add TODOs

eva_submission/eload_utils.py

@@ -70,6 +70,7 @@ def get_mongo_creds():
     properties = get_properties_from_xml_file(cfg['maven']['environment'], cfg['maven']['settings_file'])
     # Use the primary mongo host from configuration:
     # https://github.com/EBIvariation/configuration/blob/master/eva-maven-settings.xml#L111
+    # TODO: revisit once accessioning/variant pipelines can support multiple hosts
     mongo_host = split_hosts(properties['eva.mongo.host'])[1][0]
     mongo_user = properties['eva.mongo.user']
     mongo_pass = properties['eva.mongo.passwd']

nextflow/accession.nf

@@ -111,6 +111,7 @@ process accession_vcf {
     (java -Xmx7g -jar $params.jar.accession_pipeline --spring.config.name=\$filename) || \
     # If accessioning fails due to missing variants, but the only missing variants are structural variants,
     # then we should treat this as a success from the perspective of the automation.
+    # TODO revert once accessioning pipeline properly registers structural variants
         [[ \$(grep -o 'Skipped processing structural variant' ${params.logs_dir}/${log_filename}.log | wc -l) \
            == \$(grep -oP '\\d+(?= unaccessioned variants need to be checked)' ${params.logs_dir}/${log_filename}.log) ]]
     echo "done" > ${accessioned_filename}.tmp