From 97532515ea24325ba26877696991b24401733ee6 Mon Sep 17 00:00:00 2001
From: Jim Johnson <jj@umn.edu>
Date: Tue, 20 Sep 2016 10:17:14 -0500
Subject: [PATCH 1/2] API access to genome fasta index and sequence

Allows visualization components, e.g. IGV.js, to incrementally retrieve sequence as needed.
---
 lib/galaxy/webapps/galaxy/api/genomes.py | 36 ++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/lib/galaxy/webapps/galaxy/api/genomes.py b/lib/galaxy/webapps/galaxy/api/genomes.py
index ae62ad905ec..d09a7e70c41 100644
--- a/lib/galaxy/webapps/galaxy/api/genomes.py
+++ b/lib/galaxy/webapps/galaxy/api/genomes.py
@@ -43,3 +43,39 @@ class GenomesController( BaseAPIController ):
         else:
             rval = self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low )
         return rval
+
+    @web.expose_api_raw_anonymous
+    def indexes(self, trans, id, **kwd):
+        """
+        GET /api/genomes/{id}/indexes?type={table name}
+
+        Returns all available indexes for a genome id for type={table name}
+        For instance, /api/genomes/hg19/indexes?type=fasta_indexes
+        """
+        index_extensions = {'fasta_indexes': '.fai'}
+        id = get_id( id, kwd.get( 'format', None ) )
+        index_type = kwd.get('type', None)
+
+        tbl_entries = self.app.tool_data_tables.data_tables[index_type].data
+        index_file_name = [x[-1] for x in tbl_entries if id in x].pop()
+
+        if_open = open(index_file_name + index_extensions[index_type], mode='r')
+        return if_open.read()
+
+    @web.expose_api_raw_anonymous
+    def sequences(self, trans, id, num=None, chrom=None, low=None, high=None, **kwd ):
+        """
+        GET /api/genomes/{id}/sequences
+
+        This is a wrapper for accepting sequence requests that
+        want a raw return, not json
+        """
+        # import pdb
+        # pdb.set_trace()
+
+        id = get_id( id, kwd.get( 'format', None ) )
+        reference = is_true( kwd.get( 'reference', False ) )
+        if reference:
+            region = self.app.genomes.reference( trans, dbkey=id, chrom=chrom, low=low, high=high )
+            rval = { 'dataset_type': 'refseq', 'data': region.sequence }
+        return rval['data']

From efbc06eb0178f495d1581aec7a8c1467af93f2d7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 28 Sep 2016 11:29:34 -0400
Subject: [PATCH 2/2] Cleanup 97532515ea24325ba26877696991b24401733ee6.

---
 lib/galaxy/webapps/galaxy/api/genomes.py | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/genomes.py b/lib/galaxy/webapps/galaxy/api/genomes.py
index d09a7e70c41..ba525dbb49a 100644
--- a/lib/galaxy/webapps/galaxy/api/genomes.py
+++ b/lib/galaxy/webapps/galaxy/api/genomes.py
@@ -70,12 +70,8 @@ class GenomesController( BaseAPIController ):
         This is a wrapper for accepting sequence requests that
         want a raw return, not json
         """
-        # import pdb
-        # pdb.set_trace()
-
         id = get_id( id, kwd.get( 'format', None ) )
         reference = is_true( kwd.get( 'reference', False ) )
-        if reference:
-            region = self.app.genomes.reference( trans, dbkey=id, chrom=chrom, low=low, high=high )
-            rval = { 'dataset_type': 'refseq', 'data': region.sequence }
-        return rval['data']
+        assert reference
+        region = self.app.genomes.reference( trans, dbkey=id, chrom=chrom, low=low, high=high )
+        return region.sequence