JBrowse2 polishing

tools/jbrowse2/jbrowse2.py

@@ -31,7 +31,9 @@
     "}": "__cc__",
     "@": "__at__",
     "#": "__pd__",
-    "": "__cn__",
+    "\n": "__cn__",
+    "\r": "__cr__",
+    "\t": "__tc__",
 }
 
 
@@ -62,6 +64,14 @@ def etree_to_dict(t):
 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
 
 
+def unsanitize(input):
+
+    for key, value in mapped_chars.items():
+        input = input.replace(value, key)
+
+    return input
+
+
 def metadata_from_node(node):
     metadata = {}
 
@@ -74,7 +84,7 @@ def metadata_from_node(node):
             metadata[f"history_{key}"] = value
 
         for key, value in node.findall("metadata")[0].attrib.items():
-            metadata[f"metadata_{key}"] = value
+            metadata[f"metadata_{key}"] = unsanitize(value)
 
         for key, value in node.findall("tool")[0].attrib.items():
             metadata[f"tool_{key}"] = value
@@ -265,15 +275,11 @@ def _prepare_format_details(self, xml_conf):
         }
 
         if "feature" in xml_conf["formatdetails"]:
-            feat_jexl = xml_conf["formatdetails"]["feature"]
-            for key, value in mapped_chars.items():
-                feat_jexl = feat_jexl.replace(value, key)
+            feat_jexl = unsanitize(xml_conf["formatdetails"]["feature"])
             formatDetails["feature"] = feat_jexl
 
         if "subfeature" in xml_conf["formatdetails"]:
-            sfeat_jexl = xml_conf["formatdetails"]["subfeature"]
-            for key, value in mapped_chars.items():
-                sfeat_jexl = sfeat_jexl.replace(value, key)
+            sfeat_jexl = unsanitize(xml_conf["formatdetails"]["subfeature"])
             formatDetails["subfeatures"] = sfeat_jexl
 
         if "depth" in xml_conf["formatdetails"]:
@@ -773,6 +779,54 @@ def add_gff(self, parent, data, format, trackData, gffOpts, **kwargs):
             remote=trackData['remote']
         )
 
+    def add_gtf(self, parent, data, format, trackData, gffOpts, **kwargs):
+        # Not a super recommended format
+        # https://github.com/GMOD/jbrowse-components/pull/2389
+        # https://github.com/GMOD/jbrowse-components/issues/3876
+        if trackData['remote']:
+            rel_dest = data
+        else:
+            rel_dest = os.path.join("data", trackData["label"] + ".gtf")
+            dest = os.path.join(self.outdir, rel_dest)
+            shutil.copy(os.path.realpath(data), dest)
+
+        json_track_data = {
+            "type": "FeatureTrack",
+            "trackId": trackData["label"],
+            "name": trackData["key"],
+            "adapter": {
+                "type": "GtfAdapter",
+                "gtfLocation": {
+                    "uri": rel_dest,
+                    "locationType": "UriLocation"
+                },
+            },
+            "category": [trackData["category"]],
+            "assemblyNames": [parent['uniq_id']],
+        }
+
+        style_json = self._prepare_track_style(trackData)
+
+        formatdetails = self._prepare_format_details(trackData)
+
+        style_json.update(formatdetails)
+
+        track_metadata = self._prepare_track_metadata(trackData)
+
+        style_json.update(track_metadata)
+
+        json_track_data.update(style_json)
+
+        self.subprocess_check_call(
+            [
+                "jbrowse",
+                "add-track-json",
+                "--target",
+                self.outdir,
+                json.dumps(json_track_data),
+            ]
+        )
+
     def add_bed(self, parent, data, format, trackData, gffOpts, **kwargs):
         if trackData['remote']:
             rel_dest = data
@@ -1115,8 +1169,7 @@ def process_annotations(self, track, parent):
             extra_metadata,
         ) in enumerate(track["trackfiles"]):
             # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
-            for key, value in mapped_chars.items():
-                track_human_label = track_human_label.replace(value, key)
+            track_human_label = unsanitize(track_human_label)
 
             is_multi = type(dataset_path) is list
 
@@ -1180,6 +1233,14 @@ def process_annotations(self, track, parent):
                     outputTrackConfig,
                     track["conf"]["options"]["gff"],
                 )
+            elif dataset_ext in ("gtf"):
+                self.add_gtf(
+                    parent,
+                    dataset_path,
+                    dataset_ext,
+                    outputTrackConfig,
+                    track["conf"]["options"]["gff"],
+                )
             elif dataset_ext == "bed":
                 self.add_bed(
                     parent,
@@ -1288,13 +1349,10 @@ def process_annotations(self, track, parent):
                     track["conf"]["options"]["hic"]
                 )
             elif dataset_ext == "sparql":
-                sparql_query = track["conf"]["options"]["sparql"]["query"]
-                for key, value in mapped_chars.items():
-                    sparql_query = sparql_query.replace(value, key)
+                sparql_query = unsanitize(track["conf"]["options"]["sparql"]["query"])
                 sparql_query_refnames = track["conf"]["options"]["sparql"].get("query_refnames", "")
                 if sparql_query_refnames:
-                    for key, value in mapped_chars.items():
-                        sparql_query_refnames = sparql_query_refnames.replace(value, key)
+                    sparql_query_refnames = unsanitize(sparql_query_refnames)
                 self.add_sparql(
                     parent,
                     track["conf"]["options"]["sparql"]["url"],
@@ -1308,7 +1366,7 @@ def process_annotations(self, track, parent):
                     outputTrackConfig,
                 )
             else:
-                log.error(f"Do not know how to handle {dataset_ext}")
+                raise RuntimeError(f"Do not know how to handle dataset of type '{dataset_ext}'")
 
             track_labels.append(outputTrackConfig["label"])
 
@@ -1710,7 +1768,8 @@ def validate_synteny(real_root):
 
             track_labels = jc.process_annotations(track_conf, genome)
 
-            if track.attrib["visibility"] == "default_on":
+            if track.attrib["visibility"] == "default_on" and \
+               (track_conf["format"] != "synteny" or track_conf["style"]["display"] != "LinearSyntenyDisplay"):
                 for tlabel in track_labels:
                     default_tracks_on.append(tlabel)