1.1 Configuration Updates

1.1.1 Import worker configuration in settings_import.toml :

fusion_format_dir
Add the key fusion_format_dir in [vcf_to_json] section. It must point to a new folder in datafiles/vcf_to_json named fusion_format, containing a star_fusion_annotator file (cf https://gleaves.laboratoire-seqoia.fr/download/conf/workers/datafiles/vcf_to_json/)

prefix_fusion
Add the key prefix_fusion in [vcf_to_json] section. This key can have a value such as dossierfusion_ for exemple. The value must be identical between the import worker, the index worker, and gLeaves (where it is called esFusionIndexPrefix).

[vcf_to_json]
prefix_fusion="$PathToDatafiles/vcf_to_json/fusion_format"
fusion_format_dir="dossierfusion_"
1.1.2 Index worker configuration in settings_index.toml

Add the key fusion_es_mapping_file in the [elasticsearch] section.

The file must be downloaded from: https://gleaves.laboratoire-seqoia.fr/download/conf/workers/datafiles/json_to_es/ and placed in the appropriate location.

[elasticsearch]
fusion_es_mapping_file="/etc/gleaves_worker/datafiles/json_to_es/fusion_es_mapping.json"

Add the key prefix_fusion in [vcf_to_json] section. This key can have a value such as dossierfusion_ for exemple. The value must be identical between the import worker, the index worker, and gLeaves (where it is called esFusionIndexPrefix).

[vcf_to_json]
prefix_fusion="dossierfusion_"
1.1.3 gLeaves configuration :

Add the following to the rabbitmq section.

  typeMessageEnErreur: error
  typeMessageEnCoursDeTraitement: processing
  typeMessageEnAttente: waiting

Add the following section:

exportToGenno:
  username: dummy
  password: dummy
  url: dummy

1.2 Import new collections

docker cp images/update_3_68_28/hpo_bis.jsonl $containerID:/tmp

From MongoDB container :

cat /tmp/hpo_bis.jsonl | mongoimport \
  --collection hpo_bis \
  --uri="mongodb://user:password@localhost:27017/gleaves?authMechanism=SCRAM-SHA-1&authSource=admin" \
  --file /dev/stdin

1.3 Loading the last images

docker load < gleaves_3_6_28-1.tar.gz
docker load < gleaves_ad_0_1_31-1.tar.gz
docker load < gleaves_compute_rec_0_1_50-1.tar.gz
docker load < gleaves_worker_import_0_1_96-1.tar.gz
docker load < gleaves_worker_index_0_1_48-1.tar.gz