dict["id"]
- logging.debug("gff dataset hda ID: %s" % gff_dataset_hda_id)
-
- if "interproscan_file" in self.datasets_name.keys():
- if dataset_dict["name"] == self.datasets_name["interproscan_file"]:
- interproscan_dataset_hda_id = dataset_dict["id"]
- logging.debug("InterproScan dataset hda ID: %s" % gff_dataset_hda_id)
- if "blast_diamond_file" in self.datasets_name.keys():
- if dataset_dict["name"] == self.datasets_name["blast_diamond_file"]:
- blast_diamond_dataset_hda_id = dataset_dict["id"]
- logging.debug("Blast Diamond dataset hda ID: %s" % gff_dataset_hda_id)
+ if dataset_dict["history_id"] == self.history_id:
+ if dataset_dict["name"] == self.datasets_name["genome_file"]:
+ genome_dataset_hda_id = dataset_dict["id"]
+ logging.debug("Genome dataset hda id: %s" % genome_dataset_hda_id)
+ elif dataset_dict["name"] == self.datasets_name["proteins_file"]:
+ proteins_datasets_hda_id = dataset_dict["id"]
+ logging.debug("Proteins dataset hda ID: %s" % proteins_datasets_hda_id)
+ elif dataset_dict["name"] == self.datasets_name["transcripts_file"]:
+ transcripts_dataset_hda_id = dataset_dict["id"]
+ logging.debug("Transcripts dataset hda ID: %s" % transcripts_dataset_hda_id)
+ elif dataset_dict["name"] == self.datasets_name["gff_file"]:
+ gff_dataset_hda_id = dataset_dict["id"]
+ logging.debug("GFF dataset hda ID: %s" % gff_dataset_hda_id)
+
+ if "interproscan_file" in self.datasets_name.keys():
+ if dataset_dict["name"] == self.datasets_name["interproscan_file"]:
+ interproscan_dataset_hda_id = dataset_dict["id"]
+ logging.debug("InterproScan dataset hda ID: %s" % gff_dataset_hda_id)
+ if "blast_diamond_file" in self.datasets_name.keys():
+ if dataset_dict["name"] == self.datasets_name["blast_diamond_file"]:
+ blast_diamond_dataset_hda_id = dataset_dict["id"]
+ logging.debug("Blast Diamond dataset hda ID: %s" % gff_dataset_hda_id)
# Return a dict made of the hda ids
- 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,
- "interproscan_hda_id": interproscan_dataset_hda_id, "blast_diamond_hda_id": blast_diamond_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,
+ "interproscan_hda_id": interproscan_dataset_hda_id,
+ "blast_diamond_hda_id": blast_diamond_dataset_hda_id}
def get_organism_id(self):
"""
@@ -753,9 +696,9 @@ class RunWorkflow(speciesData.SpeciesData):
:return:
"""
+ tool_version = "2.3.3"
time.sleep(3)
-
# Get the ID for the current organism in chado
org = self.instance.tools.run_tool(
tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/2.3.3",
@@ -925,8 +868,7 @@ if __name__ == "__main__":
run_workflow_for_current_organism.get_instance_attributes()
# 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()
+ hda_ids = run_workflow_for_current_organism.import_datasets_into_history()
# DEBUG
# run_workflow_for_current_organism.get_invocation_report(workflow_name="Chado load Tripal synchronize")
@@ -976,6 +918,8 @@ if __name__ == "__main__":
# run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "hda",
# "id": hda_ids["gff_hda_id"]}
+ # Ensures galaxy has time to retrieve
+ time.sleep(60)
# Run the Chado load Tripal sync workflow with the parameters set above
run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
workflow_parameters=workflow_parameters,
diff --git a/speciesData.py b/speciesData.py
index a52b0e5..dc6d2a4 100644
--- a/speciesData.py
+++ b/speciesData.py
@@ -51,6 +51,10 @@ class SpeciesData:
self.genus_uppercase = self.genus[0].upper() + self.genus[1:]
self.chado_species_name = "{0} {1}".format(self.species, self.sex)
self.full_name = ' '.join(utilities.filter_empty_not_empty_items([self.genus_uppercase, self.species, self.strain, self.sex])["not_empty"])
+ self.full_name = self.full_name.replace("__", "_").replace("_ ", "_").replace(" _", "_")
+ if self.full_name.endswith("_") or self.full_name.endswith(" "):
+ self.full_name = self.full_name[0:-2]
+
self.full_name_lowercase = self.full_name.lower()
self.abbreviation = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase[0], self.species, self.strain, self.sex])["not_empty"])
self.genus_species = self.genus_lowercase + "_" + self.species
diff --git a/templates/gspecies_compose_template.yml.j2 b/templates/gspecies_compose_template.yml.j2
index c943c27..d6ca429 100644
--- a/templates/gspecies_compose_template.yml.j2
+++ b/templates/gspecies_compose_template.yml.j2
@@ -50,7 +50,9 @@ services:
TRIPAL_ENABLE_MODULES: "tripal_analysis_blast tripal_analysis_interpro tripal_analysis_go tripal_rest_api tripal_elasticsearch"
SITE_NAME: "{{ Genus_species }}"
ELASTICSEARCH_HOST: elasticsearch.{{ genus_species }}
- ENABLE_JBROWSE: /jbrowse/?data=data/{{ genus_species_sex }} # WARNING --> the variable "sex" shouldn't be in the compose file (all strains/sex are supposed to be in the same jbrowse)
+ ENABLE_JBROWSE: /jbrowse/?data=data/{{ genus_species_sex }}
+ # This ENABLE_JBROWSE variable should point to the "best assembly" by default --> tag it in the input file and use it to define this variable correctly (also called
+ # unique id in the jbrowse tool parameters == both have to be identical)
ENABLE_APOLLO: 0
ENABLE_BLAST: 1
ENABLE_DOWNLOAD: 1
--
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