Alamut alignment file link

scout/server/blueprints/alignviewers/controllers.py

@@ -13,11 +13,7 @@
     IGV_TRACKS,
 )
 from scout.server.extensions import config_igv_tracks, store
-from scout.server.utils import (
-    case_append_alignments,
-    find_index,
-    get_case_genome_build,
-)
+from scout.server.utils import case_append_alignments, find_index, get_case_genome_build
 from scout.utils.ensembl_rest_clients import EnsemblRestApiClient
 
 LOG = logging.getLogger(__name__)

scout/server/blueprints/alignviewers/views.py

@@ -75,10 +75,13 @@ def remote_cors(remote_url):
 @alignviewers_bp.route("/remote/static", methods=["OPTIONS", "GET"])
 def remote_static():
     """Stream *large* static files with special requirements."""
-    file_path = request.args.get("file", default=".", type=str)
-    institute_id = request.args.get("institute_id", default=".", type=str)
-    case_name = request.args.get("case_name", default=".", type=str)
-
+    arguments = request.args.get("args", default=".", type=str)
+    if arguments != ".":
+        institute_id, case_name, file_path = arguments.split(",")
+    else:
+        file_path = request.args.get("file", default=".", type=str)
+        institute_id = request.args.get("institute_id", default=".", type=str)
+        case_name = request.args.get("case_name", default=".", type=str)
     # Check that user is logged in
     if current_user.is_authenticated is False:
         LOG.warning("Unauthenticated user requesting resource via remote_static")

scout/server/blueprints/variant/controllers.py

@@ -1,3 +1,3 @@
 import logging
 import os
 from typing import Dict, List, Optional
@@ -35,7 +35,7 @@
 )
 from scout.server.blueprints.variants.utils import update_case_panels
 from scout.server.extensions import LoqusDB, chanjo2, config_igv_tracks, gens
-from scout.server.links import add_tx_links, disease_link, get_variant_links
+from scout.server.links import alamut_file_links, add_tx_links, disease_link, get_variant_links
 from scout.server.utils import (
     case_has_alignments,
     case_has_chanjo2_coverage,
@@ -347,6 +347,8 @@
 
     set_case_analysis_type(case_obj)
 
+    case_obj["alamut_file_links"] = alamut_file_links(institute_obj, case_obj)
+
     if variant_obj.get("genetic_models"):
         variant_models = set(model.split("_", 1)[0] for model in variant_obj["genetic_models"])
         omim_models = variant_obj.get("omim_models", set())

scout/server/blueprints/variant/templates/variant/components.html

@@ -125,18 +125,6 @@
           {{ splice_junctions_button(institute._id, case, variant._id) }}
         </div>
       {% endif %}
-      {% if variant.alamut_link %}
-        <div class="ms-1">
-          <a href="{{ variant.alamut_link }}" class="btn btn-sm btn-secondary" target="_blank" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with genome g. coordinate">Alamut g.</a>
-        </div>
-      {% endif %}
-      {% for gene in variant.genes %}
-        <div class="ms-1">
-        {% if gene.alamut_link %}
-          <a href="{{ gene.alamut_link }}" class="btn btn-sm btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with gene transcript c. coordinate">Alamut {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} c.</a>
-        {% endif %}
-        </div>
-      {% endfor %}
     </li>
     <li class="list-group-item">
       <div>
@@ -148,6 +136,32 @@
         {{ gene_coverage(institute, variant, case, config) }}
       </li>
     {% endif %}
+    {% if variant.alamut_link  %}
+    <li class="list-group-item d-flex justify-content-between">
+      <div>
+      Alamut Visual Plus 
+      </div>
+      <div>
+        Open coordinates
+      {% if variant.alamut_link %}
+          <input type="button" class="btn btn-sm btn-secondary text-white" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with genome g. coordinate" value='genome' onclick='linkOutsideSoftware("{{variant.alamut_link}}");'/>
+      {% endif %}
+      {% for gene in variant.genes %}
+        {% if gene.alamut_link %}
+          <input type="button" class="btn btn-sm btn-secondary text-white" data-bs-toggle="tooltip" title="Alamut Visual (Plus) - Open variant - with gene transcript c. coordinate" value=' {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}' onclick='linkOutsideSoftware("{{gene.alamut_link}}");'/>
+        {% endif %}
+      {% endfor %}
+      </div>
+      <div>
+      {% if case['alamut_file_links'] %}
+        Open align. file:
+      {% for sample, file_link in case['alamut_file_links'].items() %}
+          <input type="button" class="btn btn-sm btn-secondary text-white" value='{{sample}}' data-bs-toggle="tooltip" title="Open alignment file for sample {{sample}}" onclick='linkOutsideSoftware("{{file_link[0] + url_for('alignviewers.remote_static', args=institute._id + ',' + case.display_name + ',' + file_link[1], _external=True)}}");'/>
+      {% endfor %}
+      {% endif %}
+      </div>
+    </li>
+    {% endif %}
   </ul>
 {% endmacro %}
 
@@ -576,6 +590,13 @@
       }
     }
 
+    function linkOutsideSoftware(alamut_coord_link) {
+    // open Alamut browser
+    var http_req = new XMLHttpRequest();
+    http_req.open( "GET", alamut_coord_link, true);
+    http_req.send();
+
+  }
   </script>
 {% endmacro %}
 

scout/server/links.py

@@ -917,6 +917,50 @@
     )
 
 
+def alamut_file_links(
+    institute_obj: Dict[str, Any],
+    case_obj: Dict[str, Any],
+):
+    """Compose a link which loads an alignment file in the Alamut software.
+    Alamut links require some settings from the institute object.
+
+    Args:
+        institute_obj(scout.models.Institute)
+        case_obj(scout.models.Case)
+    Returns:
+        dict url_template(str): link to Alamut browser
+        links(dict): {
+            sample_display_name: url_template(str)}
+    """
+
+    if current_app.config.get("HIDE_ALAMUT_LINK"):
+        return False
+
+    if not institute_obj:
+        return False
+
+    search_verb, alamut_key_arg, alamut_inst_arg = _get_alamut_config(institute_obj)
+
+    if alamut_key_arg == "":
+        return False
+
+    url_template = (
+        "http://localhost:10000/open?{alamut_key_arg}{alamut_inst_arg}filetype={file_type}&path="
+    )
+    links = {}
+    for ind in case_obj.get("individuals"):
+        file = ind.get("bam_file")
+        if file is not None:
+            file_type = file.split(".")[-1]
+            link = url_template.format(
+                alamut_key_arg=alamut_key_arg,
+                alamut_inst_arg=alamut_inst_arg,
+                file_type=file_type,
+            )
+            links[ind.get("display_name")] = (link, file)
+    return links
+
+
 def _get_alamut_config(institute_obj: dict) -> Tuple[str, ...]:
     """
     Prepare Alamut connection string specifics from institute level configuration.