Merge pull request #11 from BD2KGenomics/feature/full_manifest

User can now mount the folder containing the token file from anywhere…
BD2KGenomics · Feb 16, 2017 · d18ca91 · d18ca91
2 parents a850b26 + 9a936d1
commit d18ca91
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Showing 3 changed files with 15 additions and 2 deletions.
diff --git a/src/main/Dockerfile b/src/main/Dockerfile
@@ -38,6 +38,8 @@ RUN pip install \
 ENV DCC_HOME /dcc
 WORKDIR ${DCC_HOME}
 RUN mkdir -p ${DCC_HOME}
+#Making directory that contains 
+RUN mkdir ${DCC_HOME}/token
 ADD bin ${DCC_HOME}/bin
 ADD cert ${DCC_HOME}/cert
 ADD lib ${DCC_HOME}/lib

diff --git a/src/main/bin/redwood-download b/src/main/bin/redwood-download
@@ -60,7 +60,7 @@ function main {
   #Seeing whether the access token is present as either a file or a by itself
   accessToken=${ACCESS_TOKEN}
   if [[ -z "$accessToken" ]]
-  then accessToken=$(cat data/${ACCESS_TOKEN_FILE})
+  then accessToken=$(cat token/${ACCESS_TOKEN_FILE})
     if [[ -z "$accessToken" ]]
     then echo "Error: Need to set environment variable ACCESS_TOKEN or ACCESS_TOKEN_FILE" && exit 1
     else echo "Using ACCESS_TOKEN_FILE"
@@ -88,6 +88,11 @@ function main {
   java ${ssl_opts}  -Dmetadata.url=${metadata_server_url} -Dstorage.url=${storage_server_url} -DaccessToken=${accessToken} -jar ${DCC_HOME}/lib/icgc-storage-client-1.0.14-SNAPSHOT/lib/icgc-storage-client.jar download --output-dir ${download} --output-layout bundle --manifest data/temp.tsv  --force
 
   rm data/temp.tsv
+  #Change ownership of the files in data/ from root to the current user.
+  user=$(stat -c '%u:%g' data/)
+  if [[ ! -z "$user" ]]
+  then  chown -R ${user} data/
+  fi
 }
 
 

diff --git a/src/main/bin/spinnaker-upload b/src/main/bin/spinnaker-upload
@@ -62,7 +62,7 @@ function main {
   #Seeing whether the access token is present as either a file or a by itself
   accessToken=${ACCESS_TOKEN}
   if [[ -z "$accessToken" ]]
-  then accessToken=$(cat data/${ACCESS_TOKEN_FILE})
+  then accessToken=$(cat token/${ACCESS_TOKEN_FILE})
     if [[ -z "$accessToken" ]]
     then echo "Error: Need to set environment variable ACCESS_TOKEN or ACCESS_TOKEN_FILE" && exit 1
     else echo "Using ACCESS_TOKEN_FILE"
@@ -85,6 +85,12 @@ function main {
     --force-upload \
     --storage-access-token ${accessToken} \
     ${tsv_file}
+  #Change ownership of the files in data/ from root to the current user.
+  cd ..
+  user=$(stat -c '%u:%g' data/)
+  if [[ ! -z "$user" ]]
+  then  chown -R ${user} data/
+  fi
 }
 
 main "$@"