Merge branch 'master' of github.com:BioContainers/biocontainers-backend

Author: osallou

biocontainers/biomongo/helpers.py

@@ -11,7 +11,7 @@
 from biocontainers.conda.conda_metrics import CondaMetrics
 from biocontainers.github.models import LocalGitReader
 
-logger = logging.getLogger('biocontainers.quayio.models')
+logger = logging.getLogger('biocontainers.biomongo.helpers')
 QUAYIO_DOMAIN = "quay.io/biocontainers/"
 DOCKER_DOMAIN = "biocontainers/"
 
@@ -226,6 +226,7 @@ def insert_dockerhub_containers(dockerhub_containers):
             tools_dic[tool.id] = tool
 
         for container in dockerhub_containers:
+            logger.info("trying to insert dockerhub container -- " + container.name())
             # The version is read from the container tag.
             current_tool = None
             for key in container.tags:
@@ -239,7 +240,7 @@ def insert_dockerhub_containers(dockerhub_containers):
                     mongo_tool_version = MongoToolVersion()
                     mongo_tool_version.name = container.name()
                     mongo_tool_version.version = version
-                    mongo_tool_version.description = container.description()
+                    mongo_tool_version.description = "" #container.description()
                     mongo_tool_version.tool_classes = [_CONSTANT_TOOL_CLASSES['CommandLineTool']]
                     mongo_tool_version.id = tool_version_id
                     mongo_tool_version.add_author(BIOCONTAINERS_USER)

biocontainers/dockerhub/models.py

@@ -85,7 +85,7 @@ def get_containers_list(self):
                 for key in json_data['results']:
                     container = DockerHubContainer(key)
                     container_list.append(container)
-                    logger.info(" Current tool has been retrieve from DockerHub -- " + container.name())
+                    logger.info("tool retrieved from DockerHub -- " + container.name())
                 string_url = json_data['next']
 
         return container_list
@@ -117,7 +117,7 @@ def get_containers(self, page=0, batch=None):
                     short_container.add_all_tags(json_data['results'])
                     container = short_container
                     container_details_list.append(container)
-                    logger.info(" Current tool has been retrieve from DockerHub -- " + container.name())
+                    logger.info("tool details retrieved from DockerHub -- " + container.name())
             except ConnectionError:
                 logger.error(" Connection has failed to DockerHub for container ID --" + short_container.name())
 

biocontainers/requirements.txt

@@ -12,4 +12,5 @@ click==7.0
 anaconda-client==1.2.2
 scikit-learn
 beautifulsoup4
-jinja2
+Jinja2==3.0.3
+MarkupSafe==2.0.1