From fe0f9ba905f11cfff4407aa574fa761e5eadf2f5 Mon Sep 17 00:00:00 2001
From: fescudie <fescudie@toulouse.inra.fr>
Date: Tue, 20 Oct 2015 09:27:09 +0200
Subject: [PATCH] Add BIOM v1 in default datatypes.

---
 config/datatypes_conf.xml.sample |  3 ++
 lib/galaxy/datatypes/text.py     | 56 ++++++++++++++++++++++++++++++++
 2 files changed, 59 insertions(+)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index b7f3b567a86..abc05ff1b13 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -423,6 +423,8 @@
     <datatype extension="plybinary" type="galaxy.datatypes.constructive_solid_geometry:PlyBinary" display_in_upload="true" />
     <datatype extension="vtkascii" type="galaxy.datatypes.constructive_solid_geometry:VtkAscii" display_in_upload="true" />
     <datatype extension="vtkbinary" type="galaxy.datatypes.constructive_solid_geometry:VtkBinary" display_in_upload="true" />
+    <!-- Metagenomic Datatype -->
+    <datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="True" subclass="True" mimetype="application/json" />
   </registration>
   <sniffers>
     <!--
@@ -483,6 +485,7 @@
     <sniffer type="galaxy.datatypes.text:Obo"/>
     <sniffer type="galaxy.datatypes.text:Arff"/>
     <sniffer type="galaxy.datatypes.text:Ipynb"/>
+    <sniffer type="galaxy.datatypes.text:Biom1"/>
     <sniffer type="galaxy.datatypes.text:Json"/>
     <sniffer type="galaxy.datatypes.sequence:RNADotPlotMatrix"/>
     <sniffer type="galaxy.datatypes.sequence:DotBracket"/>
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index 8763fdde4b4..edae572402a 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -17,6 +17,62 @@ 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"