commit/galaxy-central: 4 new changesets

12 Jan 2015

4 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/dd67f14145f7/
Changeset:   dd67f14145f7
Branch:      rna_eps_format
User:        BjoernGruening
Date:        2015-01-06 16:17:39+00:00
Summary:     Add RNA dotplot matrix file type. This is a EPS file with additional informations.
Affected #:  2 files

diff -r d50ee9520583c225e48c577ab977f18fd6cb7d6a -r dd67f14145f75cbbe9ab3e73d40088a669139f07 lib/galaxy/datatypes/sequence.py

--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -814,3 +814,34 @@
         except:
             return False
 
+
+class RNADotPlotMatrix( data.Data ):
+    file_ext = "rna_eps"
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek = 'RNA Dot Plot format (Postscript derivative)'
+            dataset.blurb = data.nice_size( dataset.get_size() )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def sniff(self, filename, image=None):
+        """Determine if the file is in RNA dot plot format."""
+        seq = False
+        coor = False
+        pairs = False
+        with open( filename ) as handle:
+            for line in handle:
+                line = line.strip()
+                if line:
+                    if line.startswith('/sequence'):
+                        seq = True
+                    elif line.startswith('/coor'):
+                        coor = True
+                    elif line.startswith('/pairs'):
+                        pairs = True
+                if seq and coor and pairs:
+                    return True
+        return False
+

diff -r d50ee9520583c225e48c577ab977f18fd6cb7d6a -r dd67f14145f75cbbe9ab3e73d40088a669139f07 lib/galaxy/datatypes/util/image_util.py
--- a/lib/galaxy/datatypes/util/image_util.py
+++ b/lib/galaxy/datatypes/util/image_util.py
@@ -71,6 +71,4 @@
         return 'pbm'
     if format == 'PGM':
         return 'pgm'
-    if format == 'EPS':
-        return 'eps'
     return None


https://bitbucket.org/galaxy/galaxy-central/commits/e89b5465e914/
Changeset:   e89b5465e914
Branch:      rna_eps_format
User:        BjoernGruening
Date:        2015-01-06 16:18:01+00:00
Summary:     add rna_eps filetype
Affected #:  1 file

diff -r dd67f14145f75cbbe9ab3e73d40088a669139f07 -r e89b5465e914bec84d946c6163b415ebd57a038e config/datatypes_conf.xml.sample
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -140,6 +140,7 @@
     <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/><datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/><datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/>
+    <datatype extension="rna_eps" type="galaxy.datatypes.sequence:RNADotPlotMatrix" mimetype="image/eps" display_in_upload="True"/><datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/><datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/><datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
@@ -302,6 +303,7 @@
     <sniffer type="galaxy.datatypes.text:Arff"/><sniffer type="galaxy.datatypes.text:Ipynb"/><sniffer type="galaxy.datatypes.text:Json"/>
+    <sniffer type="galaxy.datatypes.sequence:RNADotPlotMatrix"/><sniffer type="galaxy.datatypes.images:Jpg"/><sniffer type="galaxy.datatypes.images:Png"/><sniffer type="galaxy.datatypes.images:Tiff"/>


https://bitbucket.org/galaxy/galaxy-central/commits/f5278f9e74a2/
Changeset:   f5278f9e74a2
Branch:      rna_eps_format
User:        BjoernGruening
Date:        2015-01-06 17:54:03+00:00
Summary:     Only walk through the file if it is a EPS file.
Affected #:  1 file

diff -r e89b5465e914bec84d946c6163b415ebd57a038e -r f5278f9e74a2e2855bf6661dc998d37abc6f86ff lib/galaxy/datatypes/sequence.py
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -17,7 +17,7 @@
 from galaxy.datatypes.checkers import is_gzip
 from galaxy.datatypes.sniff import get_test_fname, get_headers
 from galaxy.datatypes.metadata import MetadataElement
-
+from galaxy.datatypes.util.image_util import check_image_type
 
 try:
     eggs.require( "bx-python" )
@@ -826,22 +826,22 @@
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
 
-    def sniff(self, filename, image=None):
+    def sniff(self, filename):
         """Determine if the file is in RNA dot plot format."""
-        seq = False
-        coor = False
-        pairs = False
-        with open( filename ) as handle:
-            for line in handle:
-                line = line.strip()
-                if line:
-                    if line.startswith('/sequence'):
-                        seq = True
-                    elif line.startswith('/coor'):
-                        coor = True
-                    elif line.startswith('/pairs'):
-                        pairs = True
-                if seq and coor and pairs:
-                    return True
-        return False
-
+        if check_image_type( filename, ['EPS'] ):
+            seq = False
+            coor = False
+            pairs = False
+            with open( filename ) as handle:
+                for line in handle:
+                    line = line.strip()
+                    if line:
+                        if line.startswith('/sequence'):
+                            seq = True
+                        elif line.startswith('/coor'):
+                            coor = True
+                        elif line.startswith('/pairs'):
+                            pairs = True
+                    if seq and coor and pairs:
+                        return True
+        return False
\ No newline at end of file


https://bitbucket.org/galaxy/galaxy-central/commits/7f27fc6cb8b6/
Changeset:   7f27fc6cb8b6
User:        dannon
Date:        2015-01-12 21:55:10+00:00
Summary:     Merged in BjoernGruening/galaxy-central-1/rna_eps_format (pull request #625)

Add RNA dotplot matrix as datatype.
Affected #:  3 files

diff -r 748cb48d79e8c3770623a0a76e2b56e332b19cc7 -r 7f27fc6cb8b6fa31b24267a25ee375ef346dde02 config/datatypes_conf.xml.sample
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -140,6 +140,7 @@
     <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/><datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/><datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/>
+    <datatype extension="rna_eps" type="galaxy.datatypes.sequence:RNADotPlotMatrix" mimetype="image/eps" display_in_upload="True"/><datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/><datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/><datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
@@ -304,6 +305,7 @@
     <sniffer type="galaxy.datatypes.text:Arff"/><sniffer type="galaxy.datatypes.text:Ipynb"/><sniffer type="galaxy.datatypes.text:Json"/>
+    <sniffer type="galaxy.datatypes.sequence:RNADotPlotMatrix"/><sniffer type="galaxy.datatypes.images:Jpg"/><sniffer type="galaxy.datatypes.images:Png"/><sniffer type="galaxy.datatypes.images:Tiff"/>

diff -r 748cb48d79e8c3770623a0a76e2b56e332b19cc7 -r 7f27fc6cb8b6fa31b24267a25ee375ef346dde02 lib/galaxy/datatypes/sequence.py
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -17,7 +17,7 @@
 from galaxy.datatypes.checkers import is_gzip
 from galaxy.datatypes.sniff import get_test_fname, get_headers
 from galaxy.datatypes.metadata import MetadataElement
-
+from galaxy.datatypes.util.image_util import check_image_type
 
 try:
     eggs.require( "bx-python" )
@@ -814,3 +814,34 @@
         except:
             return False
 
+
+class RNADotPlotMatrix( data.Data ):
+    file_ext = "rna_eps"
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek = 'RNA Dot Plot format (Postscript derivative)'
+            dataset.blurb = data.nice_size( dataset.get_size() )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def sniff(self, filename):
+        """Determine if the file is in RNA dot plot format."""
+        if check_image_type( filename, ['EPS'] ):
+            seq = False
+            coor = False
+            pairs = False
+            with open( filename ) as handle:
+                for line in handle:
+                    line = line.strip()
+                    if line:
+                        if line.startswith('/sequence'):
+                            seq = True
+                        elif line.startswith('/coor'):
+                            coor = True
+                        elif line.startswith('/pairs'):
+                            pairs = True
+                    if seq and coor and pairs:
+                        return True
+        return False
\ No newline at end of file

diff -r 748cb48d79e8c3770623a0a76e2b56e332b19cc7 -r 7f27fc6cb8b6fa31b24267a25ee375ef346dde02 lib/galaxy/datatypes/util/image_util.py
--- a/lib/galaxy/datatypes/util/image_util.py
+++ b/lib/galaxy/datatypes/util/image_util.py
@@ -71,6 +71,4 @@
         return 'pbm'
     if format == 'PGM':
         return 'pgm'
-    if format == 'EPS':
-        return 'eps'
     return None

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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