fix computed tree logic

guigolab · Sep 4, 2024 · 457fcf0 · 457fcf0
1 parent f16ed00
commit 457fcf0
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Showing 5 changed files with 16 additions and 8 deletions.
diff --git a/server/jobs/taxonomy.py b/server/jobs/taxonomy.py
@@ -3,6 +3,8 @@
 import json
 from celery import shared_task
 from helpers import taxonomy as taxonomy_helper
+
+
 ROOT_NODE = os.getenv('ROOT_NODE')
 
 @shared_task(name='helpers_handle_orphans', ignore_result=False)
@@ -14,15 +16,12 @@ def handle_orphan_organisms():
             orphan.delete()
 
 
-@shared_task(name="helpers_compute_tree", ignore_result=False)
 def compute_tree():
     node = TaxonNode.objects(taxid=ROOT_NODE).first()
     if not node:
         print(f"Taxon root with taxid: {ROOT_NODE} not found")
         return
-
     tree = taxonomy_helper.dfs_generator_iterative(node)
-
     # Resolve the path to the static folder
     current_dir = os.path.dirname(os.path.abspath(__file__))
     static_dir = os.path.join(current_dir, '../static')

diff --git a/server/rest/cronjob/cronjob_service.py b/server/rest/cronjob/cronjob_service.py
@@ -23,8 +23,7 @@
     },
     'helpers':{
         'handle_orphans':taxonomy.handle_orphan_organisms,
-        'add_lineage':taxonomy.add_lineage,
-        "tree":taxonomy.compute_tree
+        'add_lineage':taxonomy.add_lineage
     },
     'geo_locations':{
         'create_from_local_samples':geolocation.create_local_sample_coordinates,

diff --git a/server/rest/goat_report/goat_reports_service.py b/server/rest/goat_report/goat_reports_service.py
@@ -1,6 +1,6 @@
 import csv
-from db.enums import GoaTStatus,PublicationSource
-from db.models import Organism,Publication, GoaTUpdateDate
+from db.enums import GoaTStatus
+from db.models import Organism, GoaTUpdateDate
 from io import StringIO
 from itertools import islice
 from helpers import user as user_helper, taxonomy as taxonomy_helper

diff --git a/server/rest/routes.py b/server/rest/routes.py
@@ -37,6 +37,7 @@ def initialize_routes(api):
 	##TAXONOMY
 	api.add_resource(taxonomy_controller.RootTreeApi, '/api/tree')
 
+
 	api.add_resource(sample_locations_controller.SampleLocations, '/api/coordinates')
 
 	##ORGANISMS
@@ -57,8 +58,10 @@ def initialize_routes(api):
 	api.add_resource(assemblies_controller.AssemblyChrAliasesApi, '/api/assemblies/<accession>/chr_aliases')
 
 	##CRONJOBS
+	api.add_resource(taxonomy_controller.GenerateTreeApi, '/api/cronjob/helpers/tree')
 	api.add_resource(cronjobs_controller.CronJobApi, '/api/cronjob', '/api/cronjob/<model>/<action>')
 
+
 	##GEOGRAPHIC LOCATIONS
 	api.add_resource(sample_locations_controller.SampleLocationsByTaxon, '/api/taxons/<taxid>/coordinates')
 	api.add_resource(sample_locations_controller.SampleLocationsByBioSample, '/api/biosamples/<accession>/coordinates' )

diff --git a/server/rest/taxonomy/taxonomy_controller.py b/server/rest/taxonomy/taxonomy_controller.py
@@ -2,6 +2,8 @@
 from flask import Response,request
 from flask_restful import Resource
 from extensions.cache import cache
+from flask_jwt_extended import jwt_required
+from jobs import taxonomy
 import json
 
 class TreeApi(Resource):
@@ -23,4 +25,9 @@ def get(self,taxid):
 
 class RootTreeApi(Resource):
     def get(self):
-        return taxonomy_service.get_root_tree()
+        return taxonomy_service.get_root_tree()
+
+class GenerateTreeApi(Resource):
+    @jwt_required()
+    def post(self):
+        taxonomy.compute_tree()