xapers - Online in the Cloud

PROGRAM:

NAME

xapers - personal journal article indexing system

SYNOPSIS

xapers command [args ...]

DESCRIPTION

Xapers is a personal document indexing system, geared towards academic journal articles.
It provides fast search of document text and bibliographic data (synced from online
libraries) and simple document and bibtex retrieval.

Xapers takes as input document files (as PDF) and source identifiers. Documents are
copied into a local document store (~/.xapers/docs by default) and text is extracted from
the PDF and fully indexed into a Xapian database. Source identifiers are used to download
document bibliographic data from online digital libraries (see SOURCES below), which are
then parsed and indexed to prefixed terms in the database. The bibliographic data is also
stored as bibtex in the document store for easy retrieval. Documents can be arbitrarily
tagged.

A curses UI is provided for simple access to documents (see the view command below).
Xapers is ultimately a document indexing library, though, so development of alternate user
interfaces is encouraged.

Underlying Xapers is the wonderful Xapian database/search engine. See http://xapian.org/
for more information.

MAIN COMMANDS

The following are the main xapers commands. See SEARCH TERMS below for details of the
supported syntax for <search-terms>.

add [options] [<search-terms>]
Add a document, or update an existing document. Must specify at least one of --file or
--source. If search terms are provided they must match exactly one document and the
matching document is updated with the newly provided information. Available options:

--source=[<sid>|<file>]
Source identifier for document. See SOURCES below. This may also be a path to a
file that contains a single bibtex entry.

--file[=<file>]
Document file (as PDF) to add. Text of document will be extracted and indexed. A
copy of the file will be placed in the Xapers document store. If provided without
path, xapers will attempt to download file from source, assuming source supports
file downloads.

--tags=<tag>[,...]
Initial tags to apply to document. Multiple tags can be specified, comma
separated.

--prompt
Prompt user for source/file/tags, if not specified. When prompting for source
information input files are automatically scanned for source IDs and found ids are
displayed.

--view
View resulting entry in curses UI when done. See the viewP command below for more
info.

import [options] <bibtex>
Import an existing bibtex database. Each bibtex entry will be added as a new document.
If bibtex key, or any sources found in bibtex, match an existing document, that document
is instead updated (this makes the command effectively idempotent). Any "file" fields
will be parsed for document files to add. Files can be specified as a single path, or in
Mendeley/Jabref format. Available options:

--tags=<tag>[,...]
Tags to apply to all imported documents. Multiple tags can be specified, comma
separated.

tag +<tag>|-<tag> [...] [--] <search-terms>
Add/remove tags from documents. '--' can be used to separate tagging operations from
search terms.

search [options] <search-terms>
Search for documents in the database. Document information is printed to stdout.

--output=[summary|bibtex|tags|sources|keys|files]

Specify document information to be output:

summary outputs a single-line summary of the documents (default).

bibtex outputs bibtex for all documents (if available).

tags outputs all tags associated with documents.

sources outputs all sources associated with documents.

keys outputs all bibtex citation keys associated with documents.

files outputs the full paths to all files associated with documents.

Default is summary.

--limit=N

Limit number of results returned to N.

bibtex <search-terms>
Short for "search --output=bibtex <search-terms>".

count <search-terms>
Return a simple count of search results.

view [<search-terms>]
show [<search-terms>]
View search results in curses search UI. Documents matching search are displayed with
their bibliographic information and a short text summary. It allows for manipulating
document tags and for retrieved for document files and source URLs for viewing (see xdg-
open(1) for more info). Initial search terms can be provided, but further searches can be
performed from within the UI. While in the UI type "?" for available commands.

NOTE: At the moment only the top 20 search results are displayed, due to synchronous
loading restrictions. This obviously needs to be fixed.

export <directory> <search-terms>
Copy PDF files of resulting documents into <directory>, named with document titles when
available.

delete <search-terms>
Delete documents from the database. All document files will purged from the document
store.

--noprompt
Do not prompt to confirm deletion of documents.

restore
Restore a database from existing xapers root.

SOURCE COMMANDS

These commands provide access to some of the source module methods. See SOURCES below.

sources
List available sources.

source2url <sid> [<sid>...]
Parse a source identifier string and print the corresponding source URL.

source2bib <sid> [<sid>...]
Retrieve bibtex from source for a specified URL or source id, and write to stdout.

source2file <sid>
Retrieve file from source for a specified URL or source id, and write to stdout.

scandoc <file>
Scan a document file (PDF) for source IDs, and print and recognized source ids to stdout.

SOURCES

Sources are online databases from which document bibliographic data can be retrieved. In
Xapers, online libraries are assigned unique prefixes. The online libraries associate
unique document identifiers to individual documents. See 'xapers sources' for a list of
available online sources.

Xapers recognizes document a source identifier, or sid, in two forms:

full URL http://dx.doi.org/10.1364/JOSAA.29.002092
sid of form <source>:<id> doi:10.1364/JOSAA.29.002092

URLs are parsed into sources and source ids when recognized, and this information is used
to retrieve bibtex from the online library databases. The sources and sids for a given
document are stored as prefixed terms in the Xapers database (see below).

SEARCH TERMS

Xapers supports a common syntax for search terms.

Search can consist of free-form text and quoted phrases. Terms can be combined with
standard Boolean operators. All terms are combined with a logical OR by default.
Parentheses can be used to group operators, but must be protect from shell interpretation.
The string '*' will match all documents in the database.

Additionally, the following prefixed terms are understood (where <brackets> indicate user-
supplied values):

id:<docid> Xapers document ID
author:<string> string in authors (also a:)
title:<string> string in title (also t:)
tag:<tag> specific user tag
<source>:<id> specific source id (sid)
source:<source> specific source
key:<key> specific bibtex citation key
year:<year> specific publication year (also y:)
year:<since>..<until> publication year range (also y:)
year:..<until>
year:<since>..

Publication years must be four-digit integers.

See the following for more information on search terms:

http://xapian.org/docs/queryparser.html

ENVIRONMENT

The following environment variables can be used to control the behavior of xapers:

XAPERS_ROOT
Location of the Xapers document store. Defaults to "~/.xapers/docs" if not specified.

XAPERS_SOURCE_PATH
Path specification for location of additional custom Xapers source modules. Defaults to
"~/.xapers/sources" if not specified.

CONTACT

Feel free to email the author:

Jameson Rollins <[email protected]>

XAPERS(1)

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