Mercurial > repos > fubar > jbrowse2
changeset 3:2de9f585505b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b30d2e277cc360437a02fa812c577c0c8d997cff-dirty
| author | fubar |
|---|---|
| date | Tue, 09 Jan 2024 02:35:52 +0000 |
| parents | 37b2c26c7b9b |
| children | 54396f0323f4 |
| files | apache2_license.txt jbrowse2.py jbrowse2.xml macros.xml maf2bed.pl servejb2.py static/images/bam.png static/images/bigwig.png static/images/blast.png static/images/opacity.png static/images/sections.png static/images/styling.png test-data/blastxml/test.xml test-data/bw/test.xml test-data/index.html test-data/merlin.fa test-data/vcf/test.xml tool_data_table_conf.xml.sample webserver.py |
| diffstat | 18 files changed, 695 insertions(+), 289 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/apache2_license.txt Tue Jan 09 02:35:52 2024 +0000 @@ -0,0 +1,201 @@ +Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright 2023 Dan Vanderkam + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License.
--- a/jbrowse2.py Mon Jan 08 09:23:19 2024 +0000 +++ b/jbrowse2.py Tue Jan 09 02:35:52 2024 +0000 @@ -19,6 +19,9 @@ log = logging.getLogger("jbrowse") TODAY = datetime.datetime.now().strftime("%Y-%m-%d") GALAXY_INFRASTRUCTURE_URL = None +JB2REL="v2.10.0" +# version pinned for cloning + mapped_chars = { ">": "__gt__", "<": "__lt__", @@ -451,7 +454,9 @@ assemblies.append(assem) self.genome_names.append(genome_name) if self.genome_name is None: - self.genome_name = genome_name # first one for all tracks - other than paf + self.genome_name = ( + genome_name # first one for all tracks - other than paf + ) if self.config_json.get("assemblies", None): self.config_json["assemblies"] += assemblies else: @@ -506,8 +511,6 @@ "-v", " LinearGenomeView", ] - if self.debug: - log.info("### calling set-default-session with cmd=%s" % " ".join(cmd)) self.subprocess_check_call(cmd) def write_config(self): @@ -592,7 +595,7 @@ "plugins": [ { "name": "MafViewer", - "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js", + "url": "https://unpkg.com/browse/jbrowse-plugin-mafviewer@1.0.6/dist/jbrowse-plugin-mafviewer.umd.production.min.js", } ] } @@ -935,13 +938,17 @@ tId = trackData["label"] pgname = pafOpts["genome_label"] if len(pgname.split() > 1): - pgname = pgname.split()[0] # trouble from spacey names in command lines avoidance + pgname = pgname.split()[ + 0 + ] # trouble from spacey names in command lines avoidance asstrack, gname = self.make_assembly(pafOpts["genome"], pgname) self.genome_names.append(pgname) if self.config_json.get("assemblies", None): self.config_json["assemblies"].append(asstrack) else: - self.config_json["assemblies"] = [asstrack,] + self.config_json["assemblies"] = [ + asstrack, + ] style_json = self._prepare_track_style(trackData) url = "%s.paf" % (trackData["label"]) @@ -1256,7 +1263,7 @@ def clone_jbrowse(self): """Clone a JBrowse directory into a destination directory.""" dest = self.outdir - cmd = ["jbrowse", "create", "-f", dest] + cmd = ["jbrowse", "create", "-t",JB2REL, "-f", dest] self.subprocess_check_call(cmd) for fn in [ "asset-manifest.json", @@ -1268,7 +1275,7 @@ ]: cmd = ["rm", "-rf", os.path.join(self.outdir, fn)] self.subprocess_check_call(cmd) - cmd = ["cp", os.path.join(INSTALLED_TO, "servejb2.py"), self.outdir] + cmd = ["cp", os.path.join(INSTALLED_TO, "webserver.py"), self.outdir] self.subprocess_check_call(cmd)
--- a/jbrowse2.xml Mon Jan 08 09:23:19 2024 +0000 +++ b/jbrowse2.xml Tue Jan 09 02:35:52 2024 +0000 @@ -958,11 +958,11 @@ A JBrowse2 history item can be opened by viewing it (the "eye" icon). They can also be downloaded as archives ("floppy disk" icon) to share and for local viewing. One extra step is required before they can be viewed. A local python web server must be started using a script included in each archive. -Unzip the archive (*unzip [filename].zip*) and change to the first level directory. It contains a file named "servejb2.py" +Unzip the archive (*unzip [filename].zip*) and change to the first level directory. It contains a file named "webserver.py" Assuming you have python3 installed, running: -*python3 servjb2.py* +*python3 webserver.py* will serve the unarchived JBrowse2 configuration, so it can be browsed by pointing a web browser to localhost:8080
--- a/macros.xml Mon Jan 08 09:23:19 2024 +0000 +++ b/macros.xml Tue Jan 09 02:35:52 2024 +0000 @@ -27,7 +27,7 @@ <token name="@WRAPPER_VERSION@">galaxy0</token> <token name="@ATTRIBUTION@"><![CDATA[ **Attribution** -This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by the IUC +This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is developed by the IUC This xml currently fails silently when profile=22.05 is set. ]]> </token>
--- a/maf2bed.pl Mon Jan 08 09:23:19 2024 +0000 +++ b/maf2bed.pl Tue Jan 09 02:35:52 2024 +0000 @@ -1,4 +1,6 @@ #!/usr/bin/env perl +# https://unpkg.com/browse/jbrowse-plugin-mafviewer@1.0.6/dist/ +# license is Apache2_license.txt included here use warnings; use strict;
--- a/servejb2.py Mon Jan 08 09:23:19 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,159 +0,0 @@ -#!/usr/bin/env python3 - -# spec: simplest python web server with range support and multithreading that takes root path, -# port and bind address as command line arguments; by default uses the current dir as webroot, -# port 8000 and bind address of 0.0.0.0 -# borrowed from https://github.com/danvk/RangeHTTPServer -# and reborrowed from https://gist.github.com/glowinthedark/b99900abe935e4ab4857314d647a9068 - - -import argparse -import functools -import os -import re -import socketserver -import webbrowser -from http.server import SimpleHTTPRequestHandler - - -DEFAULT_PORT = 8080 - - -def copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16 * 1024): - """Like shutil.copyfileobj, but only copy a range of the streams. - - Both start and stop are inclusive. - """ - if start is not None: - infile.seek(start) - while 1: - to_read = min(bufsize, stop + 1 - infile.tell() if stop else bufsize) - buf = infile.read(to_read) - if not buf: - break - outfile.write(buf) - - -BYTE_RANGE_RE = re.compile(r"bytes=(\d+)-(\d+)?$") - - -def parse_byte_range(byte_range): - """Returns the two numbers in 'bytes=123-456' or throws ValueError. - - The last number or both numbers may be None. - """ - if byte_range.strip() == "": - return None, None - - m = BYTE_RANGE_RE.match(byte_range) - if not m: - raise ValueError("Invalid byte range %s" % byte_range) - - first, last = [x and int(x) for x in m.groups()] - if last and last < first: - raise ValueError("Invalid byte range %s" % byte_range) - return first, last - - -class RangeRequestHandler(SimpleHTTPRequestHandler): - """Adds support for HTTP 'Range' requests to SimpleHTTPRequestHandler - - The approach is to: - - Override send_head to look for 'Range' and respond appropriately. - - Override copyfile to only transmit a range when requested. - """ - - def handle(self): - try: - SimpleHTTPRequestHandler.handle(self) - except Exception: - # ignored, thrown whenever the client aborts streaming (broken pipe) - pass - - def send_head(self): - if "Range" not in self.headers: - self.range = None - return SimpleHTTPRequestHandler.send_head(self) - try: - self.range = parse_byte_range(self.headers["Range"]) - except ValueError: - self.send_error(400, "Invalid byte range") - return None - first, last = self.range - - # Mirroring SimpleHTTPServer.py here - path = self.translate_path(self.path) - f = None - ctype = self.guess_type(path) - try: - f = open(path, "rb") - except IOError: - self.send_error(404, "File not found") - return None - - fs = os.fstat(f.fileno()) - file_len = fs[6] - if first >= file_len: - self.send_error(416, "Requested Range Not Satisfiable") - return None - - self.send_response(206) - self.send_header("Content-type", ctype) - - if last is None or last >= file_len: - last = file_len - 1 - response_length = last - first + 1 - - self.send_header("Content-Range", "bytes %s-%s/%s" % (first, last, file_len)) - self.send_header("Content-Length", str(response_length)) - self.send_header("Last-Modified", self.date_time_string(fs.st_mtime)) - self.end_headers() - return f - - def end_headers(self): - self.send_header("Accept-Ranges", "bytes") - return SimpleHTTPRequestHandler.end_headers(self) - - def copyfile(self, source, outputfile): - if not self.range: - return SimpleHTTPRequestHandler.copyfile(self, source, outputfile) - - # SimpleHTTPRequestHandler uses shutil.copyfileobj, which doesn't let - # you stop the copying before the end of the file. - start, stop = self.range # set in send_head() - copy_byte_range(source, outputfile, start, stop) - - -class ThreadedTCPServer(socketserver.ThreadingMixIn, socketserver.TCPServer): - allow_reuse_address = True - - -if __name__ == "__main__": - parser = argparse.ArgumentParser( - description="Simple Python Web Server with Range Support" - ) - parser.add_argument( - "--root", - default=os.getcwd(), - help="Root path to serve files from (default: current working directory)", - ) - parser.add_argument( - "--port", - type=int, - default=DEFAULT_PORT, - help=f"Port to listen on (default: {DEFAULT_PORT})", - ) - parser.add_argument( - "--bind", default="0.0.0.0", help="IP address to bind to (default: 0.0.0.0)" - ) - args = parser.parse_args() - - handler = functools.partial(RangeRequestHandler, directory=args.root) - - webbrowser.open(f"http://{args.bind}:{args.port}") - - with ThreadedTCPServer((args.bind, args.port), handler) as httpd: - print( - f"Serving HTTP on {args.bind} port {args.port} (http://{args.bind}:{args.port}/)" - ) - httpd.serve_forever()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastxml/test.xml Tue Jan 09 02:35:52 2024 +0000 @@ -0,0 +1,138 @@ +<?xml version="1.0"?> +<root> + <metadata> + <genomes> + <genome>test-data/merlin.fa</genome> + </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>40</trackPadding> + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>false</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> + </metadata> + <tracks> + <track cat="Blah" format="blast"> + <files> + <trackFile path="test-data/blastxml/blast.xml" ext="blastxml" label="BlastP"/> + </files> + + <options> + <style> + <className>feature</className> + <description></description> + <label>Description</label> + <height>400px</height> + </style> + <blast> + <parent>test-data/blastxml/merlin.gff</parent> + <protein>true</protein> + <min_gap>10</min_gap> + </blast> + <scaling> + <method>score</method> + <algo>blast</algo> + <scales> + <type>__auto__</type> + </scales> + <scheme> + <type>opacity</type> + <color>__auto__</color> + </scheme> + </scaling> + </options> + </track> + <track cat="Blah" format="blast"> + <files> + <trackFile path="test-data/blastxml/blast.xml" ext="blastxml" label="BlastP, min_gap=3"/> + </files> + + <options> + <style> + <className>feature</className> + <description></description> + <label>Description</label> + <height>400px</height> + </style> + <blast> + <parent>test-data/blastxml/merlin.gff</parent> + <protein>true</protein> + <min_gap>3</min_gap> + </blast> + <scaling> + <method>score</method> + <algo>blast</algo> + <scales> + <type>__auto__</type> + </scales> + <scheme> + <type>opacity</type> + <color>__auto__</color> + </scheme> + </scaling> + </options> + </track> + + <track cat="Blah" format="blast"> + <files> + <trackFile path="test-data/blastxml/blast-gene1.xml" ext="blastxml" label="Non protein match/matchpart"/> + </files> + + <options> + <style> + <className>feature</className> + <description></description> + <label>Description</label> + <height>400px</height> + </style> + <blast> + <parent>test-data/blastxml/merlin.gff</parent> + <min_gap>3</min_gap> + </blast> + <scaling> + <method>ignore</method> + <algo>linear</algo> + <scheme> + <type>opacity</type> + <color>__auto__</color> + </scheme> + </scaling> + </options> + </track> + + <track cat="Blah" format="blast"> + <files> + <trackFile path="test-data/blastxml/blastn-gene1.xml" ext="blastxml" label="Non protein match/matchpart, no parent"/> + </files> + + <options> + <style> + <className>feature</className> + <description></description> + <label>Description</label> + <height>400px</height> + </style> + <blast> + <min_gap>40</min_gap> + </blast> + <scaling> + <method>score</method> + <algo>blast</algo> + <scales> + <type>__auto__</type> + </scales> + <scheme> + <type>opacity</type> + <color>__auto__</color> + </scheme> + </scaling> + </options> + </track> + + </tracks> +</root>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bw/test.xml Tue Jan 09 02:35:52 2024 +0000 @@ -0,0 +1,149 @@ +<?xml version="1.0"?> +<root> + <metadata> + <genomes> + <genome>test-data/merlin.fa</genome> + </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>40</trackPadding> + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>false</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> + </metadata> + <tracks> + <track cat="Scaling" format="wiggle"> + <files> + <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Auto Global"/> + </files> + + <options> + <wiggle> + <type>JBrowse/View/Track/Wiggle/XYPlot</type> + <variance_band>true</variance_band> + <autoscale>global</autoscale> + <color_pos>__auto__</color_pos> + <color_neg>__auto__</color_neg> + <bicolor_pivot>zero</bicolor_pivot> + <scale>linear</scale> + </wiggle> + </options> + </track> + <track cat="Scaling" format="wiggle"> + <files> + <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Auto Local"/> + </files> + + <options> + <wiggle> + <type>JBrowse/View/Track/Wiggle/XYPlot</type> + <variance_band>true</variance_band> + <autoscale>local</autoscale> + <color_pos>__auto__</color_pos> + <color_neg>__auto__</color_neg> + <bicolor_pivot>zero</bicolor_pivot> + <scale>linear</scale> + </wiggle> + </options> + </track> + <track cat="Scaling" format="wiggle"> + <files> + <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Manual"/> + </files> + + <options> + <wiggle> + <type>JBrowse/View/Track/Wiggle/XYPlot</type> + <variance_band>false</variance_band> + <autoscale>fixed</autoscale> + <min>20</min> + <max>60</max> + <color_pos>__auto__</color_pos> + <color_neg>__auto__</color_neg> + <bicolor_pivot>zero</bicolor_pivot> + <scale>linear</scale> + </wiggle> + </options> + </track> + + + <track cat="Colouring" format="wiggle"> + <files> + <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Auto A"/> + <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Auto B"/> + </files> + + <options> + <wiggle> + <type>JBrowse/View/Track/Wiggle/XYPlot</type> + <variance_band>false</variance_band> + <autoscale>local</autoscale> + + <color_pos>__auto__</color_pos> + <color_neg>__auto__</color_neg> + <bicolor_pivot>mean</bicolor_pivot> + <scale>linear</scale> + </wiggle> + </options> + </track> + <track cat="Colouring" format="wiggle"> + <files> + <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Manual"/> + </files> + + <options> + <wiggle> + <type>JBrowse/View/Track/Wiggle/XYPlot</type> + <variance_band>false</variance_band> + <autoscale>local</autoscale> + + <color_pos>#0000ff</color_pos> + <color_neg>#ff0000</color_neg> + <bicolor_pivot>mean</bicolor_pivot> + <scale>linear</scale> + </wiggle> + </options> + </track> + <track cat="Colouring" format="wiggle"> + <files> + <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Manual - Inverted"/> + </files> + + <options> + <wiggle> + <type>JBrowse/View/Track/Wiggle/XYPlot</type> + <variance_band>false</variance_band> + <autoscale>local</autoscale> + + <color_pos>#ff0000</color_pos> + <color_neg>#0000ff</color_neg> + <bicolor_pivot>mean</bicolor_pivot> + <scale>log</scale> + </wiggle> + </options> + </track> + <track cat="Colouring" format="wiggle"> + <files> + <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Nonstandard Pivot"/> + </files> + + <options> + <wiggle> + <type>JBrowse/View/Track/Wiggle/XYPlot</type> + <variance_band>false</variance_band> + <autoscale>local</autoscale> + + <color_pos>#0000ff</color_pos> + <color_neg>#ff0000</color_neg> + <bicolor_pivot>100</bicolor_pivot> + <scale>linear</scale> + </wiggle> + </options> + </track> + </tracks> +</root>
--- a/test-data/index.html Mon Jan 08 09:23:19 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,112 +0,0 @@ -<!DOCTYPE html> -<html> - <head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> - <title>JBrowse</title> - <link rel="stylesheet" type="text/css" href="css/genome.css"> -</head> -<body> - - <script type="text/javascript"> - // jshint unused: false - var dojoConfig = { - async: true, - baseUrl: './src', - has: { - 'host-node': false // Prevent dojo from being fooled by Electron - } - }; - // Move Electron's require out before loading Dojo - if(window.process&&process.versions&&process.versions.electron) { - window.electronRequire = require; - delete window.require; - } - </script> - <script type="text/javascript" src="src/dojo/dojo.js"></script> - <script type="text/javascript" src="src/JBrowse/init.js"></script> - <script type="text/javascript"> - window.onerror=function(msg){ - if( document.body ) - document.body.setAttribute("JSError",msg); - } - - // puts the main Browser object in this for convenience. feel - // free to move it into function scope if you want to keep it - // out of the global namespace - var JBrowse; - require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ], - function (Browser,ioQuery,JSON) { - // the initial configuration of this JBrowse - // instance - - // NOTE: this initial config is the same as any - // other JBrowse config in any other file. this - // one just sets defaults from URL query params. - // If you are embedding JBrowse in some other app, - // you might as well just set this initial config - // to something like { include: '../my/dynamic/conf.json' }, - // or you could put the entire - // dynamically-generated JBrowse config here. - - // parse the query vars in the page URL - var queryParams = ioQuery.queryToObject( window.location.search.slice(1) ); - - var config = { - containerID: "GenomeBrowser", - - dataRoot: queryParams.data, - queryParams: queryParams, - location: queryParams.loc, - forceTracks: queryParams.tracks, - initialHighlight: queryParams.highlight, - show_nav: queryParams.nav, - show_tracklist: queryParams.tracklist, - show_overview: queryParams.overview, - show_menu: queryParams.menu, - show_tracklabels: queryParams.tracklabels, - highResolutionMode: queryParams.highres, - stores: { url: { type: "JBrowse/Store/SeqFeature/FromConfig", features: [] } }, - makeFullViewURL: function( browser ) { - - // the URL for the 'Full view' link - // in embedded mode should be the current - // view URL, except with 'nav', 'tracklist', - // and 'overview' parameters forced to 1. - - return browser.makeCurrentViewURL({ nav: 1, tracklist: 1, overview: 1 }); - }, - updateBrowserURL: true - }; - - //if there is ?addFeatures in the query params, - //define a store for data from the URL - if( queryParams.addFeatures ) { - config.stores.url.features = JSON.parse( queryParams.addFeatures ); - } - - // if there is ?addTracks in the query params, add - // those track configurations to our initial - // configuration - if( queryParams.addTracks ) { - config.tracks = JSON.parse( queryParams.addTracks ); - } - - // if there is ?addStores in the query params, add - // those store configurations to our initial - // configuration - if( queryParams.addStores ) { - config.stores = JSON.parse( queryParams.addStores ); - } - - // create a JBrowse global variable holding the JBrowse instance - JBrowse = new Browser( config ); - }); - </script> - - </head> - - <body> - <div id="GenomeBrowser" style="height: 100%; width: 100%; padding: 0; border: 0;"></div> - <div style="display: none">JBrowseDefaultMainPage</div> - </body> -</html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf/test.xml Tue Jan 09 02:35:52 2024 +0000 @@ -0,0 +1,28 @@ +<?xml version="1.0"?> +<root> + <metadata> + <genomes> + <genome>test-data/merlin.fa</genome> + </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>40</trackPadding> + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>false</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> + </metadata> + <tracks> + <track cat="Default" format="vcf"> + <files> + <trackFile path="test-data/vcf/test.vcf" ext="vcf" label="Basic"/> + </files> + <options> + </options> + </track> + </tracks> +</root>
--- a/tool_data_table_conf.xml.sample Mon Jan 08 09:23:19 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -<tables> - <!-- Locations of all fasta files under genome directory --> - <table name="all_fasta" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/all_fasta.loc" /> - </table> -</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/webserver.py Tue Jan 09 02:35:52 2024 +0000 @@ -0,0 +1,159 @@ +#!/usr/bin/env python3 + +# spec: simplest python web server with range support and multithreading that takes root path, +# port and bind address as command line arguments; by default uses the current dir as webroot, +# port 8000 and bind address of 0.0.0.0 +# borrowed from https://github.com/danvk/RangeHTTPServer +# and reborrowed from https://gist.github.com/glowinthedark/b99900abe935e4ab4857314d647a9068 + + +import argparse +import functools +import os +import re +import socketserver +import webbrowser +from http.server import SimpleHTTPRequestHandler + + +DEFAULT_PORT = 8080 + + +def copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16 * 1024): + """Like shutil.copyfileobj, but only copy a range of the streams. + + Both start and stop are inclusive. + """ + if start is not None: + infile.seek(start) + while 1: + to_read = min(bufsize, stop + 1 - infile.tell() if stop else bufsize) + buf = infile.read(to_read) + if not buf: + break + outfile.write(buf) + + +BYTE_RANGE_RE = re.compile(r"bytes=(\d+)-(\d+)?$") + + +def parse_byte_range(byte_range): + """Returns the two numbers in 'bytes=123-456' or throws ValueError. + + The last number or both numbers may be None. + """ + if byte_range.strip() == "": + return None, None + + m = BYTE_RANGE_RE.match(byte_range) + if not m: + raise ValueError("Invalid byte range %s" % byte_range) + + first, last = [x and int(x) for x in m.groups()] + if last and last < first: + raise ValueError("Invalid byte range %s" % byte_range) + return first, last + + +class RangeRequestHandler(SimpleHTTPRequestHandler): + """Adds support for HTTP 'Range' requests to SimpleHTTPRequestHandler + + The approach is to: + - Override send_head to look for 'Range' and respond appropriately. + - Override copyfile to only transmit a range when requested. + """ + + def handle(self): + try: + SimpleHTTPRequestHandler.handle(self) + except Exception: + # ignored, thrown whenever the client aborts streaming (broken pipe) + pass + + def send_head(self): + if "Range" not in self.headers: + self.range = None + return SimpleHTTPRequestHandler.send_head(self) + try: + self.range = parse_byte_range(self.headers["Range"]) + except ValueError: + self.send_error(400, "Invalid byte range") + return None + first, last = self.range + + # Mirroring SimpleHTTPServer.py here + path = self.translate_path(self.path) + f = None + ctype = self.guess_type(path) + try: + f = open(path, "rb") + except IOError: + self.send_error(404, "File not found") + return None + + fs = os.fstat(f.fileno()) + file_len = fs[6] + if first >= file_len: + self.send_error(416, "Requested Range Not Satisfiable") + return None + + self.send_response(206) + self.send_header("Content-type", ctype) + + if last is None or last >= file_len: + last = file_len - 1 + response_length = last - first + 1 + + self.send_header("Content-Range", "bytes %s-%s/%s" % (first, last, file_len)) + self.send_header("Content-Length", str(response_length)) + self.send_header("Last-Modified", self.date_time_string(fs.st_mtime)) + self.end_headers() + return f + + def end_headers(self): + self.send_header("Accept-Ranges", "bytes") + return SimpleHTTPRequestHandler.end_headers(self) + + def copyfile(self, source, outputfile): + if not self.range: + return SimpleHTTPRequestHandler.copyfile(self, source, outputfile) + + # SimpleHTTPRequestHandler uses shutil.copyfileobj, which doesn't let + # you stop the copying before the end of the file. + start, stop = self.range # set in send_head() + copy_byte_range(source, outputfile, start, stop) + + +class ThreadedTCPServer(socketserver.ThreadingMixIn, socketserver.TCPServer): + allow_reuse_address = True + + +if __name__ == "__main__": + parser = argparse.ArgumentParser( + description="Simple Python Web Server with Range Support" + ) + parser.add_argument( + "--root", + default=os.getcwd(), + help="Root path to serve files from (default: current working directory)", + ) + parser.add_argument( + "--port", + type=int, + default=DEFAULT_PORT, + help=f"Port to listen on (default: {DEFAULT_PORT})", + ) + parser.add_argument( + "--bind", default="0.0.0.0", help="IP address to bind to (default: 0.0.0.0)" + ) + args = parser.parse_args() + + handler = functools.partial(RangeRequestHandler, directory=args.root) + + webbrowser.open(f"http://{args.bind}:{args.port}") + + with ThreadedTCPServer((args.bind, args.port), handler) as httpd: + print( + f"Serving HTTP on {args.bind} port {args.port} (http://{args.bind}:{args.port}/)" + ) + httpd.serve_forever()