Fix for tests

Author: tbooth

deploy/get_latest_ssg.sh

@@ -0,0 +1,66 @@
+#!/bin/bash
+
+# This helps you get a new version from GIT and deploy it
+# to /var/illuminatus on egcloud.  Change to that directory
+# before running it.
+# It is "safe" in that it won't clobber anything.  I promise.
+
+# To prep for first release:
+#  git init --bare --shared git_repo
+#  git --git-dir=git_repo remote add origin [email protected]:EdinburghGenomics/illuminatus.git
+#  git --git-dir=git_repo fetch --all
+
+die(){ echo $@ ; exit 1 ; }
+runcmd(){ echo "RUNNING: $@" ; "$@" ; }
+
+# Sanity checking stage...
+[ -d git_repo ] || die "No git_repo folder."\
+    "This script should normally be run in /var/illuminatus/ on egcloud"
+
+# Update the git_repo.  This doesn't affect any actual working files.
+# Note - if the tag doesn't appear to be fetched then make sure you
+# tagged it on the master branch!
+runcmd git --git-dir=git_repo fetch --all
+runcmd git --git-dir=git_repo repack -ad
+
+#Note this assumes the tags are all of the form v0.0.0 and ignores others.
+#The top tag will be the latest.
+listtags(){
+    git --git-dir=git_repo log --tags --simplify-by-decoration --pretty="format:%d" |\
+        grep -o 'tag: v[0-9][^,)]*' | awk '{print $2}'
+}
+
+# Find the latest tag in the repo
+latest_tag="`listtags | head -n1`"
+
+# Find the latest tag from the repo for which there is a directory
+latest_checked_out="NONE"
+for tag in `listtags` ; do
+    if [ -e "$tag" ] ; then
+        latest_checked_out="$tag"
+        break
+    fi
+done
+
+# Check we saw something
+[ -z "$latest_tag" ] && die "No tags found in GIT"
+
+# See if the latest tag already exists as a directory
+[ -d "$latest_tag" ] && die "The latest tag - $latest_tag - is already checked out."
+
+# So we know there is no folder for latest_tag, it's safe to create one and populate it
+runcmd mkdir "$latest_tag"
+runcmd git --git-dir=git_repo --work-tree="$latest_tag" checkout -f tags/"$latest_tag"
+
+# Sanity check
+[ -d "$latest_checked_out" ] || die "Could not read folder for tag $latest_checked_out"
+
+# Copy the config file
+cp -vn -t $latest_tag $latest_checked_out/environ.sh
+
+# Remove the test directory which we do not need, and the driver which we do not need to run
+rm -rf "$latest_tag/test" "$latest_tag/driver.sh"
+
+runcmd ln -snf $latest_tag current
+echo "Checked out version $latest_tag, and updated the symlink:"
+ls -l

test/test_samplesheet_from_ragic.py

@@ -56,10 +56,13 @@ def test_gen_ss(self):
         generated_lines = list(gen_ss(run))
 
         # The dates will differ, so mask them out
+        # Likewise the #illuminatus_version
         for linelist in [generated_lines, expected_lines]:
             for i in range(len(linelist)):
                 if linelist[i].startswith("Date,"):
                     linelist[i] = "Date,MASKED"
+                elif linelist[i].startswith("#illuminatus_version,"):
+                    linelist[i] = "#illuminatus_version,MASKED"
 
         self.assertEqual(generated_lines, expected_lines)