Add a new data type: GeoTiff

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <datatypes>
   <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
+    <datatype extension="geo.tiff" type="galaxy.datatypes.gis:GeoTiff" display_in_upload="true"/>
     <datatype extension="jp2" type="galaxy.datatypes.binary:JP2" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'ab1' format with a '.ab1' file extension.  You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Ab1"/>
     <datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/>
@@ -1076,6 +1077,7 @@
     <sniffer type="galaxy.datatypes.images:Mrc2014"/>
     <sniffer type="galaxy.datatypes.images:Jpg"/>
     <sniffer type="galaxy.datatypes.images:Png"/>
+    <sniffer type="galaxy.datatypes.gis:GeoTiff"/>
     <sniffer type="galaxy.datatypes.images:OMETiff"/>
     <sniffer type="galaxy.datatypes.images:Tiff"/>
     <sniffer type="galaxy.datatypes.images:Bmp"/>

lib/galaxy/datatypes/gis.py

@@ -2,7 +2,11 @@
 GIS classes
 """
 
+import rasterio
+
 from galaxy.datatypes.binary import Binary
+from galaxy.datatypes.images import Tiff
+from galaxy.util import nice_size
 
 
 class Shapefile(Binary):
@@ -61,3 +65,45 @@ def display_peek(self, dataset):
             return dataset.peek
         except Exception:
             return "Shapefile data"
+
+
+class GeoTiff(Tiff):
+    """ The GeoTiff data format:
+            For more information please see http://en.wikipedia.org/wiki/GeoTIFF
+    GeoTiff image format
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.geo.tif')
+    >>> GeoTiff().sniff(fname)
+    True
+    >>> fname = get_test_fname('interval.interval')
+    >>> GeoTiff().sniff(fname)
+    False
+    """
+    file_ext = "geo.tiff"
+    edam_format = "format_webprotege_012"
+    edam_data = "data_webprotege_001"
+
+    def __init__(self, **kwd):
+        super().__init__(**kwd)
+
+    def sniff(self, filename):
+        # A GeoTiff file contains a coordinate reference system (CRS) that is identified by an EPSG code.
+        try:
+            filedata = rasterio.open(filename)
+            return (filedata.meta['driver'] == 'GTiff') and (filedata.meta['crs'] is not None)
+        except Exception:
+            return False
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = "Image GeoTiff file"
+            dataset.blurb = nice_size(dataset.get_size())
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek(self, dataset):
+        try:
+            return dataset.peek
+        except Exception:
+            return "Image GeoTiff file (%s)" % (nice_size(dataset.get_size()))