| Previous changeset 109:27e9ddaaf325 (2024-06-29) Next changeset 111:0a532764dcfa (2024-07-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9de1453a009c254ab11b16ae8a56cb5c22b131bf-dirty |
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modified:
__pycache__/jbrowse2.cpython-312.pyc jbrowse2.py |
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| diff -r 27e9ddaaf325 -r c017111e976a __pycache__/jbrowse2.cpython-312.pyc |
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| Binary file __pycache__/jbrowse2.cpython-312.pyc has changed |
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| diff -r 27e9ddaaf325 -r c017111e976a jbrowse2.py --- a/jbrowse2.py Sat Jun 29 07:22:18 2024 +0000 +++ b/jbrowse2.py Sat Jun 29 09:10:04 2024 +0000 |
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| @@ -1363,10 +1363,24 @@ tId = track_conf["trackId"] if tId in default_data[gnome]["visibility"]["default_on"]: track_types[tId] = track_conf["type"] - display = {"type": "linearBasicDisplay"} + style_data = default_data[gnome]["style"].get(tId, {}) + if not style_data: + logging.debug( + "No style data for %s in available default data %s" + % (tId, default_data) + ) + else: + logging.debug( + "style data for %s = %s" + % (tId, style_data) + ) + if style_data.get('type',None) == None: + style_data["type"] = "LinearBasicDisplay" + if "displays" in track_conf: + disp = track_conf["displays"][0]["type"] + style_data["type"] = disp if track_conf.get("displays", None): - display["type"] = track_conf["displays"][0]["type"] - display["configuration"] = track_conf["displays"][0]["displayId"] + style_data["configuration"] = track_conf["displays"][0]["displayId"] else: logging.debug("no display in track_conf for %s" % tId) if track_conf.get("style_labels", None): @@ -1377,7 +1391,7 @@ { "type": track_types[tId], "configuration": tId, - "displays": [display], + "displays": [style_data], } ) first = [x for x in self.ass_first_contigs if x[0] == gnome] @@ -1395,7 +1409,7 @@ ddl = default_data.get("defaultLocation", None) if ddl: loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) - # allow commas like 100,000 but ignore as integer + # allow commas like 100,000 but ignore as integer if loc_match: refName = loc_match.group(1) drdict["refName"] = refName @@ -1701,6 +1715,17 @@ if not vis: vis = "default_off" default_session_data[primaryGenome]["visibility"][vis].append(key) + trakdat = jc.tracksToAdd[primaryGenome] + stile = {} + for trak in trakdat: + if trak["trackId"] == key: + stile = trak.get("style", {}) + if track.find("options/style"): + for item in track.find("options/style"): + if item.text: + stile[item.tag] = parse_style_conf(item) + logging.debug("stile=%s" % stile) + default_session_data[primaryGenome]["style"][key] = stile default_session_data[primaryGenome]["tracks"].append(key) default_session_data["defaultLocation"] = root.find( "metadata/general/defaultLocation" |