Forgot to add arxiv2bib + Now using argparse

arxiv2bib.py

@@ -0,0 +1,412 @@
+#! /usr/bin/env python
+#
+# Copyright (c) 2012, Nathan Grigg
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+#   notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+#   notice, this list of conditions and the following disclaimer in the
+#   documentation and/or other materials provided with the distribution.
+# * Neither the name of this package nor the
+#   names of its contributors may be used to endorse or promote products
+#   derived from this software without specific prior written permission.
+#
+# This software is provided by the copyright holders and contributors "as
+# is" and any express or implied warranties, including, but not limited
+# to, the implied warranties of merchantability and fitness for a
+# particular purpose are disclaimed. In no event shall Nathan Grigg be
+# liable for any direct, indirect, incidental, special, exemplary, or
+# consequential damages (including, but not limited to, procurement of
+# substitute goods or services; loss of use, data, or profits; or business
+# interruption) however caused and on any theory of liability, whether in
+# contract, strict liability, or tort (including negligence or otherwise)
+# arising in any way out of the use of this software, even if advised of
+# the possibility of such damage.
+#
+# (also known as the New BSD License)
+#
+# Indiscriminate automated downloads from arXiv.org are not permitted.
+# For more information, see http://arxiv.org/help/robots
+#
+# This script usually makes only one call to arxiv.org per run.
+# No caching of any kind is performed.
+
+from __future__ import print_function
+from xml.etree import ElementTree
+import sys
+import re
+import os
+
+if sys.version_info < (2, 6):
+    raise Exception("Python 2.6 or higher required")
+
+# Python 2 compatibility code
+PY2 = sys.version_info[0] == 2
+if not PY2:
+    from urllib.parse import urlencode
+    from urllib.request import urlopen
+    from urllib.error import HTTPError
+    print_bytes = lambda s: sys.stdout.buffer.write(s)
+else:
+    from urllib import urlencode
+    from urllib2 import HTTPError, urlopen
+    print_bytes = lambda s: sys.stdout.write(s)
+
+
+# Namespaces
+ATOM = '{http://www.w3.org/2005/Atom}'
+ARXIV = '{http://arxiv.org/schemas/atom}'
+
+# regular expressions to check if arxiv id is valid
+NEW_STYLE = re.compile(r'^\d{4}\.\d{4}(v\d+)?$')
+OLD_STYLE = re.compile(r"""(?x)
+^(
+   math-ph
+  |hep-ph
+  |nucl-ex
+  |nucl-th
+  |gr-qc
+  |astro-ph
+  |hep-lat
+  |quant-ph
+  |hep-ex
+  |hep-th
+  |stat
+    (\.(AP|CO|ML|ME|TH))?
+  |q-bio
+    (\.(BM|CB|GN|MN|NC|OT|PE|QM|SC|TO))?
+  |cond-mat
+    (\.(dis-nn|mes-hall|mtrl-sci|other|soft|stat-mech|str-el|supr-con))?
+  |cs
+    (\.(AR|AI|CL|CC|CE|CG|GT|CV|CY|CR|DS|DB|DL|DM|DC|GL|GR|HC|IR|IT|LG|LO|
+      MS|MA|MM|NI|NE|NA|OS|OH|PF|PL|RO|SE|SD|SC))?
+  |nlin
+    (\.(AO|CG|CD|SI|PS))?
+  |physics
+    (\.(acc-ph|ao-ph|atom-ph|atm-clus|bio-ph|chem-ph|class-ph|comp-ph|
+      data-an|flu-dyn|gen-ph|geo-ph|hist-ph|ins-det|med-ph|optics|ed-ph|
+      soc-ph|plasm-ph|pop-ph|space-ph))?
+  |math
+      (\.(AG|AT|AP|CT|CA|CO|AC|CV|DG|DS|FA|GM|GN|GT|GR|HO|IT|KT|LO|MP|MG
+      |NT|NA|OA|OC|PR|QA|RT|RA|SP|ST|SG))?
+)/\d{7}(v\d+)?$""")
+
+
+def is_valid(arxiv_id):
+    """Checks if id resembles a valid arxiv identifier."""
+    return bool(NEW_STYLE.match(arxiv_id)) or bool(OLD_STYLE.match(arxiv_id))
+
+
+class FatalError(Exception):
+    """Error that prevents us from continuing"""
+
+
+class NotFoundError(Exception):
+    """Reference not found by the arxiv API"""
+
+
+class Reference(object):
+    """Represents a single reference.
+
+    Instantiate using Reference(entry_xml). Note entry_xml should be
+    an ElementTree.Element object.
+    """
+    def __init__(self, entry_xml):
+        self.xml = entry_xml
+        self.url = self._field_text('id')
+        self.id = self._id()
+        self.authors = self._authors()
+        self.title = self._field_text('title')
+        if len(self.id) == 0 or len(self.authors) == 0 or len(self.title) == 0:
+            raise NotFoundError("No such publication", self.id)
+        self.summary = self._field_text('summary')
+        self.category = self._category()
+        self.year, self.month = self._published()
+        self.updated = self._field_text('updated')
+        self.bare_id = self.id[:self.id.rfind('v')]
+        self.note = self._field_text('journal_ref', namespace=ARXIV)
+
+    def _authors(self):
+        """Extracts author names from xml."""
+        xml_list = self.xml.findall(ATOM + 'author/' + ATOM + 'name')
+        return [field.text for field in xml_list]
+
+    def _field_text(self, id, namespace=ATOM):
+        """Extracts text from arbitrary xml field"""
+        try:
+            return self.xml.find(namespace + id).text.strip()
+        except:
+            return ""
+
+    def _category(self):
+        """Get category"""
+        try:
+            return self.xml.find(ARXIV + 'primary_category').attrib['term']
+        except:
+            return ""
+
+    def _id(self):
+        """Get arxiv id"""
+        try:
+            id_url = self._field_text('id')
+            return id_url[id_url.find('/abs/') + 5:]
+        except:
+            return ""
+
+    def _published(self):
+        """Get published date"""
+        published = self._field_text('published')
+        if len(published) < 7:
+            return "", ""
+        y, m = published[:4], published[5:7]
+        try:
+            m = ["Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul",
+                 "Aug", "Sep", "Nov", "Dec"][int(m) - 1]
+        except:
+            pass
+        return y, m
+
+    def bibtex(self):
+        """BibTex string of the reference."""
+
+        lines = ["@article{" + self.id]
+        for k, v in [("Author", " and ".join(self.authors)),
+                     ("Title", self.title),
+                     ("Eprint", self.id),
+                     ("ArchivePrefix", "arXiv"),
+                     ("PrimaryClass", self.category),
+                     ("Abstract", self.summary),
+                     ("Year", self.year),
+                     ("Month", self.month),
+                     ("Note", self.note),
+                     ("Url", self.url),
+                     ("File", self.id + ".pdf"),
+                    ]:
+            if len(v):
+                lines.append("%-13s = {%s}" % (k, v))
+
+        return ("," + os.linesep).join(lines) + os.linesep + "}"
+
+
+class ReferenceErrorInfo(object):
+    """Contains information about a reference error"""
+    def __init__(self, message, id):
+        self.message = message
+        self.id = id
+        self.bare_id = id[:id.rfind('v')]
+        # mark it as really old, so it gets superseded if possible
+        self.updated = '0'
+
+    def bibtex(self):
+        """BibTeX comment explaining error"""
+        return "@comment{%(id)s: %(message)s}" % \
+                {'id': self.id, 'message': self.message}
+
+    def __str__(self):
+        return "Error: %(message)s (%(id)s)" % \
+                {'id': self.id, 'message': self.message}
+
+
+def arxiv2bib(id_list):
+    """Returns a list of references, corresponding to elts of id_list"""
+    d = arxiv2bib_dict(id_list)
+    l = []
+    for id in id_list:
+        try:
+            l.append(d[id])
+        except:
+            l.append(ReferenceErrorInfo("Not found", id))
+
+    return l
+
+
+def arxiv_request(ids):
+    """Sends a request to the arxiv API."""
+    q = urlencode([
+         ("id_list", ",".join(ids)),
+         ("max_results", len(ids))
+         ])
+    xml = urlopen("http://export.arxiv.org/api/query?" + q)
+    # xml.read() returns bytes, but ElementTree.fromstring decodes
+    # to unicode when needed (python2) or string (python3)
+    return ElementTree.fromstring(xml.read())
+
+
+def arxiv2bib_dict(id_list):
+    """Fetches citations for ids in id_list into a dictionary indexed by id"""
+    ids = []
+    d = {}
+
+    # validate ids
+    for id in id_list:
+        if is_valid(id):
+            ids.append(id)
+        else:
+            d[id] = ReferenceErrorInfo("Invalid arXiv identifier", id)
+
+    if len(ids) == 0:
+        return d
+
+    # make the api call
+    while True:
+        xml = arxiv_request(ids)
+
+        # check for error
+        entries = xml.findall(ATOM + "entry")
+        try:
+            first_title = entries[0].find(ATOM + "title")
+        except:
+            raise FatalError("Unable to connect to arXiv.org API.")
+
+        if first_title is None or first_title.text.strip() != "Error":
+            break
+
+        try:
+            id = entries[0].find(ATOM + "summary").text.split()[-1]
+            del(ids[ids.index(id)])
+        except:
+            raise FatalError("Unable to parse an error returned by arXiv.org.")
+
+    # Parse each reference and store it in dictionary
+    for entry in entries:
+        try:
+            ref = Reference(entry)
+        except NotFoundError as error:
+            message, id = error.args
+            ref = ReferenceErrorInfo(message, id)
+        if ref.id:
+            d[ref.id] = ref
+        if ref.bare_id:
+            if not (ref.bare_id in d) or d[ref.bare_id].updated < ref.updated:
+                d[ref.bare_id] = ref
+
+    return d
+
+
+class Cli(object):
+    """Command line interface"""
+
+    def __init__(self, args=None):
+        """Parse arguments"""
+        self.args = self.parse_args(args)
+
+        if len(self.args.id) == 0:
+            self.args.id = [line.strip() for line in sys.stdin]
+
+        # avoid duplicate error messages unless verbose is set
+        if self.args.comments and not self.args.verbose:
+            self.args.quiet = True
+
+        self.output = []
+        self.messages = []
+        self.error_count = 0
+        self.code = 0
+
+    def run(self):
+        """Produce output and error messages"""
+        try:
+            bib = arxiv2bib(self.args.id)
+        except HTTPError as error:
+            if error.getcode() == 403:
+                raise FatalError("""\
+    403 Forbidden error. This usually happens when you make many
+    rapid fire requests in a row. If you continue to do this, arXiv.org may
+    interpret your requests as a denial of service attack.
+
+    For more information, see http://arxiv.org/help/robots.
+    """)
+            else:
+                raise FatalError(
+                  "HTTP Connection Error: {0}".format(error.getcode()))
+
+        self.create_output(bib)
+        self.code = self.tally_errors(bib)
+
+    def create_output(self, bib):
+        """Format the output and error messages"""
+        for b in bib:
+            if isinstance(b, ReferenceErrorInfo):
+                self.error_count += 1
+                if self.args.comments:
+                    self.output.append(b.bibtex())
+                if not self.args.quiet:
+                    self.messages.append(str(b))
+            else:
+                self.output.append(b.bibtex())
+
+    def print_output(self):
+        if not self.output:
+            return
+
+        output_string = os.linesep.join(self.output)
+        try:
+            print(output_string)
+        except UnicodeEncodeError:
+            print_bytes((output_string + os.linesep).encode('utf-8'))
+            if self.args.verbose:
+                self.messages.append(
+                  'Could not use system encoding; using utf-8')
+
+    def tally_errors(self, bib):
+        """calculate error code"""
+        if self.error_count == len(self.args.id):
+            self.messages.append("No successful matches")
+            return 2
+        elif self.error_count > 0:
+            self.messages.append("%s of %s matched succesfully" %
+              (len(bib) - self.error_count, len(bib)))
+            return 1
+        else:
+            return 0
+
+    def print_messages(self):
+        """print messages to stderr"""
+        if self.messages:
+            self.messages.append("")
+            sys.stderr.write(os.linesep.join(self.messages))
+
+    @staticmethod
+    def parse_args(args):
+        try:
+            import argparse
+        except:
+            sys.exit("Cannot load required module 'argparse'")
+
+        parser = argparse.ArgumentParser(
+          description="Get the BibTeX for each arXiv id.",
+          epilog="""\
+    Returns 0 on success, 1 on partial failure, 2 on total failure.
+    Valid BibTeX is written to stdout, error messages to stderr.
+    If no arguments are given, ids are read from stdin, one per line.""",
+          formatter_class=argparse.RawDescriptionHelpFormatter)
+        parser.add_argument('id', metavar='arxiv_id', nargs="*",
+          help="arxiv identifier, such as 1201.1213")
+        parser.add_argument('-c', '--comments', action='store_true',
+          help="Include @comment fields with error details")
+        parser.add_argument('-q', '--quiet', action='store_true',
+          help="Display fewer error messages")
+        parser.add_argument('-v', '--verbose', action="store_true",
+          help="Display more error messages")
+        return parser.parse_args(args)
+
+
+def main(args=None):
+    """Run the command line interface"""
+    cli = Cli(args)
+    try:
+        cli.run()
+    except FatalError as err:
+        sys.stderr.write(err.args[0] + os.linesep)
+        return 2
+
+    cli.print_output()
+    cli.print_messages()
+    return cli.code
+
+
+if __name__ == "__main__":
+    sys.exit(main())

main.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python2
 # -*- coding: utf8 -*-
 
+import argparse
 import os
 import shutil
 import subprocess
@@ -247,72 +248,96 @@ def resync():
 
 
 if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description="A bibliography " +
+                                     "management tool.")
+    subparsers = parser.add_subparsers(help="sub-command help")
+
+    parser_download = subparsers.add_parser('download', help="download help")
+    parser_download.add_argument('-t', '--type', default=None,
+                                 choices=['article', 'book'],
+                                 help="Type of the file to download")
+    parser_download.add_argument('url',  nargs='+',
+                                 help="url of the file to import")
+    parser_download.set_defaults(func='download')
+
+    parser_import = subparsers.add_parser('import', help="import help")
+    parser_import.add_argument('-t', '--type', default=None,
+                               choices=['article', 'book'],
+                               help="Type of the file to import")
+    parser_import.add_argument('file',  nargs='+',
+                               help="path to the file to import")
+    parser_import.set_defaults(func='import')
+
+    parser_delete = subparsers.add_parser('delete', help="delete help")
+    parser_delete.add_argument('files', metavar='entry', nargs='+',
+                               help="a filename or an identifier")
+    parser_delete.set_defaults(func='delete')
+
+    parser_list = subparsers.add_parser('list', help="list help")
+    parser_list.set_defaults(func='list')
+    # TODO
+
+    parser_search = subparsers.add_parser('search', help="search help")
+    parser_search.set_defaults(func='search')
+    # TODO
+
+    parser_open = subparsers.add_parser('open', help="open help")
+    parser_open.add_argument('ids', metavar='id',  nargs='+',
+                             help="an identifier")
+    parser_open.set_defaults(func='open')
+
+    parser_resync = subparsers.add_parser('resync', help="resync help")
+    parser_resync.set_defaults(func='resync')
+
+    args = parser.parse_args()
     try:
-        if len(sys.argv) < 2:
+        if args.func == 'download':
-            sys.exit("Usage: TODO")
+            for url in args.url:
-
+                new_name = downloadFile(url, args.t)
-        if sys.argv[1] == 'download':
+                if new_name is not False:
-            if len(sys.argv) < 3:
+                    print(url+" successfully imported as "+new_name)
-                sys.exit("Usage: " + sys.argv[0] +
+                else:
-                         " download FILE [article|book]")
+                    tools.warning("An error occurred while downloading "+url)
-
-            filetype = None
-            if len(sys.argv) > 3 and sys.argv[3] in ["article", "book"]:
-                filetype = sys.argv[3].lower()
-
-            new_name = downloadFile(sys.argv[2], filetype)
-            if new_name is not False:
-                print(sys.argv[2]+" successfully imported as "+new_name)
             sys.exit()
 
-        if sys.argv[1] == 'import':
+        if args.func == 'import':
-            if len(sys.argv) < 3:
+            for filename in args.file:
-                sys.exit("Usage: " + sys.argv[0] +
+                new_name = addFile(filename, args.t)
-                         " import FILE [article|book]")
+                if new_name is not False:
-
+                    print(sys.argv[2]+" successfully imported as " +
-            filetype = None
+                          new_name+".")
-            if len(sys.argv) > 3 and sys.argv[3] in ["article", "book"]:
+                else:
-                filetype = sys.argv[3].lower()
+                    tools.warning("An error occurred while importing " +
-
+                                  filename)
-            new_name = addFile(sys.argv[2], filetype)
-            if new_name is not False:
-                print(sys.argv[2]+" successfully imported as "+new_name+".")
             sys.exit()
 
-        elif sys.argv[1] == 'delete':
+        elif args.func == 'delete':
-            if len(sys.argv) < 3:
+            for filename in args.file:
-                sys.exit("Usage: " + sys.argv[0] + " delete FILE|ID")
+                confirm = tools.rawInput("Are you sure you want to delete " +
+                                         filename+"? [y/N] ")
 
-            confirm = tools.rawInput("Are you sure you want to delete " +
+                if confirm.lower() == 'y':
-                                     sys.argv[2]+"? [y/N] ")
+                    if not backend.deleteId(filename):
+                        if not backend.deleteFile(filename):
+                            tools.warning("Unable to delete "+filename)
+                            sys.exit(1)
 
-            if confirm.lower() == 'y':
+                    print(filename+" successfully deleted.")
-                if not backend.deleteId(sys.argv[2]):
-                    if not backend.deleteFile(sys.argv[2]):
-                        tools.warning("Unable to delete "+sys.argv[2])
-                        sys.exit(1)
-
-                print(sys.argv[2]+" successfully deleted.")
             sys.exit()
 
-        elif sys.argv[1] == 'list':
+        elif args.func == 'list':
             raise Exception('TODO')
 
-        elif sys.argv[1] == 'search':
+        elif args.func == 'search':
             raise Exception('TODO')
 
-        elif sys.argv[1] == 'open':
+        elif args.func == 'open':
-            if len(sys.argv) < 3:
+            for filename in args.ids:
-                sys.exit("Usage: " + sys.argv[0] +
-                         " open ID1 ID2 …")
-            for filename in sys.argv[2:]:
                 if not openFile(filename):
                     sys.exit("Unable to open file associated " +
-                            "to ident "+filename)
+                             "to ident "+filename)
 
-        elif sys.argv[1] == 'resync':
+        elif args.func == 'resync':
-            if len(sys.argv) > 2 and sys.argv[2] == 'help':
-                sys.exit("Usage: " + sys.argv[0] + " resync")
             confirm = tools.rawInput("Resync files and bibtex index? [y/N] ")
             if confirm.lower() == 'y':
                 resync()