From 48bc8e8d50e0d2d5f3dc1e4b7cbda91aa6fbfcc2 Mon Sep 17 00:00:00 2001 From: Athitheya Gobinathan Date: Thu, 9 May 2024 17:42:07 -0400 Subject: [PATCH 1/4] Updated mongoDB image version to 4.2 --- docker-compose.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yaml b/docker-compose.yaml index 5565bc2..905b068 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -36,7 +36,7 @@ services: - "5672:5672" mongodb: - image: mongo:3.2 + image: mongo:4.2 restart: unless-stopped volumes: - ${PROTES_DATA_DIR:-../data/pro_tes}/db:/data/db From a9f26f76276e6bacdc48580020e9865321f12dda Mon Sep 17 00:00:00 2001 From: Athitheya Gobinathan Date: Tue, 14 May 2024 11:29:35 -0400 Subject: [PATCH 2/4] build: updated mongoDB to 7.0 --- docker-compose.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yaml b/docker-compose.yaml index 905b068..2bbac44 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -36,7 +36,7 @@ services: - "5672:5672" mongodb: - image: mongo:4.2 + image: mongo:7.0 restart: unless-stopped volumes: - ${PROTES_DATA_DIR:-../data/pro_tes}/db:/data/db From 63236b726db114c593ec3680bef29ec1e72da832 Mon Sep 17 00:00:00 2001 From: Athitheya Gobinathan Date: Tue, 14 May 2024 11:31:58 -0400 Subject: [PATCH 3/4] test: changed deprecated insert() to insert_one() --- pro_tes/ga4gh/tes/task_runs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pro_tes/ga4gh/tes/task_runs.py b/pro_tes/ga4gh/tes/task_runs.py index 8bfccc3..34b9cad 100644 --- a/pro_tes/ga4gh/tes/task_runs.py +++ b/pro_tes/ga4gh/tes/task_runs.py @@ -417,7 +417,7 @@ def _write_doc_to_db( ) document.worker_id = uuid() try: - self.db_client.insert(document.dict(exclude_none=True)) + self.db_client.insert_one(document.dict(exclude_none=True)) except DuplicateKeyError: continue assert document is not None From 6a1b3eb37a4ea88c47b69a873c62f738685679f5 Mon Sep 17 00:00:00 2001 From: Athitheya Gobinathan Date: Mon, 20 May 2024 15:15:23 -0400 Subject: [PATCH 4/4] build: updated foca to 0.13.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 983ac80..104f329 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ celery-types>=0.20.0 connexion>=2.11.2,<3 -foca>=0.12.1 +foca>=0.13.0 geopy>=2.2.0 gunicorn>=20.1.0,<21 ip2geotools>=0.1.6