Merge pull request #11801 from qiagu/ometiff2

Make Avivator GEDA and sniffer for ome.tiff datatype

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

@@ -207,7 +207,9 @@
     <datatype extension="svs" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
     <datatype extension="scn" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
     <datatype extension="bif" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
-    <datatype extension="ome.tiff" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="true"/>
+    <datatype extension="ome.tiff" type="galaxy.datatypes.images:OMETiff" display_in_upload="true">
+      <display file="image/avivator.xml"/>
+    </datatype>
     <datatype extension="vms" type="galaxy.datatypes.images:Hamamatsu" mimetype="image/hamamatsu"/>
     <datatype extension="vmu" type="galaxy.datatypes.images:Hamamatsu" subclass="true" display_in_upload="false"/>
     <datatype extension="ndpi" type="galaxy.datatypes.images:Hamamatsu" subclass="true" display_in_upload="false"/>
@@ -1055,6 +1057,7 @@
     <sniffer type="galaxy.datatypes.images:Mrc2014"/>
     <sniffer type="galaxy.datatypes.images:Jpg"/>
     <sniffer type="galaxy.datatypes.images:Png"/>
+    <sniffer type="galaxy.datatypes.images:OMETiff"/>
     <sniffer type="galaxy.datatypes.images:Tiff"/>
     <sniffer type="galaxy.datatypes.images:Bmp"/>
     <sniffer type="galaxy.datatypes.images:Gif"/>

lib/galaxy/datatypes/display_applications/configs/image/avivator.xml

@@ -0,0 +1,7 @@
+<display id="avivator" version="1.0.0" name="display at">
+    <link id="main" name="Avivator">
+        <url>http://avivator.gehlenborglab.org/?image_url=${qp($tiff_file.url)}</url>
+        <param type="data" name="tiff_file" url="galaxy_${DATASET_HASH}.ome.tiff" allow_cors="true"/>
+        <param type="data" name="offsets_file" url="galaxy_${DATASET_HASH}.offsets.json" metadata="offsets" allow_cors="true"/>
+    </link>
+</display>

lib/galaxy/datatypes/images.py

@@ -2,6 +2,7 @@
 Image classes
 """
 import base64
+import json
 import logging
 import zipfile
 from io import StringIO
@@ -9,8 +10,13 @@ from urllib.parse import quote_plus
 
 import mrcfile
 import numpy as np
+import tifffile
 
 from galaxy.datatypes.binary import Binary
+from galaxy.datatypes.metadata import (
+    FileParameter,
+    MetadataElement,
+)
 from galaxy.datatypes.text import Html as HtmlFromText
 from galaxy.util import nice_size
 from galaxy.util.image_util import check_image_type
@@ -80,6 +86,28 @@ class Tiff(Image):
     file_ext = "tiff"
 
 
+class OMETiff(Tiff):
+    file_ext = "ome.tiff"
+    MetadataElement(name="offsets", desc="Offsets File", param=FileParameter, file_ext="json", readonly=True, no_value=None, visible=False, optional=True)
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        spec_key = 'offsets'
+        offsets_file = dataset.metadata.offsets
+        if not offsets_file:
+            offsets_file = dataset.metadata.spec[spec_key].param.new_file(dataset=dataset)
+        with tifffile.TiffFile(dataset.file_name) as tif:
+            offsets = [page.offset for page in tif.pages]
+        with open(offsets_file.file_name, 'w') as f:
+            json.dump(offsets, f)
+        dataset.metadata.offsets = offsets_file
+
+    def sniff(self, filename):
+        with tifffile.TiffFile(filename) as tif:
+            if tif.is_ome:
+                return True
+        return False
+
+
 class Hamamatsu(Image):
     file_ext = "vms"
 

lib/galaxy/dependencies/dev-requirements.txt

@@ -234,6 +234,7 @@ svgwrite==1.4.1; python_version >= "3.6"
 tempita==0.5.2
 tenacity==7.0.0
 testfixtures==6.17.1
+tifffile==2020.9.3
 toml==0.10.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6"
 tornado==6.1; python_version >= "3.5"
 tqdm==4.59.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"

lib/galaxy/dependencies/pinned-requirements.txt

@@ -188,6 +188,7 @@ stevedore==3.3.0; python_version >= "3.6"
 svgwrite==1.4.1; python_version >= "3.6"
 tempita==0.5.2
 tenacity==7.0.0
+tifffile==2020.9.3
 tornado==6.1; python_version >= "3.5"
 tqdm==4.59.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
 typing-extensions==3.7.4.3; python_version >= "3.6" and python_version < "3.8"

packages/data/requirements.txt

@@ -16,4 +16,5 @@ social-auth-core[openidconnect]==3.3.0
 SQLAlchemy>=1.3.0,<1.4.0  # https://github.com/kvesteri/sqlalchemy-utils/issues/474
 sqlalchemy-migrate
 sqlalchemy-utils
+tifffile<=2020.9.3  # Last version compatible with python 3.6
 WebOb

pyproject.toml

@@ -76,6 +76,7 @@ sqlparse = "*"
 starlette = "*"
 starlette-context = {version = "*", python = ">=3.7"}
 svgwrite = "*"
+tifffile = "<=2020.9.3"  # Last version compatible with python 3.6
 uvicorn = "*"
 WebOb = "*"
 Whoosh = "*"