diff jbrowse2.py @ 7:b04fd993b31e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717

--- a/jbrowse2.py	Tue Jan 09 06:55:34 2024 +0000
+++ b/jbrowse2.py	Wed Jan 17 07:50:52 2024 +0000
@@ -17,6 +17,10 @@
 
 logging.basicConfig(level=logging.INFO)
 log = logging.getLogger("jbrowse")
+
+JB2VER = "v2.10.0"
+# version pinned for cloning
+
 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
 GALAXY_INFRASTRUCTURE_URL = None
 JB2REL = "v2.10.0"
@@ -371,7 +375,6 @@
 
 class JbrowseConnector(object):
     def __init__(self, outdir, genomes):
-        self.debug = False
         self.usejson = True
         self.giURL = GALAXY_INFRASTRUCTURE_URL
         self.outdir = outdir
@@ -387,16 +390,14 @@
 
     def subprocess_check_call(self, command, output=None):
         if output:
-            if self.debug:
-                log.debug("cd %s && %s >  %s", self.outdir, " ".join(command), output)
+            log.debug("cd %s && %s >  %s", self.outdir, " ".join(command), output)
             subprocess.check_call(command, cwd=self.outdir, stdout=output)
         else:
             log.debug("cd %s && %s", self.outdir, " ".join(command))
             subprocess.check_call(command, cwd=self.outdir)
 
     def subprocess_popen(self, command):
-        if self.debug:
-            log.debug(command)
+        log.debug(command)
         p = subprocess.Popen(
             command,
             cwd=self.outdir,
@@ -414,8 +415,7 @@
             raise RuntimeError("Command failed with exit code %s" % (retcode))
 
     def subprocess_check_output(self, command):
-        if self.debug:
-            log.debug(" ".join(command))
+        log.debug(" ".join(command))
         return subprocess.check_output(command, cwd=self.outdir)
 
     def symlink_or_copy(self, src, dest):
@@ -465,9 +465,14 @@
                 self.config_json["assemblies"] = assemblies
 
     def make_assembly(self, fapath, gname):
-        faname = gname + ".fa.gz"
+        hashData = [
+            fapath,
+            gname,
+        ]
+        hashData = "|".join(hashData).encode("utf-8")
+        ghash = hashlib.md5(hashData).hexdigest()
+        faname = ghash + ".fa.gz"
         fadest = os.path.join(self.outdir, faname)
-        # fadest = os.path.realpath(os.path.join(self.outdir, faname))
         cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
             fapath,
             fadest,
@@ -556,7 +561,7 @@
         # can be served - if public.
         # dsId = trackData["metadata"]["dataset_id"]
         # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
-        hname = trackData["name"]
+        hname = trackData["label"]
         dest = os.path.join(self.outdir, hname)
         cmd = ["cp", data, dest]
         # these can be very big.
@@ -603,8 +608,6 @@
         tId = trackData["label"]
         fname = "%s.bed" % tId
         dest = "%s/%s" % (self.outdir, fname)
-        # self.symlink_or_copy(data, dest)
-        # Process MAF to bed-like. Need build to munge chromosomes
         gname = self.genome_name
         cmd = [
             "bash",
@@ -722,11 +725,11 @@
         trackDict["style"] = style_json
         self.tracksToAdd.append(trackDict)
         self.trackIdlist.append(tId)
-
         os.unlink(gff3)
 
     def add_bigwig(self, data, trackData):
-        url = "%s.bw" % trackData["name"]
+        url = "%s.bigwig" % trackData["label"]
+        # slashes in names cause path trouble
         dest = os.path.join(self.outdir, url)
         cmd = ["cp", data, dest]
         self.subprocess_check_call(cmd)
@@ -735,7 +738,7 @@
         trackDict = {
             "type": "QuantitativeTrack",
             "trackId": tId,
-            "name": url,
+            "name": trackData["name"],
             "assemblyNames": [
                 self.genome_name,
             ],
@@ -754,6 +757,7 @@
         trackDict["style"] = style_json
         self.tracksToAdd.append(trackDict)
         self.trackIdlist.append(tId)
+        logging.debug("#### wig trackData=%s" % str(trackData))
 
     def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
         tId = trackData["label"]
@@ -959,35 +963,24 @@
                 asstrack,
             ]
 
-        style_json = self._prepare_track_style(trackData)
         url = "%s.paf" % (trackData["label"])
         dest = "%s/%s" % (self.outdir, url)
         self.symlink_or_copy(os.path.realpath(data), dest)
-
-        if self.usejson:
-            trackDict = {
-                "type": "SyntenyTrack",
-                "trackId": tId,
+        trackDict = {
+            "type": "SyntenyTrack",
+            "trackId": tId,
+            "assemblyNames": [self.genome_name, pgname],
+            "name": tname,
+            "adapter": {
+                "type": "PAFAdapter",
+                "pafLocation": {"uri": url},
                 "assemblyNames": [self.genome_name, pgname],
-                "name": tname,
-                "adapter": {
-                    "type": "PAFAdapter",
-                    "pafLocation": {"uri": url},
-                    "assemblyNames": [self.genome_name, pgname],
-                },
-                "config": style_json,
-            }
-            self.tracksToAdd.append(trackDict)
-            self.trackIdlist.append(tId)
-        else:
-            self._add_track(
-                trackData["label"],
-                trackData["key"],
-                trackData["category"],
-                dest,
-                assemblies=[self.genome_name, pgname],
-                config=style_json,
-            )
+            },
+        }
+        style_json = self._prepare_track_style(trackDict)
+        trackDict["style"] = style_json
+        self.tracksToAdd.append(trackDict)
+        self.trackIdlist.append(tId)
 
     def add_hicab(self, data, trackData, hicOpts, **kwargs):
         rel_dest = os.path.join("data", trackData["label"] + ".hic")
@@ -995,14 +988,12 @@
 
         self.symlink_or_copy(os.path.realpath(data), dest)
 
-        style_json = self._prepare_track_style(trackData)
-
         self._add_track(
             trackData["label"],
             trackData["key"],
             trackData["category"],
             rel_dest,
-            config=style_json,
+            config={},
         )
 
     def add_sparql(self, url, query, query_refnames, trackData):
@@ -1061,12 +1052,7 @@
             }
 
             outputTrackConfig["key"] = track_human_label
-            if self.debug:
-                log.info(
-                    "Processing category = %s, track_human_label = %s",
-                    category,
-                    track_human_label,
-                )
+
             # We add extra data to hash for the case of REST + SPARQL.
             if (
                 "conf" in track
@@ -1076,7 +1062,7 @@
                 rest_url = track["conf"]["options"]["url"]
             else:
                 rest_url = ""
-
+            outputTrackConfig["trackset"] = track.get("trackset", {})
             # I chose to use track['category'] instead of 'category' here. This
             # is intentional. This way re-running the tool on a different date
             # will not generate different hashes and make comparison of outputs
@@ -1165,26 +1151,22 @@
 
         for track_conf in self.tracksToAdd:
             track_types[track_conf["trackId"]] = track_conf["type"]
-
-        for on_track in data["visibility"]["default_on"]:
-            style_data = {"type": "LinearBasicDisplay", "height": 100}
-            if on_track in data["style"]:
-                if "display" in data["style"][on_track]:
-                    style_data["type"] = data["style"][on_track]["display"]
-                    del data["style"][on_track]["display"]
-                style_data.update(data["style"][on_track])
-            if on_track in data["style_labels"]:
-                # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work
-                # TODO move this to per track displays?
-                style_data["labels"] = data["style_labels"][on_track]
-
-            tracks_data.append(
-                {
-                    "type": track_types[on_track],
-                    "configuration": on_track,
-                    "displays": [style_data],
-                }
-            )
+            tId = track_conf["trackId"]
+            if tId in data["visibility"]["default_on"]:
+                style_data = {"type": "LinearBasicDisplay"}
+                if "displays" in track_conf:
+                    style_data["type"] = track_conf["displays"][0]["type"]
+                if track_conf.get("style_labels", None):
+                    # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work
+                    # TODO move this to per track displays?
+                    style_data["labels"] = track_conf["style_labels"]
+                tracks_data.append(
+                    {
+                        "type": track_types[tId],
+                        "configuration": tId,
+                        "displays": [style_data],
+                    }
+                )
 
         # The view for the assembly we're adding
         view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
@@ -1199,7 +1181,7 @@
         elif self.genome_name is not None:
             refName = self.genome_name
             start = 0
-            end = 100000  # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708
+            end = 10000  # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708
 
         if refName is not None:
             # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
@@ -1265,8 +1247,11 @@
 
     def clone_jbrowse(self):
         """Clone a JBrowse directory into a destination directory."""
+        # dest = os.path.realpath(self.outdir)
         dest = self.outdir
-        cmd = ["jbrowse", "create", "-t", JB2REL, "-f", dest]
+        cmd = ["rm", "-rf", dest + "/*"]
+        self.subprocess_check_call(cmd)
+        cmd = ["jbrowse", "create", dest, "-t", JB2VER, "-f"]
         self.subprocess_check_call(cmd)
         for fn in [
             "asset-manifest.json",
@@ -1278,7 +1263,7 @@
         ]:
             cmd = ["rm", "-rf", os.path.join(self.outdir, fn)]
             self.subprocess_check_call(cmd)
-        cmd = ["cp", os.path.join(INSTALLED_TO, "webserver.py"), self.outdir]
+        cmd = ["cp", os.path.join(INSTALLED_TO, "jb2_webserver.py"), self.outdir]
         self.subprocess_check_call(cmd)
 
 
@@ -1386,21 +1371,17 @@
                     {},  # No metadata for multiple bigwig
                 )
             )
-
         track_conf["category"] = track.attrib["cat"]
         track_conf["format"] = track.attrib["format"]
-        track_conf["style"] = {
-            item.tag: parse_style_conf(item) for item in track.find("options/style")
-        }
-
-        track_conf["style"] = {
-            item.tag: parse_style_conf(item) for item in track.find("options/style")
-        }
-
-        track_conf["style_labels"] = {
-            item.tag: parse_style_conf(item)
-            for item in track.find("options/style_labels")
-        }
+        if track.find("options/style"):
+            track_conf["style"] = {
+                item.tag: parse_style_conf(item) for item in track.find("options/style")
+            }
+        if track.find("options/style_labels"):
+            track_conf["style_labels"] = {
+                item.tag: parse_style_conf(item)
+                for item in track.find("options/style_labels")
+            }
 
         track_conf["conf"] = etree_to_dict(track.find("options"))
         keys = jc.process_annotations(track_conf)
@@ -1410,10 +1391,14 @@
                 default_session_data["visibility"][
                     track.attrib.get("visibility", "default_off")
                 ].append(key)
-                default_session_data["style"][key] = track_conf[
-                    "style"
-                ]  # TODO do we need this anymore?
-                default_session_data["style_labels"][key] = track_conf["style_labels"]
+                if track_conf.get("style", None):
+                    default_session_data["style"][key] = track_conf[
+                        "style"
+                    ]  # TODO do we need this anymore?
+                if track_conf.get("style_lables", None):
+                    default_session_data["style_labels"][key] = track_conf.get(
+                        "style_labels", None
+                    )
 
         default_session_data["defaultLocation"] = root.find(
             "metadata/general/defaultLocation"
@@ -1444,7 +1429,6 @@
     jc.config_json["tracks"] = jc.tracksToAdd
     if jc.usejson:
         jc.write_config()
-    # jc.add_default_view()
     jc.add_default_session(default_session_data)
 
     # jc.text_index() not sure what broke here.