Merge branch 'release_18.01' into dev

Conflicts:
	scripts/common_startup.sh

client/package.json

@@ -36,7 +36,7 @@
     "build-production": "NODE_ENV=production gulp stage-libs && concurrently \"yarn run style\" \"yarn run webpack-production\" \"yarn run gulp clean && yarn run gulp-production\" && yarn run save-build-hash",
     "build-production-maps": "NODE_ENV=production gulp stage-libs && concurrently \"yarn run style\" \"yarn run webpack-production-maps\" \"yarn run gulp clean && yarn run gulp-production-maps\" && yarn run save-build-hash",
     "webpack": "webpack -d",
-    "save-build-hash": "git rev-parse HEAD > ../static/client_build_hash.txt",
+    "save-build-hash": "(git rev-parse HEAD 2>/dev/null || echo '') >../static/client_build_hash.txt",
     "webpack-watch": "webpack -d --watch",
     "webpack-production": "webpack -p",
     "webpack-production-maps": "GXY_BUILD_SOURCEMAPS=1 webpack -p",

config/datatypes_conf.xml.sample

@@ -675,6 +675,9 @@
     <datatype extension="allegro_ihaplo" type="galaxy.datatypes.tabular:Tabular" />
     <datatype extension="allegro_descent" type="galaxy.datatypes.tabular:Tabular" />
     <datatype extension="allegro_fparam" type="galaxy.datatypes.genetics:AllegroLOD" />
+    <!-- IDEAS datatypes -->
+    <datatype extension="ideaspre" type="galaxy.datatypes.genetics:IdeasPre" display_in_upload="true"/>
+    <!-- End IDEAS datatypes -->
   </registration>
   <sniffers>
     <!--

lib/galaxy/datatypes/genetics.py

@@ -518,6 +518,73 @@ class Snptest(Rgenetics):
     file_ext = "snptest"
 
 
+class IdeasPre(Html):
+    """
+    This datatype defines the input format required by IDEAS:
+    https://academic.oup.com/nar/article/44/14/6721/2468150
+    The IDEAS preprocessor tool produces an output using this
+    format.  The extra_files_path of the primary input dataset
+    contains the following files and directories.
+    - chromosome_windows.txt (optional)
+    - chromosomes.bed (optional)
+    - IDEAS_input_config.txt
+    - compressed archived tmp directory containing a number of compressed bed files.
+    """
+
+    MetadataElement(name="base_name", desc="Base name for this dataset", default='IDEASData', readonly=True, set_in_upload=True)
+    MetadataElement(name="chrom_bed", desc="Bed file specifying window positions", default=None, readonly=True)
+    MetadataElement(name="chrom_windows", desc="Chromosome window positions", default=None, readonly=True)
+    MetadataElement(name="input_config", desc="IDEAS input config", default=None, readonly=True)
+    MetadataElement(name="tmp_archive", desc="Compressed archive of compressed bed files", default=None, readonly=True)
+
+    composite_type = 'auto_primary_file'
+    allow_datatype_change = False
+    file_ext = 'ideaspre'
+
+    def __init__(self, **kwd):
+        Html.__init__(self, **kwd)
+        self.add_composite_file('chromosome_windows.txt', description='Chromosome window positions', is_binary=False, optional=True)
+        self.add_composite_file('chromosomes.bed', description='Bed file specifying window positions', is_binary=False, optional=True)
+        self.add_composite_file('IDEAS_input_config.txt', description='IDEAS input config', is_binary=False)
+        self.add_composite_file('tmp.tar.gz', description='Compressed archive of compressed bed files', is_binary=True)
+
+    def set_meta(self, dataset, **kwd):
+        Html.set_meta(self, dataset, **kwd)
+        for fname in os.listdir(dataset.extra_files_path):
+            if fname.startswith("chromosomes"):
+                dataset.metadata.chrom_bed = os.path.join(dataset.extra_files_path, fname)
+            elif fname.startswith("chromosome_windows"):
+                dataset.metadata.chrom_windows = os.path.join(dataset.extra_files_path, fname)
+            elif fname.startswith("IDEAS_input_config"):
+                dataset.metadata.input_config = os.path.join(dataset.extra_files_path, fname)
+            elif fname.startswith("tmp"):
+                dataset.metadata.tmp_archive = os.path.join(dataset.extra_files_path, fname)
+        self.regenerate_primary_file(dataset)
+
+    def generate_primary_file(self, dataset=None):
+        rval = ['<html><head></head><body>']
+        rval.append('<h3>Files prepared for IDEAS</h3>')
+        rval.append('<ul>')
+        for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
+            fn = composite_name
+            rval.append('<li><a href="%s>%s</a></li>' % (fn, fn))
+        rval.append('</ul></body></html>\n')
+        return "\n".join(rval)
+
+    def regenerate_primary_file(self, dataset):
+        # Cannot do this until we are setting metadata.
+        rval = ['<html><head></head><body>']
+        rval.append('<h3>Files prepared for IDEAS</h3>')
+        rval.append('<ul>')
+        for fname in os.listdir(dataset.extra_files_path):
+            fn = os.path.split(fname)[-1]
+            rval.append('<li><a href="%s">%s</a></li>' % (fn, fn))
+        rval.append('</ul></body></html>')
+        with open(dataset.file_name, 'w') as f:
+            f.write("\n".join(rval))
+            f.write('\n')
+
+
 class Pheno(Tabular):
     """
     base class for pheno files

scripts/common_startup.sh

@@ -78,7 +78,7 @@ for rmfile in $RMFILES; do
 done
 
 # Determine branch (if using git)
-if command -v git >/dev/null; then
+if command -v git >/dev/null && [ -d .git ]; then
     GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
     case $GIT_BRANCH in
         release_*|master)
@@ -93,7 +93,7 @@ if command -v git >/dev/null; then
     esac
 else
     GIT_BRANCH=0
-    SKIP_CLIENT_BUILD=1
+    DEV_WHEELS=1
 fi
 
 : ${GALAXY_CONFIG_FILE:=config/galaxy.yml}
@@ -120,7 +120,7 @@ if [ $SET_VENV -eq 1 -a $CREATE_VENV -eq 1 ]; then
             # Ensure Python is a supported version before creating .venv
             python ./scripts/check_python.py || exit 1
             if command -v virtualenv >/dev/null; then
-                virtualenv -p $(command -v python) "$GALAXY_VIRTUAL_ENV"
+                virtualenv -p "$(command -v python)" "$GALAXY_VIRTUAL_ENV"
             else
                 vvers=13.1.2
                 vurl="https://pypi.python.org/packages/source/v/virtualenv/virtualenv-${vvers}.tar.gz"
@@ -192,13 +192,19 @@ fi
 # Check client build state.
 if [ $SKIP_CLIENT_BUILD -eq 0 ]; then
     if [ -f static/client_build_hash.txt ]; then
-        # Compare hash.
-        githash=$(git rev-parse HEAD)
-        statichash=$(cat static/client_build_hash.txt)
-        if [ "$githash" = "$statichash" ]; then
+        # If git is not used and static/client_build_hash.txt is present, next
+        # client rebuilds must be done manually by the admin
+        if [ "$GIT_BRANCH" = "0" ]; then
             SKIP_CLIENT_BUILD=1
         else
-            echo "The Galaxy client is out of date and will be built now."
+            # Compare hash.
+            githash=$(git rev-parse HEAD)
+            statichash=$(cat static/client_build_hash.txt)
+            if [ "$githash" = "$statichash" ]; then
+                SKIP_CLIENT_BUILD=1
+            else
+                echo "The Galaxy client is out of date and will be built now."
+            fi
         fi
     else
         echo "The Galaxy client has not yet been built and will be built now."
@@ -209,11 +215,11 @@ fi
 if [ $SKIP_CLIENT_BUILD -eq 0 ]; then
     # Ensure dependencies are installed
     if [ -n "$VIRTUAL_ENV" ]; then
-        if ! in_venv `command -v node`; then
+        if ! in_venv "$(command -v node)"; then
             echo "Installing node into $VIRTUAL_ENV with nodeenv."
             nodeenv -p
         fi
-        if ! in_venv `command -v yarn`; then
+        if ! in_venv "$(command -v yarn)"; then
             echo "Installing yarn into $VIRTUAL_ENV with npm."
             npm install --global yarn
         fi