diff --git a/server/api/tasks.py b/server/api/tasks.py
index 5d0ad4ebfc25e653a5c98ba6ce17d3507ee48ddc..7e52416e4787930bed5450be09a0d47bb1d30d40 100644
--- a/server/api/tasks.py
+++ b/server/api/tasks.py
@@ -32,8 +32,10 @@ def run_analyis(
# current_history = gi.histories.create_history()
# history_id = current_history["id"]
chained_tasks = chain(
- create_history.si(f"{settings.HOSTLABEL} - {project_name} - {analysis_name}", analysis_id),
- upload_file_to_galaxy.s(experiment_file_path, "excel.xls",),
+ create_history.si(
+ f"{settings.HOSTLABEL} - {project_name} - {analysis_name}", analysis_id
+ ),
+ upload_file_to_galaxy.s(experiment_file_path, "excel.xls"),
genome_scan_wf.s(tools_params, wf_id),
load_lod_score.s(),
load_significance_threshold.s(),
@@ -78,7 +80,6 @@ def upload_file_to_galaxy(ids, file_path, file_type):
analysis_id, history_id = ids
# gi = GalaxyInstance(url=url, key=key, verify=False)
upload_response = gi.tools.upload_file(file_path, history_id, file_type=file_type)
-
upload_data_id = upload_response["outputs"][0]["id"]
upload_job = upload_response["jobs"][0]
upload_job_id = upload_job["id"]
@@ -101,7 +102,7 @@ def upload_file_to_galaxy(ids, file_path, file_type):
f"error : {data['misc_info']}"
)
shutil.rmtree(Path(file_path).parent)
- return (analysis_id, history_id, upload_data_id)
+ return analysis_id, history_id, upload_data_id
@celery_app.task()
@@ -132,7 +133,7 @@ def genome_scan_wf(ids, tools_params, wf_id):
# f"Error during Galaxy workflow job - name : "
# f"id : {workflow_job_id}, "
# )
- return analysis_id, history_id
+ return analysis_id, history_id, workflow_job_id
except StopIteration:
raise Exception(f"Do not find the workflow : {genome_scan_wf_metadata['name']}")
@@ -174,7 +175,7 @@ def download_formatted_qtl2_data(history_id):
@celery_app.task()
def load_lod_score(ids):
- analysis_id, history_id = ids
+ analysis_id, history_id, _ = ids
dataset_pattern = "lod.csv"
try:
datasets = gi.histories.show_history(history_id, contents=True)
@@ -200,13 +201,12 @@ def load_lod_score(ids):
lod_entry = LodScore(analysis=analysis, lod_scores=lod_scores)
lod_entry.save()
# LodScore.objects.bulk_create([lod_scores])
- return analysis_id, history_id
+ return analysis_id, history_id, lod_entry.id
@celery_app.task()
def load_refine_peaks(ids):
- print(ids)
- analysis_id, history_id = ids
+ analysis_id, history_id, _ = ids
dataset_pattern = "refine-peaks.csv"
try:
# TODO: test to put a fake history in order to catch exception and
@@ -237,15 +237,15 @@ def load_refine_peaks(ids):
peak.save()
peak_ids.append(peak.id)
- return analysis_id, history_id
+ return analysis_id, history_id, peak_ids
@celery_app.task()
def load_significance_threshold(ids):
- analysis_id, history_id = ids
+ analysis_id, history_id, _ = ids
# gi = GalaxyInstance(url=url, key=key, verify=False)
dataset_pattern = "significance-threshold.csv"
- ids = []
+ significance_threshold_ids = []
try:
# TODO: test to put a fake history in order to catch exception and
# do whatever needed
@@ -259,7 +259,6 @@ def load_significance_threshold(ids):
except StopIteration:
raise Exception(f"Do not find the dataset : {dataset_pattern}")
for dataset in filtered_datasets:
- print(dataset["name"])
try:
downloaded_ds = gi.datasets.download_dataset(dataset["id"])
except HTTPError:
@@ -274,14 +273,14 @@ def load_significance_threshold(ids):
bulk = threshold_gen(signi_thres, analysis)
for threshold_db in bulk:
threshold_db.save()
- ids.append(threshold_db.id)
+ significance_threshold_ids.append(threshold_db.id)
# LodScoreSignificanceThreshold.objects.bulk_create(bulk, batch_size=10000)
- return analysis_id, history_id
+ return analysis_id, history_id, significance_threshold_ids
@celery_app.task()
def load_coefficient(ids):
- analysis_id, history_id = ids
+ analysis_id, history_id, _ = ids
dataset_pattern = "coef.csv"
try:
# TODO: test to put a fake history in order to catch exception and
@@ -318,12 +317,12 @@ def load_coefficient(ids):
coef_gen = coefficient_gen(file_list[1:])
coef_db = Coefficient(peak=peak, coefficients=list(coef_gen))
coef_db.save()
- return analysis_id, history_id
+ return analysis_id, history_id, coef_db.id
@celery_app.task()
def load_haplotypes(ids):
- analysis_id, history_id = ids
+ analysis_id, history_id, _ = ids
dataset_pattern = "haplo.csv"
try:
datasets = gi.histories.show_history(history_id, contents=True)
@@ -356,12 +355,12 @@ def load_haplotypes(ids):
haplo_gen = haplotype_gen(file_list[1:])
haplotype_db = Haplotypes(peak=peak, haplotypes=list(haplo_gen))
haplotype_db.save()
- return analysis_id, history_id
+ return analysis_id, history_id, haplotype_db.id
@celery_app.task()
def load_top_snps(ids):
- analysis_id, history_id = ids
+ analysis_id, history_id, _ = ids
dataset_pattern = "top_snps.csv"
try:
datasets = gi.histories.show_history(history_id, contents=True)
@@ -393,12 +392,12 @@ def load_top_snps(ids):
top_snps = list(top_snps_gen(file_list[1:]))
top_snps_db = TopSnps(peak=peak, top_snps=top_snps)
top_snps_db.save()
- return analysis_id, history_id
+ return analysis_id, history_id, top_snps_db.id
@celery_app.task()
def load_snps_association(ids):
- analysis_id, history_id = ids
+ analysis_id, history_id, _ = ids
dataset_pattern = "snps_assoc.csv"
try:
datasets = gi.histories.show_history(history_id, contents=True)
@@ -432,7 +431,7 @@ def load_snps_association(ids):
snps_assoc = list(snps_association_gen(file_list[1:]))
snps_assoc_db = SnpsAssociation(peak=peak, snps_association=snps_assoc)
snps_assoc_db.save()
- return analysis_id, history_id
+ return analysis_id, history_id, snps_assoc_db.id
def threshold_gen(thresholds, analysis):