From 39f849889ed106bc11eb48e803201f31ffcdccd4 Mon Sep 17 00:00:00 2001
From: Alexander OSTROVSKY <alexanderostrovsky@Chell.local>
Date: Thu, 15 Jun 2023 14:21:46 -0700
Subject: [PATCH 1/2] Add Visium datatype for squidpy and spatialomics tools

---
 .../config/sample/datatypes_conf.xml.sample   |  1 +
 lib/galaxy/datatypes/binary.py                | 22 +++++++++++++++++++
 2 files changed, 23 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index cfd58ef2285..dd056fdca9e 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -185,6 +185,7 @@
     <datatype extension="grib" type="galaxy.datatypes.binary:Grib" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="loom" type="galaxy.datatypes.binary:Loom" description="An HDF5-based Loom File" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="h5ad" type="galaxy.datatypes.binary:Anndata" description="An HDF5-based anndata File" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="visium.tar.gz" type="galaxy.datatypes.binary:Visium" subclass="true" display_in_upload="true" description="Visium is a tar.gz archive with at least a 'Spatial' subfolder, a filtered h5 file and a raw h5 file." />
     <datatype extension="mz5" type="galaxy.datatypes.binary:H5" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="hyphy_results.json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
     <datatype extension="hivtrace" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index b56c7bee39e..231ebba84ed 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -317,6 +317,28 @@ class Meryldb(CompressedArchive):
             log.warning("%s, sniff Exception: %s", self, e)
         return False
 
+class Visium(CompressedArchive):
+    """Visium is a tar.gz archive with at least a 'Spatial' subfolder, a filtered h5 file and a raw h5 file."""
+
+    file_ext = "visium.tar.gz"
+
+    def sniff(self, filename: str) -> bool:
+        """
+            Check data structure:
+            Contains h5 files
+            Contains spatial folder
+        """
+        try:
+            if filename and tarfile.is_tarfile(filename):
+                with tarfile.open(filename, "r") as temptar:
+                    _tar_content = temptar.getnames()
+                    if "spatial" in _tar_content:
+                        if len([_ for _ in _tar_content if _.endswith("matrix.h5")]) == 2:
+                            return True
+        except Exception as e:
+            log.warning("%s, sniff Exception: %s", self, e)
+        return False
+
 
 class Bref3(Binary):
     """Bref3 format is a binary format for storing phased, non-missing genotypes for a list of samples."""

From 3be998011e0ffcbf5fbd6e9180f0e63632255a54 Mon Sep 17 00:00:00 2001
From: Alexander OSTROVSKY <alexanderostrovsky@Chell.local>
Date: Fri, 16 Jun 2023 09:01:16 -0700
Subject: [PATCH 2/2] formatting

---
 lib/galaxy/datatypes/binary.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 231ebba84ed..de4565a58c3 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -317,6 +317,7 @@ class Meryldb(CompressedArchive):
             log.warning("%s, sniff Exception: %s", self, e)
         return False
 
+
 class Visium(CompressedArchive):
     """Visium is a tar.gz archive with at least a 'Spatial' subfolder, a filtered h5 file and a raw h5 file."""
 
@@ -324,9 +325,9 @@ class Visium(CompressedArchive):
 
     def sniff(self, filename: str) -> bool:
         """
-            Check data structure:
-            Contains h5 files
-            Contains spatial folder
+        Check data structure:
+        Contains h5 files
+        Contains spatial folder
         """
         try:
             if filename and tarfile.is_tarfile(filename):