fixed bug where the automatic classification did not consider assays …

…& fixed no_proxy setting for requests
GC-HBOC · Dec 1, 2024 · bd5ad8c · bd5ad8c
1 parent 7c5d501
commit bd5ad8c
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Showing 10 changed files with 51 additions and 33 deletions.
diff --git a/src/annotation_service/annotation_jobs/automatic_classification_job.py b/src/annotation_service/annotation_jobs/automatic_classification_job.py
@@ -306,14 +306,16 @@ def get_autoclass_json(self, variant_id, conn: Connection) -> str:
 
         splicing_assays = assays_dict.get("splicing")
 
+        #print(splicing_assays)
+
         all_splicing_assays = []
         if splicing_assays is not None:
-            for assay in all_splicing_assays:
+            for assay in splicing_assays:
                 if assay.metadata.get("minigene") is None or assay.metadata.get("patient_rna") is None or assay.metadata.get("allele_specific") is None: # skip legacy assays
                     continue
-                minigene = assay.metadata.get("minigene", "") == "True"
-                patient_rna = assay.metadata.get("patient_rna", "") == "True"
-                allelic = assay.metadata.get("allele_specific", "False")
+                minigene = assay.get_metadata_value("minigene", "False") == "True"
+                patient_rna = assay.get_metadata_value("patient_rna", "False") == "True"
+                allelic = assay.get_metadata_value("allele_specific", "False")
                 quantification = functions.percent_to_decimal(assay.metadata.get("minimal_percentage", None))
                 all_splicing_assays.append({"minigene": minigene,
                                             "patient_rna": patient_rna,
@@ -339,8 +341,8 @@ def get_autoclass_json(self, variant_id, conn: Connection) -> str:
             for assay in functional_assays:
                 if assay.metadata.get("functional_category") is None or assay.metadata.get("functional_category") is None: # skip legacy assays
                     continue
-                is_pathogenic = assay.metadata.get("functional_category", "") == "pathogenic"
-                is_benign =  assay.metadata.get("functional_category", "") == "benign"
+                is_pathogenic = assay.get_metadata_value("functional_category", "") == "pathogenic"
+                is_benign = assay.get_metadata_value("functional_category", "") == "benign"
                 all_functional_assays.append({"pathogenic": is_pathogenic,
                                               "benign": is_benign})
         result["functional_data"] = all_functional_assays
@@ -391,8 +393,7 @@ def get_autoclass_json(self, variant_id, conn: Connection) -> str:
 
         result_json = json.dumps(result)
 
-        with open("/var/www/html/heredivar-demo/logs/herediclassify_jsons/test.json", "w") as f:
-            f.write(result_json)
+        #print(result_json)
 
         return result_json
 

diff --git a/src/annotation_service/main.py b/src/annotation_service/main.py
@@ -14,40 +14,40 @@
 def get_default_job_config():
     job_config = {
         # heredicare annotations
-        'do_heredicare': True,
+        'do_heredicare': False,
 
         # external programs
-        'do_phylop': True,
-        'do_spliceai': True,
-        'do_hexplorer': True,
-        'do_maxentscan': True,
+        'do_phylop': False,
+        'do_spliceai': False,
+        'do_hexplorer': False,
+        'do_maxentscan': False,
 
         # consequences
-        'do_consequence': True,
-        'do_vep': True,
+        'do_consequence': False,
+        'do_vep': False,
 
         #vcf annotate from vcf
-        'do_dbsnp': True,
-        'do_revel': True,
-        'do_cadd': True,
-        'do_clinvar': True,
-        'do_gnomad': True,
-        'do_brca_exchange': True,
-        'do_flossies': True,
+        'do_dbsnp': False,
+        'do_revel': False,
+        'do_cadd': False,
+        'do_clinvar': False,
+        'do_gnomad': False,
+        'do_brca_exchange': False,
+        'do_flossies': False,
 
-        'do_tp53_database': True,
-        'do_priors': True,
-        'do_bayesdel': True,
-        'do_cosmic': True,
+        'do_tp53_database': False,
+        'do_priors': False,
+        'do_bayesdel': False,
+        'do_cosmic': False,
 
         # assays
-        'do_cspec_brca_assays': True,
+        'do_cspec_brca_assays': False,
 
         # additional annotations
-        'do_cancerhotspots': True,
-        'do_taskforce_domains': True,
-        'do_coldspots': True,
-        'do_litvar': True,
+        'do_cancerhotspots': False,
+        'do_taskforce_domains': False,
+        'do_coldspots': False,
+        'do_litvar': False,
         'do_auto_class': True
 
         # outdated

diff --git a/src/common/models.py b/src/common/models.py
@@ -734,6 +734,11 @@ class Assay:
 
     metadata: Any # dict of Assay Metadata
 
+    def get_metadata_value(self, metadata_type, default):
+        if metadata_type in self.metadata:
+            return self.metadata.get(metadata_type).value
+        return default
+
     def get_header(self):
         ## Separator-symbol-hierarchy: ; -> & -> | -> $ -> +
         header = {'assays': '##INFO=<ID=assays,Number=.,Type=String,Description="All types of assays (e. g. functional or splicing) which were submitted to HerediVar. Assays are separated by "&" symbols. Format:assay_type|date|link|metadata. Metadata itself is a $ separated list of key+value pairs.">\n'}

diff --git a/src/frontend_celery/config.py b/src/frontend_celery/config.py
@@ -29,6 +29,7 @@ class Config(object):
 
     HOST = os.environ.get('HOST')
     PORT = os.environ.get('PORT')
+    os.environ["no_proxy"] = os.environ.get("NO_PROXY", "")
 
     LOGIN_REQUIRED = os.environ.get('LOGIN_REQUIRED', "True").lower() in ["true"]
 

diff --git a/src/frontend_celery/start_celery.sh b/src/frontend_celery/start_celery.sh
@@ -55,6 +55,7 @@ export WEBAPP_ENV=$we
 vep_install_dir=$ROOT/tools/ensembl-vep-release-107.0
 cpan_dir=$vep_install_dir/cpan
 export PERL5LIB=$vep_install_dir/Bio/:$cpan_dir/lib/perl5/:$PERL5LIB
+export no_proxy=$NO_PROXY
 
 
 if [ -z "${WEBAPP_ENV}" ]

diff --git a/src/frontend_celery/start_herediclass.sh b/src/frontend_celery/start_herediclass.sh
@@ -51,7 +51,7 @@ set -o allexport
 extension=env_
 source $ROOT/.$extension$WEBAPP_ENV
 set +o allexport
-
+export no_proxy=$NO_PROXY
 
 autoclass_path=$ROOT/tools/herediclass
 cd $autoclass_path

diff --git a/src/frontend_celery/start_keycloak.sh b/src/frontend_celery/start_keycloak.sh
@@ -58,7 +58,7 @@ set -o allexport
 extension=env_
 source $ROOT/.$extension$WEBAPP_ENV
 set +o allexport
-
+export no_proxy=$NO_PROXY
 
 
 if [ "${WEBAPP_ENV}" == "dev" ]

diff --git a/src/frontend_celery/start_redis.sh b/src/frontend_celery/start_redis.sh
@@ -56,6 +56,7 @@ set -o allexport
 extension=env_
 source $ROOT/.$extension$WEBAPP_ENV
 set +o allexport
+export no_proxy=$NO_PROXY
 
 cd tools/redis-stable
 src/redis-server --port $REDIS_PORT
diff --git a/src/frontend_celery/start_webapp.sh b/src/frontend_celery/start_webapp.sh
@@ -65,6 +65,7 @@ then
    extension=env_
    source $ROOT/.$extension$WEBAPP_ENV
    set +o allexport
+   export no_proxy=$NO_PROXY
 
    logsdir=$ROOT/logs
    mkdir -p $logsdir/gunicorn-access-logs

diff --git a/src/frontend_celery/webapp/templates/index.html b/src/frontend_celery/webapp/templates/index.html
@@ -93,6 +93,14 @@ <h4>Overview</h4>
 <div class="bst bsb">
     <h4>Changelog</h4>
 
+    <div class="underline">v 1.14.5 ()</div>
+    <div>
+        Bugfixes:
+        <ul>
+            <li>Fixed a bug where assay annotations would not be considered for automatic classification</li>
+        </ul>
+    </div>
+
     <div class="underline">v 1.14.4 (03.11.2024)</div>
     <div>
         General changes: