jbrowse2: jbrowse2.py comparison

comparison jbrowse2.py @ 98:b1260bca5fdc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6

author	bgruening
date	Wed, 05 Jun 2024 10:00:07 +0000
parents	74074746ccd8
children	990291e918c7

comparison

equal deleted inserted replaced

-:74074746ccd8
+:b1260bca5fdc
 #!/usr/bin/env python
 import argparse
 import binascii
 import datetime
+# import hashlib
 import json
 import logging
 import os
 import re
 import shutil
 logging.basicConfig(level=logging.DEBUG)
 log = logging.getLogger("jbrowse")
 JB2VER = "v2.11.0"
-# version pinned if cloning - but not cloning now
+# version pinned if cloning - but not used until now
 logCommands = True
-# useful for seeing what's being written but NOT for production setups
+# 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__))
 GALAXY_INFRASTRUCTURE_URL = None
 mapped_chars = {
 ">": "__gt__",
 "}": "__cc__",
 "@": "__at__",
 "#": "__pd__",
 "": "__cn__",
 }
+INDEX_TEMPLATE = """<!doctype html>
+<html lang="en" style="height:100%">
+<head>
+<meta charset="utf-8"/>
+<link rel="shortcut icon" href="./favicon.ico"/>
+<meta name="viewport" content="width=device-width,initial-scale=1"/>
+<meta name="theme-color" content="#000000"/>
+<meta name="description" content="A fast and flexible genome browser"/>
+<link rel="manifest" href="./manifest.json"/>
+<title>JBrowse</title>
+</script>
+</head>
+<body style="overscroll-behavior:none; height:100%; margin: 0;">
+<iframe
+id="jbframe"
+title="JBrowse2"
+frameborder="0"
+width="100%"
+height="100%"
+src='index_noview.html?config=config.json__SESSION_SPEC__'>
+</iframe>
+</body>
+</html>
+"""
 class ColorScaling(object):
 COLOR_FUNCTION_TEMPLATE = """
 def get_cwd(self, cwd):
 if cwd:
 return self.outdir
 else:
 return subprocess.check_output(["pwd"]).decode("utf-8").strip()
-# return None
 def subprocess_check_call(self, command, output=None, cwd=True):
 if output:
 if logCommands:
 log.debug(
 retcode = p.returncode
 if retcode != 0:
 log.error(command)
 log.error(output)
 log.error(err)
-raise RuntimeError("Command failed with exit code %s" % (retcode))
+raise RuntimeError(f"Command ( {command} ) failed with exit code {retcode}")
 def subprocess_check_output(self, command):
 if logCommands:
 log.debug(" ".join(command))
 return subprocess.check_output(command, cwd=self.outdir)
 with urllib.request.urlopen(url, context=scontext) as f:
 fl = f.readlines()
 nrow = len(fl)
 except Exception:
 nrow = 0
-logging.debug("### getNrow %s returning %d" % (url, nrow))
+logging.debug("getNrow %s returning %d" % (url, nrow))
 return nrow
 def process_genomes(self, genomes):
 assembly = []
 assmeta = []
 self.assmeta[primaryGenome] = assmeta
 self.tracksToAdd[primaryGenome] = []
 return primaryGenome
 def make_assembly(self, fapath, gname, useuri):
-"""added code to grab the first contig name and length for broken default session from Anthony and Helena's code
-that poor Bjoern is trying to figure out.
-"""
 if useuri:
 faname = fapath
 scontext = ssl.SSLContext(ssl.PROTOCOL_TLS_CLIENT)
 scontext.check_hostname = False
 scontext.verify_mode = ssl.VerifyMode.CERT_NONE
 "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js",
 }
 ]
 }
 categ = trackData["category"]
-fname = tId
+fname = f"{tId}"
-dest = "%s/%s" % (self.outdir, fname)
+dest = os.path.join(self.outdir, fname)
 gname = trackData["assemblyNames"]
 cmd = [
 "bash",
 os.path.join(INSTALLED_TO, "convertMAF.sh"),
 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
 self.trackIdlist.append(tId)
 def add_vcf(self, data, trackData):
 tId = trackData["label"]
-# url = "%s/api/datasets/%s/display" % (
-# self.giURL,
-# trackData["metadata"]["dataset_id"],
-# )
 categ = trackData["category"]
 useuri = trackData["useuri"].lower() == "yes"
 if useuri:
 url = data
 else:
 track_human_label = track_human_label.replace(" ", "_")
 outputTrackConfig = {
 "category": category,
 "style": {},
 }
+# hashData = [
+#    str(dataset_path),
+#    track_human_label,
+#    track["category"],
+# ]
+# hashData = "|".join(hashData).encode("utf-8")
+# hash_string = hashlib.md5(hashData).hexdigest()
 outputTrackConfig["assemblyNames"] = track["assemblyNames"]
 outputTrackConfig["key"] = track_human_label
 outputTrackConfig["useuri"] = useuri
 outputTrackConfig["path"] = dataset_path
 outputTrackConfig["ext"] = dataset_ext
 outputTrackConfig["trackset"] = track.get("trackset", {})
 outputTrackConfig["label"] = track["label"]
+# outputTrackConfig["label"] = "%s_%i_%s_%s" % (
+#    dataset_ext,
+#    trackIndex,
+#    track_human_label,
+#    hash_string,
+# )
 outputTrackConfig["metadata"] = extra_metadata
 outputTrackConfig["name"] = track_human_label
 if track["label"] in self.trackIdlist:
 logging.error(
 "### not adding %s already in %s"
 "hic",
 dataset_path,
 hic_path,
 ]
 )
-logging.debug(
-"### ext=cool: wasCool=%s, hic_path=%s"
-% (outputTrackConfig["wasCool"], hic_path)
-)
 self.add_hic(
 hic_path,
 outputTrackConfig,
 )
 elif dataset_ext in ("bed",):
 dataset_path,
 outputTrackConfig,
 )
 elif dataset_ext == "bam":
 real_indexes = track["conf"]["options"]["bam"]["bam_index"]
-logging.debug("**** add bam got %s for indexes" % real_indexes)
 self.add_bam(
 dataset_path,
 outputTrackConfig,
 bam_indexes=real_indexes,
 )
 elif dataset_ext == "cram":
 real_indexes = track["conf"]["options"]["cram"]["cram_index"]
-logging.debug("**** add cram got %s for indexes" % real_indexes)
 self.add_cram(
 dataset_path,
 outputTrackConfig,
 cram_indexes=real_indexes,
 )
 dataset_path,
 outputTrackConfig,
 track["conf"]["options"]["paf"],
 )
 else:
-logging.warn("Do not know how to handle %s", dataset_ext)
+logging.warning("Do not know how to handle %s", dataset_ext)
 # Return non-human label for use in other fields
 yield outputTrackConfig["label"]
 def add_default_session(self, default_data):
 """
 default session settings are hard and fragile.
 .add_default_view() and other configuration code adapted from
 https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
 """
 # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
-bpPerPx = 50 # this is tricky since browser window width is unknown - this seems a compromise that sort of works....
 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)
 "type": track_types[tId],
 "configuration": tId,
 "displays": [style_data],
 }
 )
+view_json = {
+"type": "LinearGenomeView",
+"offsetPx": 0,
+"minimized": False,
+"tracks": tracks_data,
+}
 first = [x for x in self.ass_first_contigs if x[0] == gnome]
-drdict = {
+if len(first) > 0:
+[gnome, refName, end] = first[0]
+start = 0
+end = int(end)
+drdict = {
+"refName": refName,
+"start": start,
+"end": end,
 "reversed": False,
 "assemblyName": gnome,
 }
-if len(first) > 0:
-[gnome, refName, end] = first[0]
-drdict["refName"] = refName
-drdict["start"] = 0
-end = int(end)
-drdict["end"] = end
 else:
 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
 else:
 logging.info(
 "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
 % ddl
 )
-view_json = {
-"type": "LinearGenomeView",
-"offsetPx": 0,
-"bpPerPx" : bpPerPx,
-"minimized": False,
-"tracks": tracks_data
-}
 if drdict.get("refName", None):
 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
 view_json["displayedRegions"] = [
 drdict,
 ]
 session_views.append(view_json)
 session_name = default_data.get("session_name", "New session")
 for key, value in mapped_chars.items():
 session_name = session_name.replace(value, key)
 session_json["name"] = session_name
 if "views" not in session_json:
 session_json["views"] = session_views
 else:
 session_json["views"] += session_views
 pp = json.dumps(session_views, indent=2)
 config_json["defaultSession"] = session_json
 self.config_json.update(config_json)
 logging.debug("defaultSession=%s" % (pp))
 with open(self.config_json_file, "w") as config_file:
 Xrefs to understand the choices:
 https://github.com/GMOD/jbrowse-components/issues/2708
 https://github.com/GMOD/jbrowse-components/discussions/3568
 https://github.com/GMOD/jbrowse-components/pull/4148
 """
-INDEX_TEMPLATE = """<!doctype html>
-<html lang="en" style="height:100%">
-<head>
-<meta charset="utf-8"/>
-<link rel="shortcut icon" href="./favicon.ico"/>
-<meta name="viewport" content="width=device-width,initial-scale=1"/>
-<meta name="theme-color" content="#000000"/>
-<meta name="description" content="A fast and flexible genome browser"/>
-<link rel="manifest" href="./manifest.json"/>
-<title>JBrowse</title>
-</script>
-</head>
-<body style="overscroll-behavior:none; height:100%; margin: 0;">
-<iframe
-id="jbframe"
-title="JBrowse2"
-frameborder="0"
-width="100%"
-height="100%"
-src='index_noview.html?config=config.json__SESSION_SPEC__'>
-</iframe>
-</body>
-</html>
-"""
 new_index = "Nothing written"
 session_spec = {"views": []}
 logging.debug("def ass_first=%s\ndata=%s" % (self.ass_first_contigs, data))
 for first_contig in self.ass_first_contigs:
 logging.debug("first contig=%s" % self.ass_first_contigs)
 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, realclone=False):
-"""Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now
+"""
-Leave as True between version updates on temporary tools - requires manual conda trigger :(
+Clone a JBrowse directory into a destination directory.
+`realclone=true` will use the `jbrowse create` command.
+To allow running on internet-less compute and for reproducibility
+use frozen code with `realclone=false
 """
 dest = self.outdir
 if realclone:
 self.subprocess_check_call(
 ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"]

Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 98:b1260bca5fdc draft