From 2599eb1ebf04f1c5ce144d4c2aa4b4546df549db Mon Sep 17 00:00:00 2001
From: Simon Bray <sbray1371@gmail.com>
Date: Tue, 12 Nov 2019 09:13:04 +0100
Subject: [PATCH 1/3] add new gmx datatypes: ndx, xvg, edr

---
 .../config/sample/datatypes_conf.xml.sample   |   4 +++
 lib/galaxy/datatypes/binary.py                |  23 +++++++++++++++---
 lib/galaxy/datatypes/test/md.edr              | Bin 0 -> 10 bytes
 3 files changed, 24 insertions(+), 3 deletions(-)
 create mode 100644 lib/galaxy/datatypes/test/md.edr

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index f78512d133d..3787399ff14 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -641,8 +641,11 @@
     <datatype extension="top" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
     <datatype extension="itp" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
     <datatype extension="mdp" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
+    <datatype extension="ndx" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
+    <datatype extension="xvg" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
     <datatype extension="xtc" type="galaxy.datatypes.binary:Xtc" display_in_upload="true"/>
     <datatype extension="cpt" type="galaxy.datatypes.binary:Cpt" display_in_upload="true"/>
+    <datatype extension="edr" type="galaxy.datatypes.binary:Edr" display_in_upload="true"/>
     <datatype extension="gro" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
     <datatype extension="vel" type="galaxy.datatypes.binary:Vel" display_in_upload="true"/>
     <datatype extension="grd" type="galaxy.datatypes.molecules:grd" display_in_upload="true"/>
@@ -821,6 +824,7 @@
     <sniffer type="galaxy.datatypes.binary:Dcd"/>
     <sniffer type="galaxy.datatypes.binary:Xtc"/>
     <sniffer type="galaxy.datatypes.binary:Cpt"/>
+    <sniffer type="galaxy.datatypes.binary:Edr"/>
     <sniffer type="galaxy.datatypes.binary:Vel"/>
     <sniffer type="galaxy.datatypes.annotation:Augustus"/>
     <sniffer type="galaxy.datatypes.triples:Rdf"/>
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 519001ae6b1..36de357131d 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -957,7 +957,7 @@ class Trr(GmxBinary):
     """
 
     file_ext = "trr"
-    magic_number = 1993  # magic number reference: https://github.com/gromacs/gromacs/blob/1c6639f0636d2ffc3d665686756d77227c8ae6d1/src/gromacs/fileio/trrio.cpp
+    magic_number = 1993  # magic number reference: https://github.com/gromacs/gromacs/blob/master/src/gromacs/fileio/trrio.cpp
 
 
 class Cpt(GmxBinary):
@@ -974,7 +974,7 @@ class Cpt(GmxBinary):
     """
 
     file_ext = "cpt"
-    magic_number = 171817  # magic number reference: https://github.com/gromacs/gromacs/blob/cec211b2c835ba6e8ea849fb1bf67d7fc19693a4/src/gromacs/fileio/checkpoint.cpp
+    magic_number = 171817  # magic number reference: https://github.com/gromacs/gromacs/blob/master/src/gromacs/fileio/checkpoint.cpp
 
 
 class Xtc(GmxBinary):
@@ -991,7 +991,24 @@ class Xtc(GmxBinary):
     """
 
     file_ext = "xtc"
-    magic_number = 1995  # reference: https://github.com/gromacs/gromacs/blob/cec211b2c835ba6e8ea849fb1bf67d7fc19693a4/src/gromacs/fileio/xtcio.cpp
+    magic_number = 1995  # reference: https://github.com/gromacs/gromacs/blob/master/src/gromacs/fileio/xtcio.cpp
+
+
+class Edr(GmxBinary):
+    """
+    Class describing an edr file from the GROMACS suite
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('md.edr')
+    >>> Xtc().sniff(fname)
+    True
+    >>> fname = get_test_fname('md.trr')
+    >>> Xtc().sniff(fname)
+    False
+    """
+
+    file_ext = "edr"
+    magic_number = -55555  # reference: https://github.com/gromacs/gromacs/blob/master/src/gromacs/fileio/enxio.cpp
 
 
 class Biom2(H5):
diff --git a/lib/galaxy/datatypes/test/md.edr b/lib/galaxy/datatypes/test/md.edr
new file mode 100644
index 0000000000000000000000000000000000000000..d95e137947a9aa773f60142d1b55c5845eec297d
GIT binary patch
literal 10
RcmezWU+pgg0|P4q0{|N#11A6g

literal 0
HcmV?d00001


From 8f45f7c59a285e540e957bda7c67203af19f23b4 Mon Sep 17 00:00:00 2001
From: Simon Bray <sbray1371@gmail.com>
Date: Tue, 12 Nov 2019 09:15:14 +0100
Subject: [PATCH 2/3] fix

---
 lib/galaxy/datatypes/binary.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 36de357131d..21156a9fa47 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -1000,10 +1000,10 @@ class Edr(GmxBinary):
 
     >>> from galaxy.datatypes.sniff import get_test_fname
     >>> fname = get_test_fname('md.edr')
-    >>> Xtc().sniff(fname)
+    >>> Edr().sniff(fname)
     True
     >>> fname = get_test_fname('md.trr')
-    >>> Xtc().sniff(fname)
+    >>> Edr().sniff(fname)
     False
     """
 

From a115122deaa7a2eb23077a79cdd57dc056e4bda0 Mon Sep 17 00:00:00 2001
From: Simon Bray <sbray1371@gmail.com>
Date: Tue, 12 Nov 2019 14:04:43 +0100
Subject: [PATCH 3/3] point gromacs magic number refs to a specific commit

---
 lib/galaxy/datatypes/binary.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 21156a9fa47..a8d5d73d7b1 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -957,7 +957,7 @@ class Trr(GmxBinary):
     """
 
     file_ext = "trr"
-    magic_number = 1993  # magic number reference: https://github.com/gromacs/gromacs/blob/master/src/gromacs/fileio/trrio.cpp
+    magic_number = 1993  # magic number reference: https://github.com/gromacs/gromacs/blob/cec211b2c835ba6e8ea849fb1bf67d7fc19693a4/src/gromacs/fileio/trrio.cpp
 
 
 class Cpt(GmxBinary):
@@ -974,7 +974,7 @@ class Cpt(GmxBinary):
     """
 
     file_ext = "cpt"
-    magic_number = 171817  # magic number reference: https://github.com/gromacs/gromacs/blob/master/src/gromacs/fileio/checkpoint.cpp
+    magic_number = 171817  # magic number reference: https://github.com/gromacs/gromacs/blob/cec211b2c835ba6e8ea849fb1bf67d7fc19693a4/src/gromacs/fileio/checkpoint.cpp
 
 
 class Xtc(GmxBinary):
@@ -991,7 +991,7 @@ class Xtc(GmxBinary):
     """
 
     file_ext = "xtc"
-    magic_number = 1995  # reference: https://github.com/gromacs/gromacs/blob/master/src/gromacs/fileio/xtcio.cpp
+    magic_number = 1995  # reference: https://github.com/gromacs/gromacs/blob/cec211b2c835ba6e8ea849fb1bf67d7fc19693a4/src/gromacs/fileio/xtcio.cpp
 
 
 class Edr(GmxBinary):
@@ -1008,7 +1008,7 @@ class Edr(GmxBinary):
     """
 
     file_ext = "edr"
-    magic_number = -55555  # reference: https://github.com/gromacs/gromacs/blob/master/src/gromacs/fileio/enxio.cpp
+    magic_number = -55555  # reference: https://github.com/gromacs/gromacs/blob/cec211b2c835ba6e8ea849fb1bf67d7fc19693a4/src/gromacs/fileio/enxio.cpp
 
 
 class Biom2(H5):