Dockerfiles has been added

Author: ypriverol

biocontainers/biomongo/__pycache__/helpers.cpython-34.pyc

@@ -139,7 +139,7 @@ def insert_dockerhub_containers(dockerhub_containers):
                     mongo_tool_version.name = container.name()
                     mongo_tool_version.version = version
                     mongo_tool_version.description = container.description()
-                    mongo_tool_version.tool_classes = ['TOOL']
+                    mongo_tool_version.tool_classes = [_CONSTANT_TOOL_CLASSES['CommandLineTool']]
                     mongo_tool_version.id = tool_version_id
                 else:
                     mongo_tool_version = tool_versions_dic[tool_version_id]
@@ -166,7 +166,9 @@ def insert_dockerhub_containers(dockerhub_containers):
                     mongo_tool.name = container.name()
                     mongo_tool.id = container.name()
                     mongo_tool.description = container.description()
+                    mongo_tool.tool_classes = [_CONSTANT_TOOL_CLASSES['CommandLineTool']]
                     tools_dic[tool_id] = mongo_tool
+
                 else:
                     mongo_tool = tools_dic[tool_id]
 

biocontainers/biomongo/helpers.py

@@ -76,7 +76,7 @@ def get_list_containers(self):
                 for key in json_data['results']:
                     container = DockerHubContainer(key)
                     self.container_list.append(container)
-                    print(container.name())
+                    logger.info(" Current tool has been retrieve from DockerHub -- " + container.name())
                 string_url = json_data['next']
 
         return self.container_list
@@ -109,9 +109,9 @@ def get_containers(self, page=None, batch=None):
                     short_container.add_all_tags(json_data['results'])
                     container = short_container
                     containers_list.append(container)
-                    print(container.name())
+                    logger.info(" Current tool has been retrieve from DockerHub -- " + container.name())
             except ConnectionError:
-                logger.error("Connection has failed to DockerHub for container ID --" + container.id)
+                logger.error(" Connection has failed to DockerHub for container ID --" + container.id)
 
         self.container_list = containers_list
         return self.container_list

biocontainers/common/__pycache__/models.cpython-34.pyc

@@ -1,3 +1,4 @@
+import argparse
 import configparser
 import logging
 
@@ -51,7 +52,7 @@ def import_dockerhub_containers(config, config_profile):
     reader.dockerhub_list_url(config[config_profile]['DOCKER_HUB'])
     reader.dockerhub_tags_url(config[config_profile]['DOCKER_HUB_TAG'])
     reader.namespace(config[config_profile]['NAMESPACE'])
-    dockerhub_containers = reader.get_containers(batch=200)
+    dockerhub_containers = reader.get_containers()
 
     mongo_helper = InsertContainers(config[config_profile]['DATABASE_URI'])
     mongo_helper.insert_dockerhub_containers(dockerhub_containers)

biocontainers/dockerhub/__pycache__/models.cpython-34.pyc

@@ -118,7 +118,6 @@ def tools_id_versions_get(id):  # noqa: E501
         for mongo_tool_version in mongo_tool_versions:
             tool_versions.append(transform_tool_version(mongo_tool_version, mongo_tool.id))
 
-
     return tool_versions
 
 
@@ -134,7 +133,7 @@ def tools_id_versions_version_id_containerfile_get(id, version_id):  # noqa: E50
 
     :rtype: List[FileWrapper]
     """
-    return 'do some magic!'
+    return 'No yet implemented!'
 
 
 def tools_id_versions_version_id_get(id, version_id):  # noqa: E501
@@ -149,7 +148,18 @@ def tools_id_versions_version_id_get(id, version_id):  # noqa: E501
 
     :rtype: ToolVersion
     """
-    return 'do some magic!'
+    mongo_tool = MongoTool.get_tool_by_id(id)
+    tool_versions = []
+    if mongo_tool is not None:
+        mongo_tool_versions = mongo_tool.get_tool_versions()
+        for mongo_tool_version in mongo_tool_versions:
+            tool_versions.append(transform_tool_version(mongo_tool_version, mongo_tool.id))
+
+    for tool_version in tool_versions:
+        if tool_version.id == version_id:
+            return tool_version
+
+    return None
 
 
 def tools_id_versions_version_id_type_descriptor_get(type, id, version_id):  # noqa: E501
@@ -166,7 +176,7 @@ def tools_id_versions_version_id_type_descriptor_get(type, id, version_id):  # n
 
     :rtype: FileWrapper
     """
-    return 'do some magic!'
+    return 'Not yet Implemented!'
 
 
 def tools_id_versions_version_id_type_descriptor_relative_path_get(type, id, version_id, relative_path):  # noqa: E501
@@ -185,7 +195,7 @@ def tools_id_versions_version_id_type_descriptor_relative_path_get(type, id, ver
 
     :rtype: FileWrapper
     """
-    return 'do some magic!'
+    return 'Not yet implemented!'
 
 
 def tools_id_versions_version_id_type_files_get(type, id, version_id):  # noqa: E501
@@ -202,7 +212,7 @@ def tools_id_versions_version_id_type_files_get(type, id, version_id):  # noqa:
 
     :rtype: List[ToolFile]
     """
-    return 'do some magic!'
+    return 'Not Yet Implemented'
 
 
 def tools_id_versions_version_id_type_tests_get(type, id, version_id):  # noqa: E501
@@ -219,4 +229,4 @@ def tools_id_versions_version_id_type_tests_get(type, id, version_id):  # noqa:
 
     :rtype: List[FileWrapper]
     """
-    return 'do some magic!'
+    return 'Not Yet Implemented'

biocontainers/dockerhub/models.py

@@ -0,0 +1,5 @@
+FROM mongo:3.6
+
+ADD first_run.sh /first_run.sh
+
+ENTRYPOINT ["bash", "/first_run.sh"]

biocontainers/pipelines.py

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# Create User
+echo "Creating user: \"$USER\"..."
+mongo  --host $MONGODB_HOST --username $ADMIN_USER --password $ADMIN_PASSWORD --eval "db.createUser({ user: '$MONGODB_USER', pwd: '$MONGODB_PASS', roles: [ { role: '$MONGODB_ROLES', db: '$MONGO_DB' } ] });"
+
+
+echo "========================================================================"
+echo "MongoDB User: \"$USER\""
+echo "MongoDB Password: \"$PASS\""
+echo "MongoDB Database: \"$DB\""
+echo "MongoDB Role: \"$ROLE\""
+echo "========================================================================"

biocontainers_flask/server/__pycache__/util.cpython-34.pyc

@@ -0,0 +1,33 @@
+
+################## BASE IMAGE ######################
+
+FROM python:2.7.15-alpine3.6
+
+################## METADATA ######################
+
+LABEL base_image="python:2.7.15-alpine3.6"
+LABEL version="1"
+LABEL software="biocontainers-pipelines-py"
+LABEL software.version="1.0.0"
+LABEL about.summary="The pipelines retrieve all the biocontainers sources dockerhub, quay.io and other resources"
+LABEL about.home="https://biocontainers.pro"
+LABEL about.license="SPDX:Apache-2"
+
+################## MAINTAINER ######################
+
+MAINTAINER Yasset Perez-Riverol <[email protected]>
+
+################## INSTALLATION ######################
+
+RUN apk update && apk add wget git python
+RUN git clone --single-branch -b master https://github.com/BioContainers/biocontainers-backend.git
+RUN cd /biocontainers-backend && python pip -r requirements.txt
+
+FROM openjdk:8-jre-stretch
+
+RUN echo "deb http://repo.mongodb.org/apt/debian stretch/mongodb-org/4.0 main" | tee /etc/apt/sources.list.d/mongodb-org-4.0.list
+RUN apt-get update && apt-get install -y --allow-unauthenticated mongodb-org-shell
+
+COPY --from=0 /registry-backend/registry-pipelines/target/registry-pipelines-1.0-SNAPSHOT.jar /registry-pipelines.jar
+
+

biocontainers_flask/server/controllers/__pycache__/__init__.cpython-34.pyc

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+java -jar /registry-pipelines.jar --mongodb.biocontainers.db.database=$BIOCONT_DB_NAME \
+  --mongodb.biocontainers.db.user=$MONGODB_USER \
+  --mongodb.biocontainers.db.password=$MONGODB_PASS \
+  --mongodb.biocontainers.db.authenticationDatabase=$MONGODB_ADMIN_DB \
+  --mongodb.biocontainers.db.host=$MONGODB_HOST \
+  --mongodb.biocontainers.db.port=27017

biocontainers_flask/server/controllers/__pycache__/ga4_gh_controller.cpython-34.pyc

@@ -0,0 +1,27 @@
+To test on minikube:
+
+```
+minikube start
+helm init --wait
+helm install -f ../../helm-example-configs/minikube.yaml ../../biocontainer-registry
+```
+
+Then check pods and if failing, see the logs:
+
+```
+kubectl get pods
+# check for pod name
+kubectl logs -f <pod-name>
+```
+
+To make changes on the container:
+
+```
+# point docker engine to minikubes to avoid building and pushing to dockerhub between tests:
+eval $(minikube docker-env)
+# with this user you won't need to change the minikube yaml config, but change it if you want to push
+docker build -t pcm32/biocontainers-api:8-stretch .
+# Delete the pod (change pod name below)
+kubectl delete pods/<pod-name>
+# Get logs from new pod, after looking into `kubectl get pods`
+```

biocontainers_flask/server/controllers/__pycache__/utils.cpython-34.pyc

@@ -0,0 +1,35 @@
+
+################## BASE IMAGE ######################
+
+FROM openjdk:8-jdk-alpine
+
+################## METADATA ######################
+
+LABEL base_image="biocontainers:debian-stretch-backports"
+LABEL version="1"
+LABEL software="biocontainers-api-py"
+LABEL software.version="1.0.0"
+LABEL about.summary="The biocontainers API provides an entry point to retrieve all containers"
+LABEL about.home="https://biocontainers.pro"
+LABEL about.license="SPDX:Apache-2"
+
+################## MAINTAINER ######################
+
+MAINTAINER Yasset Perez-Riverol <[email protected]>
+
+################## INSTALLATION ######################
+
+RUN apk update && apk add maven wget git
+RUN git clone --single-branch -b master https://github.com/BioContainers/registry-backend.git
+RUN cd /registry-backend && mvn install -DskipTests
+
+FROM openjdk:8-jre-stretch
+
+RUN echo "deb http://repo.mongodb.org/apt/debian stretch/mongodb-org/4.0 main" | tee /etc/apt/sources.list.d/mongodb-org-4.0.list
+RUN apt-get update && apt-get install -y --allow-unauthenticated mongodb-org-shell
+
+COPY --from=0 /registry-backend/biocontainers-api/target/biocontainers-api-1.0-SNAPSHOT.jar /api-service.jar
+
+ADD run.sh /usr/local/bin/run.sh
+RUN chmod u+x /usr/local/bin/run.sh
+ENTRYPOINT ["run.sh"]

biocontainers_flask/server/controllers/ga4_gh_controller.py

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+#   --mongodb.biocontainers.db.authenticationDatabase= \
+#  --mongodb.biocontainers.db.port= \
+
+cat > mongo_exec.js <<- EOM
+db = db.getSiblingDB('admin');
+try {
+  db.createUser({ user: "$MONGODB_USER" , pwd: "$MONGODB_PASS", roles: ["userAdminAnyDatabase", "dbAdminAnyDatabase", "readWriteAnyDatabase"] });
+} catch(err) {
+  print("Could not create user: "+err.message )
+  print("Trying to add role to existing user")
+  db.grantRolesToUser( "$MONGODB_USER", ["userAdminAnyDatabase", "dbAdminAnyDatabase", "readWriteAnyDatabase"] );
+}
+/* uncomment for debugging
+printjson( db.getUser( "$MONGODB_USER", {
+   showCredentials: false,
+   showPrivileges: true,
+   showAuthenticationRestrictions: true
+} ) )
+*/
+EOM
+
+cat mongo_exec.js
+
+
+mongo --host $MONGODB_HOST -u root -p $MONGO_ROOT_PASS --authenticationDatabase \
+  $MONGODB_ADMIN_DB mongo_exec.js
+
+java -jar /api-service.jar --mongodb.biocontainers.db.database=$BIOCONT_DB_NAME \
+  --mongodb.biocontainers.db.user=$MONGODB_USER \
+  --mongodb.biocontainers.db.password=$MONGODB_PASS \
+  --mongodb.biocontainers.db.authenticationDatabase=$MONGODB_ADMIN_DB \
+  --mongodb.biocontainers.db.host=$MONGODB_HOST \
+  --mongodb.biocontainers.db.port=27017

biocontainers_flask/server/models/__pycache__/__init__.cpython-34.pyc

@@ -0,0 +1,27 @@
+To test on minikube:
+
+```
+minikube start
+helm init --wait
+helm install -f ../../helm-example-configs/minikube.yaml ../../biocontainer-registry
+```
+
+Then check pods and if failing, see the logs:
+
+```
+kubectl get pods
+# check for pod name
+kubectl logs -f <pod-name>
+```
+
+To make changes on the container:
+
+```
+# point docker engine to minikubes to avoid building and pushing to dockerhub between tests:
+eval $(minikube docker-env)
+# with this user you won't need to change the minikube yaml config, but change it if you want to push
+docker build -t pcm32/biocontainers-api:8-stretch .
+# Delete the pod (change pod name below)
+kubectl delete pods/<pod-name>
+# Get logs from new pod, after looking into `kubectl get pods`
+```