comparison jbrowse2.py @ 10:c60b17456297 draft

planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04

9:a26c41e304c3

        # We need to know the track type from the config.json generated just before
        track_types = {}
        with open(self.config_json_file, "r") as config_file:
            config_json = json.load(config_file)

        for track_conf in self.tracksToAdd:
            track_types[track_conf["trackId"]] = track_conf["type"]
            tId = track_conf["trackId"]
            if tId in data["visibility"]["default_on"]:

                    "assemblyName": self.genome_name,
                }
            ]

        session_name = data.get("session_name", "New session")

        # Merge with possibly existing defaultSession (if upgrading a jbrowse instance)
        session_json = {}
        if "defaultSession" in config_json:
            session_json = config_json["defaultSession"]

            session_json["views"] = []

        session_json["views"].append(view_json)

        config_json["defaultSession"] = session_json

        with open(self.config_json_file, "w") as config_file:
            json.dump(config_json, config_file, indent=2)

    def add_general_configuration(self, data):
        """
        Add some general configuration to the config.json file
        """

        config_path = self.config_json_file
        config_json = {}
        if os.path.exists(config_path):
            with open(config_path, "r") as config_file:
                config_json = json.load(config_file)

        config_data = {}

        config_data["disableAnalytics"] = data.get("analytics", "false") == "true"

        config_data["theme"] = {

            "typography": {"fontSize": int(data.get("font_size", 10))},
        }
        if not config_json.get("configuration", None):
            config_json["configuration"] = {}
        config_json["configuration"].update(config_data)

        with open(config_path, "w") as config_file:
            json.dump(config_json, config_file, indent=2)

    def clone_jbrowse(self):
        """Clone a JBrowse directory into a destination directory."""
        # dest = os.path.realpath(self.outdir)
        dest = self.outdir

        except TypeError:
            track_conf["style"] = {}
            pass
        track_conf["conf"] = etree_to_dict(track.find("options"))
        jc.add_general_configuration(general_data)
    x = open(args.xml, "r").read()
    jc.config_json["tracks"] = jc.tracksToAdd
    jc.write_config()
    jc.add_default_session(default_session_data)

    # jc.text_index() not sure what broke here.

10:c60b17456297

        # We need to know the track type from the config.json generated just before
        track_types = {}
        with open(self.config_json_file, "r") as config_file:
            config_json = json.load(config_file)
        if self.config_json:
            config_json.update(self.config_json)

        for track_conf in self.tracksToAdd:
            track_types[track_conf["trackId"]] = track_conf["type"]
            tId = track_conf["trackId"]
            if tId in data["visibility"]["default_on"]:

                    "assemblyName": self.genome_name,
                }
            ]

        session_name = data.get("session_name", "New session")
        for key, value in mapped_chars.items():
            session_name = session_name.replace(value, key)
        # Merge with possibly existing defaultSession (if upgrading a jbrowse instance)
        session_json = {}
        if "defaultSession" in config_json:
            session_json = config_json["defaultSession"]

            session_json["views"] = []

        session_json["views"].append(view_json)

        config_json["defaultSession"] = session_json
        self.config_json.update(config_json)

        with open(self.config_json_file, "w") as config_file:
            json.dump(self.config_json, config_file, indent=2)

    def add_general_configuration(self, data):
        """
        Add some general configuration to the config.json file
        """

        config_path = self.config_json_file
        if os.path.exists(config_path):
            with open(config_path, "r") as config_file:
                config_json = json.load(config_file)
        else:
            config_json = {}
        if self.config_json:
            config_json.update(self.config_json)
        config_data = {}

        config_data["disableAnalytics"] = data.get("analytics", "false") == "true"

        config_data["theme"] = {

            "typography": {"fontSize": int(data.get("font_size", 10))},
        }
        if not config_json.get("configuration", None):
            config_json["configuration"] = {}
        config_json["configuration"].update(config_data)
        self.config_json.update(config_json)
        with open(config_path, "w") as config_file:
            json.dump(self.config_json, config_file, indent=2)

    def clone_jbrowse(self):
        """Clone a JBrowse directory into a destination directory."""
        # dest = os.path.realpath(self.outdir)
        dest = self.outdir

        except TypeError:
            track_conf["style"] = {}
            pass
        track_conf["conf"] = etree_to_dict(track.find("options"))
        jc.add_general_configuration(general_data)
    jc.config_json["tracks"] = jc.tracksToAdd
    jc.write_config()
    jc.add_default_session(default_session_data)

    # jc.text_index() not sure what broke here.