Add BIOM v1 in default datatypes

lib/galaxy/datatypes/text.py

@@ -17,62 +17,6 @@ from galaxy.util import nice_size, string_as_bool
 log = logging.getLogger(__name__)
 
 
-class Biom(Text):
-    file_ext = "biom"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        if not dataset.dataset.purged:
-            dataset.peek = get_file_peek(dataset.file_name,
-                                         is_multi_byte=is_multi_byte)
-            dataset.blurb = "Biological Observation Matrix"
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
-
-    def display_peek(self, dataset):
-        try:
-            return dataset.peek
-        except:
-            return "BIOM file (%s)" % (nice_size(dataset.get_size()))
-
-
-class Biom1(Biom):
-    edam_format = "format_3464"
-    file_ext = "biom1"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(Biom1, self).set_peek(dataset, is_multi_byte)
-        if not dataset.dataset.purged:
-            dataset.blurb = "Biological Observation Matrix v1"
-
-    def sniff(self, filename):
-        return self._looks_like_biom(filename)
-
-    def _looks_like_biom(self, filepath, check_limit_size=104857600):
-        """
-        @param filepath: [str] The path to the evaluated file.
-        @param check_limit_size: [int] The maximum size of the checked file (in
-                                 bytes).
-        @note: If the size is superior than this number the format cannot be
-               validated.
-        """
-        is_biom = False
-        try:
-            if os.path.getsize(filepath) < check_limit_size:
-                biom = json.load(open(filepath, "r"))
-                is_biom = True
-                biom_expected_fields = ["id", "format", "format_url", "type",
-                                        "generated_by", "date", "rows",
-                                        "columns", "matrix_type",
-                                        "matrix_element_type", "shape", "data"]
-                for expected_field in biom_expected_fields:
-                    if not expected_field in biom:
-                        is_biom = False
-        except:
-                is_biom = False
-        return is_biom
-
-
 class Json( Text ):
     edam_format = "format_3464"
     file_ext = "json"
@@ -178,6 +122,46 @@ class Ipynb( Json ):
         pass
 
 
+class Biom1(Json):
+    file_ext = "biom1"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(Biom1, self).set_peek(dataset, is_multi_byte)
+        if not dataset.dataset.purged:
+            dataset.blurb = "Biological Observation Matrix v1"
+
+    def sniff(self, filename):
+        is_biom = False
+        if self._looks_like_json( filename ):
+            is_biom = self._looks_like_biom(filename)
+        return is_biom
+
+    def _looks_like_biom(self, filepath, load_size=50000):
+        """
+        @param filepath: [str] The path to the evaluated file.
+        @param load_size: [int] The size of the file block load in RAM (in
+                          bytes).
+        """
+        is_biom = False
+        segment_size = int(load_size / 2)
+        try:
+            with open(filepath, "r") as fh:
+                prev_str = ""
+                segment_str = fh.read(segment_size)
+                if segment_str.strip().startswith('{'):
+                    while segment_str and not is_biom:
+                        current_str = prev_str + segment_str
+                        if '"format"' in current_str:
+                            current_str = re.sub(r'\s', '', current_str)
+                            if '"format":"BiologicalObservationMatrix' in current_str:
+                                is_biom = True
+                        prev_str = segment_str
+                        segment_str = fh.read(segment_size)
+        except:
+            pass
+        return is_biom
+
+
 class Obo( Text ):
     """
         OBO file format description