From b46072ee1d83548dfb4e07d510e7234ef5959fa9 Mon Sep 17 00:00:00 2001
From: elichad <eli.chadwick.256@gmail.com>
Date: Tue, 8 Mar 2022 14:04:40 +0000
Subject: [PATCH] sniff tests and 'no ase' message

---
 lib/galaxy/datatypes/molecules.py | 23 +++++++++++++++++------
 lib/galaxy/datatypes/sniff.py     | 14 +++++++++++++-
 2 files changed, 30 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index 36d2e0d47d8..5083dfcbe57 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -957,7 +957,11 @@ class Cell(GenericMolFile):
             info_list.append(f"Atoms in file:\n{metadata.number_of_atoms}")
             info += "\n--\n".join(info_list)
         else:
-            info += f"Atoms in file:\n{metadata.number_of_atoms}"
+            info = """
+                Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.
+                You can still use this dataset in tools and workflows.
+                For full metadata, ask your admin to install the 'ase' Python package.
+            """
 
         return info
 
@@ -1156,8 +1160,12 @@ class CIF(GenericMolFile):
                 formulae = "\n".join(metadata.chemical_formula)
                 info_list.append(f"Chemical formula for each structure in this file:\n{formulae}")
             info = "\n--\n".join(info_list)
-        # else:
-        #   info = f"Atoms in file:\n{metadata.number_of_atoms}"
+        else:
+            info = """
+                Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.
+                You can still use this dataset in tools and workflows.
+                For full metadata, ask your admin to install the 'ase' Python package.
+            """
 
         return info
 
@@ -1365,9 +1373,12 @@ class XYZ(GenericMolFile):
                 formulae = "\n".join(metadata.chemical_formula)
                 info_list.append(f"Chemical formula for each structure in this file:\n{formulae}")
             info = "\n--\n".join(info_list)
-        # else:
-        # TODO: message along the lines of "ask your admin to install ase"?
-        #   info = f"Atoms in file:\n{metadata.number_of_atoms}"
+        else:
+            info = """
+                Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.
+                You can still use this dataset in tools and workflows.
+                For full metadata, ask your admin to install the 'ase' Python package.
+            """
 
         return info
 
diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index 95b133a2136..87a1c9218c6 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -372,7 +372,10 @@ def guess_ext(fname, sniff_order, is_binary=False):
     >>> fname = get_test_fname('5e5z.pdb')
     >>> guess_ext(fname, sniff_order)
     'pdb'
-    >>> fname = get_test_fname('Si.cell')
+    >>> fname = get_test_fname('Si_uppercase.cell')
+    >>> guess_ext(fname, sniff_order)
+    'cell'
+    >>> fname = get_test_fname('Si_lowercase.cell')
     >>> guess_ext(fname, sniff_order)
     'cell'
     >>> fname = get_test_fname('Si.cif')
@@ -381,6 +384,15 @@ def guess_ext(fname, sniff_order, is_binary=False):
     >>> fname = get_test_fname('Si.xyz')
     >>> guess_ext(fname, sniff_order)
     'xyz'
+    >>> fname = get_test_fname('Si_multi.xyz')
+    >>> guess_ext(fname, sniff_order)
+    'xyz'
+    >>> fname = get_test_fname('Si.extxyz')
+    >>> guess_ext(fname, sniff_order)
+    'extxyz'
+    >>> fname = get_test_fname('Si_multi.extxyz')
+    >>> guess_ext(fname, sniff_order)
+    'extxyz'
     >>> fname = get_test_fname('mothur_datatypetest_true.mothur.otu')
     >>> guess_ext(fname, sniff_order)
     'mothur.otu'