implement fetching of current biobox images. refs #1

Author: Tobias Laufkötter

app/api.py

@@ -1,6 +1,6 @@
 from flask import jsonify, abort, request, make_response
 
-from app import app
+from app import app, bioboxes
 
 BAD_REQUEST = 400
 NOT_IMPLEMENTED = 405
@@ -18,7 +18,7 @@ def not_implemented(error):
 
 @app.route('/bioboxgui/api/bioboxes', methods=[GET_METHOD])
 def get_bioboxes():
-    abort(NOT_IMPLEMENTED)
+    return jsonify({'images': [box.get_dict() for box in bioboxes.get_current_bioboxes()]})
 
 
 @app.route('/bioboxgui/api/bioboxes', methods=[POST_METHOD])

app/bioboxes.py

@@ -0,0 +1,134 @@
+import requests
+import yaml
+
+
+class Yaml():
+    """
+    is the parent of every class that can be generated from yaml files.
+    """
+    MUST_HAVE = []
+
+    def __init__(self, yaml_dict):
+        """
+        Forms an object from the given dictionary.
+
+        :param yaml_dict: a dictionary as it is parsed from yaml code.
+        :return: Yaml base
+        """
+        self.validate_yaml(yaml_dict)
+
+    def validate_yaml(self, yaml_dict):
+        """
+        validates the given dictionary against the MUST_HAVE keys.
+
+        :param yaml_dict: a dictionary as it is parsed from yaml code.
+        :return: None
+        :raises: LookupError when key requirements aren't fulfilled.
+        """
+        for key in self.MUST_HAVE:
+            if yaml_dict.has_key(key) and yaml_dict.get(key):
+                pass
+            else:
+                raise LookupError, 'error with the "%s" key' % key
+
+
+class Biobox(Yaml):
+    """
+    represents a generic biobox container description.
+    """
+    KEY_IMAGE = 'image'
+    KEY_ID = 'pmid'
+    KEY_HOME_PAGE = 'homepage'
+    KEY_MAILING_LIST = 'mailing_list'
+    KEY_DESCRIPTION = 'description'
+    KEY_TASKS = 'tasks'
+    KEY_TITLE = 'title'
+
+    MUST_HAVE = [
+        KEY_IMAGE,
+        KEY_ID,
+        KEY_DESCRIPTION,
+        KEY_TASKS,
+        KEY_TITLE
+    ]
+
+    def __init__(self, yaml_dict):
+        """
+        Forms an object from the given dictionary.
+
+        :param interface: the interface of the biobox.
+        :param yaml_dict: a dictionary as it is parsed from yaml code.
+        :return: Yaml base
+        """
+        Yaml.__init__(self, yaml_dict)
+        self.image = self.Image(yaml_dict.get(self.KEY_IMAGE))
+        self.tasks = [self.Task(task) for task in yaml_dict.get(self.KEY_TASKS)]
+        self.pmid = yaml_dict.get(self.KEY_ID)
+        self.homepage = yaml_dict.get(self.KEY_HOME_PAGE)
+        self.mailing_list = yaml_dict.get(self.KEY_MAILING_LIST)
+        self.description = yaml_dict.get(self.KEY_DESCRIPTION)
+        self.title = yaml_dict.get(self.KEY_TITLE)
+
+    def get_dict(self):
+        dictionary = self.__dict__
+        dictionary[self.KEY_IMAGE] = self.image.__dict__
+        dictionary[self.KEY_TASKS] = [task.__dict__ for task in self.tasks]
+        return dictionary
+
+    class Image(Yaml):
+        """
+        is a helper class for :class:`Biobox`.
+        """
+        KEY_CONTAINER_URI = 'dockerhub'
+        KEY_REPO_URL = 'repo'
+        KEY_SRC_URL = 'source'
+
+        MUST_HAVE = [
+            KEY_CONTAINER_URI,
+            KEY_REPO_URL
+        ]
+
+        def __init__(self, yaml_dict):
+            """
+            Forms an object from the given dictionary.
+
+            :param yaml_dict: a dictionary as it is parsed from yaml code.
+            :return: Yaml base
+            """
+            Yaml.__init__(self, yaml_dict)
+            self.dockerhub = yaml_dict.get(self.KEY_CONTAINER_URI)
+            self.repo = yaml_dict.get(self.KEY_REPO_URL)
+            self.source = yaml_dict.get(self.KEY_SRC_URL)
+
+    class Task(Yaml):
+        KEY_NAME = 'name'
+        KEY_INTERFACE = 'interface'
+
+        MUST_HAVE = [
+            KEY_NAME,
+            KEY_INTERFACE
+        ]
+
+        def __init__(self, yaml_dict):
+            Yaml.__init__(self, yaml_dict)
+            self.name = yaml_dict.get(self.KEY_NAME)
+            self.interface = yaml_dict.get(self.KEY_INTERFACE)
+
+
+def get_current_bioboxes():
+    response = requests.get('https://raw.githubusercontent.com/pbelmann/data/feature/new-image-list/images.yml')
+    return from_list(yaml.load(response.text))
+
+
+def from_list(yaml_dict):
+    """
+    creates bioboxes from an interface list.
+    :param yaml_dict: the list with bioboxes as it is parsed from a yaml file.
+    :return: a list with lists of :class:`Biobox`.
+    """
+    interfaces = []
+    for yaml_box in yaml_dict.get('images'):
+        biobox = Biobox(yaml_box)
+        interfaces.append(biobox)
+
+    return interfaces

requirements.txt

@@ -1 +1,15 @@
-flask
+Flask==0.10.1
+Flask-HTTPAuth==2.7.0
+Flask-SQLAlchemy==2.1
+google-common==0.0.1
+itsdangerous==0.24
+Jinja2==2.8
+MarkupSafe==0.23
+mesos==0.26.0
+mesos.interface==0.26.0
+protobuf==2.6.1
+PyYAML==3.11
+requests==2.9.1
+SQLAlchemy==1.0.11
+Werkzeug==0.11.3
+wheel==0.24.0