start testing for download feature

cycledash/auth.py

@@ -3,6 +3,7 @@
 from flask.ext.login import login_user, logout_user
 from sqlalchemy import exc
 import voluptuous
+import base64
 
 from cycledash import db, bcrypt, login_manager
 from cycledash.helpers import prepare_request_data, safely_redirect_to_next
@@ -107,3 +108,33 @@ def register():
             login_user(user)
             return redirect('/')
     return render_template('register.html', errors=errors)
+
+def check_login_from_key(api_key):
+    username, password = api_key.split(":")
+    return check_login(username, password)
+
+def load_user_from_request(request):
+    """Support for basic authorization."""
+    # first, try to login using the api_key url arg
+    api_key = request.args.get('api_key')
+    if api_key:
+        user = check_login_from_key(api_key)
+        if user:
+            return user
+
+    # next, try to login using Basic Auth
+    api_key = request.headers.get('Authorization')
+    if api_key:
+        api_key = api_key.replace('Basic ', '', 1)
+        try:
+            api_key = base64.b64decode(api_key)
+        except TypeError:
+            pass
+        user = check_login_from_key(api_key)
+        if user:
+            return user
+
+    # finally, return None if both methods did not login the user
+    return None
+
+login_manager.request_loader(load_user_from_request)

tests/python/test_download.py

@@ -0,0 +1,46 @@
+import mock
+import nose
+import json
+
+from cycledash import app, db
+from common.helpers import tables
+
+from test_projects_api import create_project_with_name
+from test_bams_api import create_bam_with_name
+from test_runs_api import create_run_with_uri
+from workers.genotype_extractor import _extract
+
+import helpers
+
+class TestDownload(helpers.ResourceTest):
+    """ Creates a project from a test file, extracts the genotype
+        and tries to download it back. """
+
+    @classmethod
+    def setUpClass(cls):
+        cls.project = create_project_with_name('Downloadable project')
+        cls.run = create_run_with_uri(cls.project['id'],
+                                       '/tests/data/somatic_hg19_14muts.vcf')
+        _extract(cls.run['id'])
+        return super(TestDownload, cls).setUpClass()
+
+    def tearDown(self):
+        with tables(db.engine, 'projects', 'vcfs', 'genotypes') \
+                as (con, projects, runs, genotypes):
+            genotypes.delete().execute()
+            runs.delete().execute()
+            projects.delete().execute()
+
+    def test_download(self):
+        # match the URL with the default download button href
+        downUrl = ("/runs/" + str(self.run['id']) + "/download?query="
+                   "%7B%22range%22%3A%7B%22start%22%3Anull%2C%22end%22%3Anull"
+                   "%2C%22contig%22%3Anull%7D%2C%22filters%22%3A%5B%5D%2C%22"
+                   "sortBy%22%3A%5B%7B%22order%22%3A%22asc%22%2C%22"
+                   "columnName%22%3A%22contig%22%7D%2C%7B%22order"
+                   "%22%3A%22asc%22%2C%22columnName%22%3A%22position"
+                   "%22%7D%5D%2C%22page%22%3A0%2C%22limit%22%3A250%2C%22"
+                   "compareToVcfId%22%3Anull%7D")
+        r = self.get(downUrl)
+        assert r.status_code == 200  # no fail
+        assert len(r.data) == 1193  # might differ from the original file