From b6c0b0074dfb4ba44ef0ffb19f3dfc155b3bee67 Mon Sep 17 00:00:00 2001
From: elichad <eli.chadwick.256@gmail.com>
Date: Wed, 9 Mar 2022 11:42:59 +0000
Subject: [PATCH] use fingerprint for extxyz sniffer

---
 lib/galaxy/datatypes/molecules.py         | 37 ++++-------------------
 lib/galaxy/datatypes/sniff.py             |  3 --
 lib/galaxy/datatypes/test/Si_multi.extxyz | 20 ------------
 3 files changed, 6 insertions(+), 54 deletions(-)
 delete mode 100644 lib/galaxy/datatypes/test/Si_multi.extxyz

diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index f721569f492..fcc39ef5bd4 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -1401,42 +1401,17 @@ class ExtendedXYZ(XYZ):
         >>> fname = get_test_fname('Si.extxyz')
         >>> ExtendedXYZ().sniff(fname)
         True
-        >>> from galaxy.datatypes.sniff import get_test_fname
-        >>> fname = get_test_fname('Si_multi.extxyz')
-        >>> ExtendedXYZ().sniff(fname)
-        True
         >>> fname = get_test_fname('Si.xyz')
         >>> ExtendedXYZ().sniff(fname)
         False
         """
         with open(filename) as f:
-            xyz_lines = f.readlines(1000)[:-1]
-
-        try:
-            blocks = self.read_blocks(xyz_lines)
-        except (TypeError, ValueError):
-            return False
-        except IndexError as e:
-            if "pop from empty list" in str(e):
-                # xyz_lines ran out mid-block – check full file
-                with open(filename) as f:
-                    xyz_lines = f.readlines()
-                try:
-                    blocks = self.read_blocks(xyz_lines)
-                except (TypeError, ValueError, IndexError):
-                    # any error is now a failure
-                    return False
-            else:
-                # some other IndexError - invalid input
-                return False
-
-        # check blocks are valid
-        for block in blocks:
-            if block["number_of_atoms"] is None:
-                return False
-
-        # all checks passed
-        return True
+            # fingerprint is 'Properties="<name>:<type>:<number>:..."' in the second line
+            # e.g. Properties="species:S:1:pos:R:3:vel:R:3:select:I:1"
+            f.readline()
+            comment = f.readline()
+            properties = re.search(r"Properties=\"?([a-zA-Z0-9:]+)\"?", comment) # returns None if no match
+            return True if properties else False
 
     def read_blocks(self, lines):
         """
diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index 87a1c9218c6..3fa67dfa4d0 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -390,9 +390,6 @@ def guess_ext(fname, sniff_order, is_binary=False):
     >>> 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'
diff --git a/lib/galaxy/datatypes/test/Si_multi.extxyz b/lib/galaxy/datatypes/test/Si_multi.extxyz
deleted file mode 100644
index 5c4d0b987fd..00000000000
--- a/lib/galaxy/datatypes/test/Si_multi.extxyz
+++ /dev/null
@@ -1,20 +0,0 @@
-8
-Lattice="5.44 0.0 0.0 0.0 5.44 0.0 0.0 0.0 5.44" Properties="species:S:1:pos:R:3:vel:R:3:select:I:1" Time=0.0
-Si        0.00000000      0.00000000      0.00000000      0.00000000      0.00000000      0.00000000       1
-Si        1.36000000      1.36000000      1.36000000      0.00000000      0.00000000      0.00000000       1
-Si        2.72000000      2.72000000      0.00000000      0.00000000      0.00000000      0.00000000       1
-Si        4.08000000      4.08000000      1.36000000      0.00000000      0.00000000      0.00000000       1
-Si        2.72000000      0.00000000      2.72000000      0.00000000      0.00000000      0.00000000       1
-Si        4.08000000      1.36000000      4.08000000      0.00000000      0.00000000      0.00000000       1
-Si        0.00000000      2.72000000      2.72000000      0.00000000      0.00000000      0.00000000       1
-Si        1.36000000      4.08000000      4.08000000      0.00000000      0.00000000      0.00000000       1
-8
-Lattice="5.44 0.0 0.0 0.0 5.44 0.0 0.0 0.0 5.44" Properties="species:S:1:pos:R:3:vel:R:3:select:I:1" Time=0.0
-Si        0.00000000      0.00000000      0.00000000      0.00000000      0.00000000      0.00000000       1
-Si        1.36000000      1.36000000      1.36000000      0.00000000      0.00000000      0.00000000       1
-Si        2.72000000      2.72000000      0.00000000      0.00000000      0.00000000      0.00000000       1
-Si        4.08000000      4.08000000      1.36000000      0.00000000      0.00000000      0.00000000       1
-Si        2.72000000      0.00000000      2.72000000      0.00000000      0.00000000      0.00000000       1
-Si        4.08000000      1.36000000      4.08000000      0.00000000      0.00000000      0.00000000       1
-Si        0.00000000      2.72000000      2.72000000      0.00000000      0.00000000      0.00000000       1
-Si        1.36000000      4.08000000      4.08000000      0.00000000      0.00000000      0.00000000       1