Make default dockerfile ship with compliance

Add space
Change back to port 80
Set example data
Move compliance data up a directory to avoid collisions

Dockerfile

@@ -57,7 +57,7 @@ EXPOSE 80
 # Prepare container for deployment
 # The directory that the user will land in when executing an interactive shell
 WORKDIR /srv/ga4gh/server
-RUN python scripts/prepare_compliance_data.py -o ga4gh_example_data
+RUN python scripts/prepare_compliance_data.py -o ../ga4gh-compliance-data
 
 # Default action: Bring up a webserver instance to run as a daemon
 CMD ["/usr/sbin/apache2ctl", "-D", "FOREGROUND"]

deploy/001-ga4gh.conf

@@ -5,10 +5,11 @@
     CustomLog ${APACHE_LOG_DIR}/access.log combined
     WSGIDaemonProcess ga4gh python-eggs=/var/cache/apache2/python-egg-cache \
         processes=10 threads=1
-    WSGIScriptAlias /ga4gh /srv/ga4gh/application.wsgi
+    WSGIScriptAlias / /srv/ga4gh/application.wsgi
     <Directory /srv/ga4gh>
         WSGIProcessGroup ga4gh
         WSGIApplicationGroup %{GLOBAL}
         Require all granted
     </Directory>
-</VirtualHost>
+</VirtualHost>
+

deploy/config.py

@@ -1,3 +1,3 @@
 import os
-DATA_SOURCE = os.getenv('GA4GH_DATA_SOURCE', "/data/registry.db")
+DATA_SOURCE = os.getenv('GA4GH_DATA_SOURCE', "/srv/ga4gh/ga4gh-compliance-data/registry.db")
 DEBUG = os.getenv('GA4GH_DEBUG', "")

docs/installation.rst

@@ -224,7 +224,7 @@ From the client, the server is accessible at ``http://server/``, and the ``/tmp/
 
 .. code-block:: bash
 
-  #make a development dir and place the example client script in it
+  # make a development dir and place the example client script in it
   $ mkdir /tmp/mydev
   $ curl https://raw.githubusercontent.com/ga4gh/server/master/scripts/demo_example.py > /tmp/mydev/demo_example.py
   $ chmod +x /tmp/mydev/demo_example.py

scripts/prepare_compliance_data.py

@@ -207,7 +207,8 @@ def run(self):
             readSrc.close()
             pysam.index(destFilePath)
             readGroupSet = reads.HtslibReadGroupSet(dataset, name)
-            readGroupSet.populateFromFile(os.path.abspath(destFilePath), os.abspath(destFilePath + ".bai"))
+            readGroupSet.populateFromFile(os.path.abspath(
+                destFilePath), os.path.abspath(destFilePath + ".bai"))
             readGroupSet.setReferenceSet(referenceSet)
             dataset.addReadGroupSet(readGroupSet)
             bioSamples = [hg00096BioSample, hg00099BioSample, hg00101BioSample]
@@ -272,8 +273,9 @@ def run(self):
         self.repo.insertFeatureSet(featuresetG2P)
 
         # add g2p phenotypeAssociationSet
-        phenotypeAssociationSet = g2p_associationset\
-            .RdfPhenotypeAssociationSet(dataset, "cgd", outputG2PPath)
+        phenotypeAssociationSet = \
+            g2p_associationset.RdfPhenotypeAssociationSet(
+                dataset, "cgd", os.path.abspath(outputG2PPath))
         self.repo.insertPhenotypeAssociationSet(phenotypeAssociationSet)
 
         self.repo.commit()
@@ -312,7 +314,8 @@ def addVariantSet(
             dataset, variantFileName.split('_')[1])
         variantSet.setReferenceSet(referenceSet)
         variantSet.populateFromFile(
-            [os.path.abspath(outputVcf + ".gz")], [os.path.abspath(outputVcf + ".gz.tbi")])
+            [os.path.abspath(outputVcf + ".gz")],
+            [os.path.abspath(outputVcf + ".gz.tbi")])
         variantSet.checkConsistency()
         for callSet in variantSet.getCallSets():
             for bioSample in bioSamples: