Merge branch 'release/1.0.19'

Dockerfile

@@ -20,16 +20,17 @@ RUN apt-get update && apt-get install --yes \
     libxml2-dev \
     libxslt-dev \
     lib32z1-dev \
-    python-setuptools \
     build-essential
 
 RUN pip install --upgrade pip
-RUN pip install jsonschema jsonmerge openpyxl sets json-spec elasticsearch semver
+
+COPY requirements.txt .
+RUN pip install -r requirements.txt
 
 #install cwltool in the container
 #use the version required by dockstore
 RUN pip install setuptools==28.8.0
-RUN pip install cwl-runner cwltool==1.0.20170217172322 schema-salad==2.2.20170222151604 avro==1.8.1
+RUN pip install cwl-runner==1.0 cwltool==1.0.20170217172322 schema-salad==2.2.20170222151604 avro==1.8.1
 RUN pip install functools32==3.2.3.post2
 
 #Patch the cwltool code that sets up the docker run command line

DockstoreRunner.py

@@ -330,7 +330,7 @@ def download_and_transform_json(self, json_encoded):
                 #create list of individual command 'words' for input to run commmand function
                 self.run_command(cmd, self.MAX_ATTEMPTS, self.DELAY_IN_SECONDS)
 
-                cmd = "icgc-storage-client download --output-dir {} --object-id {} --output-layout bundle".format(self.tmp_dir, file_uuid)
+                cmd = "icgc-storage-client download --output-dir {} --object-id {} --output-layout bundle --force".format(self.tmp_dir, file_uuid)
                 #create list of individual command 'words' for input to run commmand function
                 self.run_command(cmd, self.MAX_ATTEMPTS, self.DELAY_IN_SECONDS)
 

requirements.txt

@@ -0,0 +1,30 @@
+CacheControl==0.11.7
+definitions==0.2.0
+elasticsearch==5.4.0
+et-xmlfile==1.0.1
+isodate==0.5.4
+jdcal==1.3
+json-spec==0.10.1
+jsonmerge==1.3.0
+jsonschema==2.6.0
+lockfile==0.12.2
+lxml==3.7.3
+mistune==0.7.4
+nltk==3.2.4
+numpy==1.12.1
+openpyxl==2.4.7
+pathlib==1.0.1
+pyparsing==2.2.0
+PyYAML==3.12
+rdflib==4.2.2
+rdflib-jsonld==0.4.0
+requests==2.14.2
+ruamel.ordereddict==0.4.9
+ruamel.yaml==0.14.12
+semver==2.7.6
+sets==0.3.2
+shellescape==3.4.1
+six==1.10.0
+typing==3.5.3.0
+urllib3==1.21.1
+