From bc6ece1317bb6dc9cc1ab55e68ad224213e19574 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Mon, 23 Jan 2023 15:05:07 +0100
Subject: [PATCH] update igv session generating (#1585)

---
 CHANGELOG.rst                   |  1 +
 samplesheets/studyapps/utils.py | 21 ++-------------------
 2 files changed, 3 insertions(+), 19 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index db5ec38f..d34c7899 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -46,6 +46,7 @@ Changed
 - **Samplesheets**
     - Upgrade critical Vue app dependencies (#1527, #1571)
     - Remove redundant node UUIDs from render tables (#708)
+    - Improve IGV session file XML generating (#1585)
 
 Fixed
 -----
diff --git a/samplesheets/studyapps/utils.py b/samplesheets/studyapps/utils.py
index 27723e71..36cc8639 100644
--- a/samplesheets/studyapps/utils.py
+++ b/samplesheets/studyapps/utils.py
@@ -77,9 +77,8 @@ def get_igv_session_url(source, app_name, merge=False):
     file_url = reverse(
         '{}:igv'.format(app_name), kwargs={'genericmaterial': source.sodar_uuid}
     )
-    return '{}/load?{}merge={}&file={}{}.xml'.format(
+    return '{}/load?merge={}&file={}{}.xml'.format(
         IGV_URL_BASE,
-        'genome=b37&' if not merge else '',
         str(merge).lower(),
         file_prefix,
         file_url,
@@ -121,18 +120,14 @@ def get_igv_xml(bam_urls, vcf_urls, vcf_title, request):
             'version': '8',
         },
     )
-
     # Resources
     xml_resources = ET.SubElement(xml_session, 'Resources')
-
     # VCF resource
     for vcf_name, vcf_url in vcf_urls.items():
         ET.SubElement(xml_resources, 'Resource', attrib={'path': vcf_url})
-
     # BAM resources
     for bam_name, bam_url in bam_urls.items():
         ET.SubElement(xml_resources, 'Resource', attrib={'path': bam_url})
-
     # VCF panel (under Session)
     for vcf_name, vcf_url in vcf_urls.items():
         xml_vcf_panel = ET.SubElement(
@@ -165,7 +160,6 @@ def get_igv_xml(bam_urls, vcf_urls, vcf_title, request):
                 'windowFunction': 'count',
             },
         )
-
     # BAM panels
     for bam_name, bam_url in bam_urls.items():
         # Generating unique panel name with hashlib
@@ -179,7 +173,6 @@ def get_igv_xml(bam_urls, vcf_urls, vcf_title, request):
                 'width': '1129',
             },
         )
-
         xml_bam_panel_track_coverage = ET.SubElement(
             xml_bam_panel,
             'Track',
@@ -198,7 +191,6 @@ def get_igv_xml(bam_urls, vcf_urls, vcf_title, request):
                 'visible': 'true',
             },
         )
-
         # xml_bam_panel_track_datarange
         ET.SubElement(
             xml_bam_panel_track_coverage,
@@ -212,7 +204,6 @@ def get_igv_xml(bam_urls, vcf_urls, vcf_title, request):
                 'type': 'LINEAR',
             },
         )
-
         xml_bam_panel_track = ET.SubElement(
             xml_bam_panel,
             'Track',
@@ -229,7 +220,6 @@ def get_igv_xml(bam_urls, vcf_urls, vcf_title, request):
                 'visible': 'true',
             },
         )
-
         # xml_bam_panel_track_renderoptions
         ET.SubElement(
             xml_bam_panel_track,
@@ -247,13 +237,11 @@ def get_igv_xml(bam_urls, vcf_urls, vcf_title, request):
                 'sortByTag': '',
             },
         )
-
     xml_feature_panel = ET.SubElement(
         xml_session,
         'Panel',
         attrib={'height': '40', 'name': 'FeaturePanel', 'width': '1129'},
     )
-
     # xml_feature_panel_track
     ET.SubElement(
         xml_feature_panel,
@@ -271,7 +259,6 @@ def get_igv_xml(bam_urls, vcf_urls, vcf_title, request):
             'visible': 'true',
         },
     )
-
     xml_feature_panel_track2 = ET.SubElement(
         xml_feature_panel,
         'Track',
@@ -284,7 +271,7 @@ def get_igv_xml(bam_urls, vcf_urls, vcf_title, request):
             'displayMode': 'COLLAPSED',
             'featureVisibilityWindow': '-1',
             'fontSize': '10',
-            'id': 'b37_genes',
+            'id': 'genes',
             'name': 'Gene',
             'renderer': 'BASIC_FEATURE',
             'sortable': 'false',
@@ -292,7 +279,6 @@ def get_igv_xml(bam_urls, vcf_urls, vcf_title, request):
             'windowFunction': 'count',
         },
     )
-
     # xml_feature_panel_track2_datarange
     ET.SubElement(
         xml_feature_panel_track2,
@@ -306,7 +292,6 @@ def get_igv_xml(bam_urls, vcf_urls, vcf_title, request):
             'type': 'LINEAR',
         },
     )
-
     # xml_panel_layout
     ET.SubElement(
         xml_session,
@@ -316,12 +301,10 @@ def get_igv_xml(bam_urls, vcf_urls, vcf_title, request):
             '0.6595744680851063,0.9273049645390071'
         },
     )
-
     xml_hidden_attrs = ET.SubElement(xml_session, 'HiddenAttributes')
     ET.SubElement(xml_hidden_attrs, 'Attribute', attrib={'name': 'DATA FILE'})
     ET.SubElement(xml_hidden_attrs, 'Attribute', attrib={'name': 'DATA TYPE'})
     ET.SubElement(xml_hidden_attrs, 'Attribute', attrib={'name': 'NAME'})
-
     xml_str = ET.tostring(
         xml_session,
         encoding='utf-8',