comparison jbrowse2.py @ 108:5d1259b88c27 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9de1453a009c254ab11b16ae8a56cb5c22b131bf

107:a074cd6b5905

import argparse
import binascii
import copy
import datetime
# import hashlib
import json
import logging
import os
import re
import shutil

from collections import defaultdict

logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger("jbrowse")

JB2VER = "v2.11.1"
# version pinned if cloning - but not cloning now
logCommands = True
# useful for seeing what's being written but not for production setups
TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))

        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd[gname].append(copy.copy(trackDict))
        self.trackIdlist.append(copy.copy(tId))
        if self.config_json.get("plugins", None):
            self.config_json["plugins"].append(mafPlugin[0])
        else:
            self.config_json.update(mafPlugin)

    def _blastxml_to_gff3(self, xml, min_gap=10):
        gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)

        trackDict["style"] = style_json
        self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
        self.trackIdlist.append(copy.copy(tId))

    def add_bed(self, data, ext, trackData):
        tId = trackData["label"]
        categ = trackData["category"]
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            url = data
        else:
            url = tId + ".gz"
            dest = os.path.join(self.outdir, url)
            self._sort_bed(data, dest)
        trackDict = {
            "type": "FeatureTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [trackData["assemblyNames"]],
            "adapter": {
                "category": [
                    categ,
                ],
                "type": "BedTabixAdapter",
                "bedGzLocation": {
                    "uri": url,
                },
                "index": {
                    "location": {
                        "uri": url + ".tbi",
                    }
                },
            },
            "displays": [
                {
                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearBasicDisplay" % tId,
                },
                {
                    "type": "LinearPileupDisplay",
                    "displayId": "%s-LinearPileupDisplay" % tId,
                },

                },
            ],
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
        self.trackIdlist.append(copy.copy(tId))

    def add_paf(self, data, trackData, pafOpts, **kwargs):
        tname = trackData["name"]

            tracks_data = []
            for track_conf in self.tracksToAdd[gnome]:
                tId = track_conf["trackId"]
                if tId in default_data[gnome]["visibility"]["default_on"]:
                    track_types[tId] = track_conf["type"]
                    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("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],
                        }
                    )
            first = [x for x in self.ass_first_contigs if x[0] == gnome]
            drdict = {
                    "reversed": False,

                    shutil.rmtree(path)
                else:
                    os.remove(path)
            except OSError as e:
                log.error("Error: %s - %s." % (e.filename, e.strerror))
        shutil.copyfile(os.path.join(INSTALLED_TO, "jb2_webserver.py"), os.path.join(dest, "jb2_webserver.py"))


def parse_style_conf(item):
    if item.text.lower() in ["false", "true", "yes", "no"]:
        return item.text.lower in ("yes", "true")

                pass

            trackfiles = track.findall("files/trackFile")
            if trackfiles:
                for x in trackfiles:
                    track_conf["label"] = "%s_%d" % (
                        x.attrib["label"].replace(" ", "_").replace(",", "_").replace("/","_"),
                        trackI,
                    )
                    trackI += 1

                            "bigwig_multiple",
                            "MultiBigWig",  # Giving an hardcoded name for now
                            {},  # No metadata for multiple bigwig
                        )
                    )

            track_conf["category"] = track.attrib["cat"]
            track_conf["format"] = track.attrib["format"]
            track_conf["conf"] = etree_to_dict(track.find("options"))
            keys = jc.process_annotations(track_conf)
            if keys:
                for key in keys:
                    vis = track.attrib.get("visibility", "default_off")
                    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
                    if track.find("options/style_labels"):
                        default_session_data[primaryGenome]["style_labels"][key] = {
                            item.tag: parse_style_conf(item)
                            for item in track.find("options/style_labels")
                        }
                    default_session_data[primaryGenome]["tracks"].append(key)
    default_session_data["defaultLocation"] = root.find(
        "metadata/general/defaultLocation"
    ).text
    default_session_data["session_name"] = root.find(

108:5d1259b88c27

import argparse
import binascii
import copy
import datetime
import json
import logging
import os
import re
import shutil

from collections import defaultdict

logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger("jbrowse")

JB2VER = "v2.12.3"
# version pinned if cloning - but not cloning now
logCommands = True
# useful for seeing what's being written but not for production setups
TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))

        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd[gname].append(copy.copy(trackDict))
        self.trackIdlist.append(copy.copy(tId))
        if self.config_json.get("plugins", None):
            self.config_json["plugins"].append(mafPlugin["plugins"][0])
        else:
            self.config_json.update(mafPlugin)

    def _blastxml_to_gff3(self, xml, min_gap=10):
        gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)

        trackDict["style"] = style_json
        self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
        self.trackIdlist.append(copy.copy(tId))

    def add_bed(self, data, ext, trackData):
        bedPlugin = {"name": "BedScorePlugin", "umdLoc": { "uri": "bedscoreplugin.js" } }
        tId = trackData["label"]
        categ = trackData["category"]
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            url = data
        else:
            url = tId + ".gz"
            dest = os.path.join(self.outdir, url)
            self._sort_bed(data, dest)
        if True or trackData.get("usebedscore",None):
            bedgzlocation = {
                    "uri": url,
                    "columnNames": ["chr","start","end","name","score"],
                    "scoreColumn": "score",
                }
        else:
            bedgzlocation = {
                    "uri": url,
                }
        trackDict = {
            "type": "FeatureTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [trackData["assemblyNames"]],
            "adapter": {
                "category": [
                    categ,
                ],
                "type": "BedTabixAdapter",
                "bedGzLocation": bedgzlocation,
                "index": {
                    "location": {
                        "uri": url + ".tbi",
                    },
                },
            },
            "displays": [
                {
                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearBasicDisplay" % tId,
                    "renderer": {
                        "type": "SvgFeatureRenderer",
                        "color1": "jexl:customColor(feature)",
                        },
                },
                {
                    "type": "LinearPileupDisplay",
                    "displayId": "%s-LinearPileupDisplay" % tId,
                },

                },
            ],
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        if self.config_json.get("plugins", None):
            self.config_json["plugins"].append(bedPlugin)
        else:
            self.config_json["plugins"] = [bedPlugin,]
        self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
        self.trackIdlist.append(copy.copy(tId))

    def add_paf(self, data, trackData, pafOpts, **kwargs):
        tname = trackData["name"]

            tracks_data = []
            for track_conf in self.tracksToAdd[gnome]:
                tId = track_conf["trackId"]
                if tId in default_data[gnome]["visibility"]["default_on"]:
                    track_types[tId] = track_conf["type"]
                    display = {"type": "linearBasicDisplay"}
                    if "displays" in track_conf:
                        display["type"] = track_conf["displays"][0]["type"]
                    display["configuration"] = track_conf["displays"][0]["displayId"]
                    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": [display],
                        }
                    )
            first = [x for x in self.ass_first_contigs if x[0] == gnome]
            drdict = {
                    "reversed": False,

                    shutil.rmtree(path)
                else:
                    os.remove(path)
            except OSError as e:
                log.error("Error: %s - %s." % (e.filename, e.strerror))
        for neededfile in ["jb2_webserver.py", "bedscoreplugin.js"]:
            shutil.copyfile(os.path.join(INSTALLED_TO, neededfile), os.path.join(dest, neededfile))


def parse_style_conf(item):
    if item.text.lower() in ["false", "true", "yes", "no"]:
        return item.text.lower in ("yes", "true")

                pass

            trackfiles = track.findall("files/trackFile")
            if trackfiles:
                for x in trackfiles:
                    isBed = False
                    if x.attrib['ext'] == "bed":
                        isBed = True                   
                    track_conf["label"] = "%s_%d" % (
                        x.attrib["label"].replace(" ", "_").replace(",", "_").replace("/","_"),
                        trackI,
                    )
                    trackI += 1

                            "bigwig_multiple",
                            "MultiBigWig",  # Giving an hardcoded name for now
                            {},  # No metadata for multiple bigwig
                        )
                    )
            track_conf["category"] = track.attrib["cat"]
            track_conf["format"] = track.attrib["format"]
            track_conf["conf"] = etree_to_dict(track.find("options"))
            keys = jc.process_annotations(track_conf)
            if keys:
                for key in keys:
                    vis = track.attrib.get("visibility", "default_off")
                    if not vis:
                        vis = "default_off"
                    default_session_data[primaryGenome]["visibility"][vis].append(key)
                    default_session_data[primaryGenome]["tracks"].append(key)
    default_session_data["defaultLocation"] = root.find(
        "metadata/general/defaultLocation"
    ).text
    default_session_data["session_name"] = root.find(