ADS Management
Note
To enable the ADS functionality, first you need to obtain an ADS token [1], and set it into the ads_tokend
config parameter. To do this:
Create an account and login into the new ADS system.
Get your token (or generate a new one) from here.
Set the
ads_token
bibmanager parameter:
# Set ads_token to 'my_ads_token':
bibm config ads_token my_ads_token
ads-search
Do a query on ADS.
Usage
bibm ads-search [-h] [-n] [-a] [-f] [-o]
Description
This command enables ADS queries. The query syntax is identical to a query in the new ADS’s one-box search engine: https://ui.adsabs.harvard.edu. Here there is a detailed documentations for ADS searches: https://adsabs.github.io/help/search/search-syntax See below for typical query examples.
-a/--add
flag, the code will prompt to add
entries to the database right after showing the ADS search results.
Similarly, set the -f/--fetch
or -o/--open
flags to prompt
to fetch or open PDF files right after showing the ADS search
results. Note that you can combine these to add and fetch/open at
the same time (e.g., bibm ads-search -a -o
), or you can
fetch/open PDFs that are not in the database (e.g., bibm
ads-search -o
).Note
Note that a query will display at most ‘ads_display’ entries on
screen at once (see bibm config ads_display
). If a query matches
more entries, the user can execute bibm ads-search -n
to display the next set of entries.
Caution
When making an ADS query, note that ADS requires the field values (when necessary) to use double quotes. For example: author:”^Fortney, J”.
Options
Examples
# Search entries for given author (press tab to prompt the autocompleter):
bibm ads-search
(Press 'tab' for autocomplete)
author:"^Fortney, J"
Title: Exploring A Photospheric Radius Correction to Model Secondary Eclipse
Spectra for Transiting Exoplanets
Authors: Fortney, Jonathan J.; et al.
adsurl: https://ui.adsabs.harvard.edu/abs/2019arXiv190400025F
bibcode: 2019arXiv190400025F
Title: Laboratory Needs for Exoplanet Climate Modeling
Authors: Fortney, J. J.; et al.
adsurl: https://ui.adsabs.harvard.edu/abs/2018LPICo2065.2068F
bibcode: 2018LPICo2065.2068F
...
Showing entries 1--20 out of 74 matches. To show the next set, execute:
bibm ads-search -n
Basic author search examples:
# Search by author in article:
bibm ads-search
(Press 'tab' for autocomplete)
author:"Fortney, J"
# Search by first author:
bibm ads-search
(Press 'tab' for autocomplete)
author:"^Fortney, J"
# Search multiple authors:
bibm ads-search
(Press 'tab' for autocomplete)
author:("Fortney, J" AND "Showman, A")
Search combining multiple fields:
# Search by author AND year:
bibm ads-search
(Press 'tab' for autocomplete)
author:"Fortney, J" year:2010
# Search by author AND year range:
bibm ads-search
(Press 'tab' for autocomplete)
author:"Fortney, J" year:2010-2019
# Search by author AND words/phrases in title:
bibm ads-search
(Press 'tab' for autocomplete)
author:"Fortney, J" title:Spitzer
# Search by author AND words/phrases in abstract:
bibm ads-search
(Press 'tab' for autocomplete)
author:"Fortney, J" abs:"HD 209458b"
Restrict searches to articles or peer-reviewed articles:
# Search by author AND request only articles:
bibm ads-search
(Press 'tab' for autocomplete)
author:"Fortney, J" property:article
# Search by author AND request only peer-reviewed articles:
bibm ads-search
(Press 'tab' for autocomplete)
author:"Fortney, J" property:refereed
Add entries and fetch/open PDFs right after the ADS search:
# Search and prompt to open a PDF right after (fetched PDF is not stored in database):
bibm ads-search -o
(Press 'tab' for autocomplete)
author:"^Fortney, J" property:refereed year:2015-2019
Title: Exploring a Photospheric Radius Correction to Model Secondary Eclipse
Spectra for Transiting Exoplanets
Authors: Fortney, Jonathan J.; et al.
adsurl: https://ui.adsabs.harvard.edu/abs/2019ApJ...880L..16F
bibcode: 2019ApJ...880L..16F
...
Fetch/open entry from ADS:
Syntax is: key: KEY_VALUE FILENAME
or: bibcode: BIBCODE_VALUE FILENAME
bibcode: 2019ApJ...880L..16F Fortney2019.pdf
# Search and prompt to add entry to database right after:
bibm ads-search -a
(Press 'tab' for autocomplete)
author:"^Fortney, J" property:refereed year:2015-2019
Title: Exploring a Photospheric Radius Correction to Model Secondary Eclipse
Spectra for Transiting Exoplanets
Authors: Fortney, Jonathan J.; et al.
adsurl: https://ui.adsabs.harvard.edu/abs/2019ApJ...880L..16F
bibcode: 2019ApJ...880L..16F
...
Add entry from ADS:
Enter pairs of ADS bibcodes and BibTeX keys, one pair per line
separated by blanks (press META+ENTER or ESCAPE ENTER when done):
2019ApJ...880L..16F FortneyEtal2019apjPhotosphericRadius
# Search and prompt to add entry and fetch/open its PDF right after:
bibm ads-search -a -f
(Press 'tab' for autocomplete)
author:"^Fortney, J" property:refereed year:2015-2019
Title: Exploring a Photospheric Radius Correction to Model Secondary Eclipse
Spectra for Transiting Exoplanets
Authors: Fortney, Jonathan J.; et al.
adsurl: https://ui.adsabs.harvard.edu/abs/2019ApJ...880L..16F
bibcode: 2019ApJ...880L..16F
...
Add entry from ADS:
Enter pairs of ADS bibcodes and BibTeX keys, one pair per line
separated by blanks (press META+ENTER or ESCAPE ENTER when done):
2019ApJ...880L..16F FortneyEtal2019apjPhotosphericRadius
ads-add
Add entries from ADS by bibcode into the bibmanager database.
Usage
bibm ads-add [-h] [-f] [-o] [bibcode key] [tag1 [tag2 ...]]
Description
This command add BibTeX entries from ADS by specifying pairs of ADS bibcodes and BibTeX keys.
Executing this command without arguments (i.e., bibm ads-add
) launches
an interactive prompt session allowing the user to enter multiple
bibcode, key pairs.
By default, added entries replace previously existent entries in the bibmanager database.
-f/--fetch
or -o/--open
, the
code will attempt to fetch and fetch/open (respectively) the
associated PDF files of the added entries.bibm ads-add
or later via the prompt you can specify
tags for the entries to be add.Options
Examples
# Let's search and add the greatest astronomy PhD thesis of all times:
bibm ads-search
(Press 'tab' for autocomplete)
author:"^payne, cecilia" doctype:phdthesis
Title: Stellar Atmospheres; a Contribution to the Observational Study of High
Temperature in the Reversing Layers of Stars.
Authors: Payne, Cecilia Helena
adsurl: https://ui.adsabs.harvard.edu/abs/1925PhDT.........1P
bibcode: 1925PhDT.........1P
# Add the entry to the bibmanager database:
bibm ads-add 1925PhDT.........1P Payne1925phdStellarAtmospheres
The user can optionally assign tags or request to fetch/open PDFs:
# Add the entry and assign a 'stars' tag to it:
bibm ads-add 1925PhDT.........1P Payne1925phdStellarAtmospheres stars
# Add the entry and fetch its PDF:
bibm ads-add -f 1925PhDT.........1P Payne1925phdStellarAtmospheres
# Add the entry and fetch/open its PDF:
bibm ads-add -o 1925PhDT.........1P Payne1925phdStellarAtmospheres
Alternatively, the call can be done without arguments, which allow the user to request multiple entries at once (and as above, set tags to each entry as desired):
# A call without bibcode,key arguments (interactive prompt):
bibm ads-add
Enter pairs of ADS bibcodes and BibTeX keys (plus optional tags)
Use one line for each BibTeX entry, separate fields with blank spaces.
(press META+ENTER or ESCAPE ENTER when done):
1925PhDT.........1P Payne1925phdStellarAtmospheres stars
# Multiple entries at once, assigning tags (interactive prompt):
bibm ads-add
Enter pairs of ADS bibcodes and BibTeX keys (plus optional tags)
Use one line for each BibTeX entry, separate fields with blank spaces.
(press META+ENTER or ESCAPE ENTER when done):
1925PhDT.........1P Payne1925phdStellarAtmospheres stars
1957RvMP...29..547B BurbidgeEtal1957rvmpStellarSynthesis stars nucleosynthesis
ads-update
Update bibmanager database cross-checking entries with ADS.
Usage
bibm ads-update [-h] [update_keys]
Description
This command triggers an ADS search of all entries in the bibmanager
database that have a bibcode
. Replacing these entries with
the output from ADS.
The main utility of this command is to auto-update entries that
were added as arXiv version, with their published version.
For arXiv updates, this command updates automatically the year and
journal of the key (where possible). This is done by searching for
the year and the string ‘arxiv’ in the key, using the bibcode info.
For example, an entry with key ‘NameEtal2010arxivGJ436b’ whose bibcode
changed from ‘2010arXiv1007.0324B’ to ‘2011ApJ…731…16B’, will have
a new key ‘NameEtal2011apjGJ436b’.
To disable this feature, set the update_keys
optional argument to ‘no’.
Options
Examples
Note
These example outputs assume that you merged the sample bibfile
already, i.e.: bibm merge ~/.bibmanager/examples/sample.bib
# Look at this entry with old info from arXiv:
bibm search -v
author:"^Beaulieu"
Title: Methane in the Atmosphere of the Transiting Hot Neptune GJ436b?, 2010
Authors: {Beaulieu}, J.-P.; et al.
bibcode: 2010arXiv1007.0324B
ADS url: http://adsabs.harvard.edu/abs/2010arXiv1007.0324B
arXiv url: http://arxiv.org/abs/arXiv:1007.0324
key: BeaulieuEtal2010arxivGJ436b
# Update bibmanager entries that are in ADS:
bibm ads-update
Merged 0 new entries.
(Not counting updated references)
There were 1 entries updated from ArXiv to their peer-reviewed version.
These ones changed their key:
BeaulieuEtal2010arxivGJ436b -> BeaulieuEtal2011apjGJ436b
# Let's take a look at this entry again:
bibm search -v
author:"^Beaulieu"
Title: Methane in the Atmosphere of the Transiting Hot Neptune GJ436B?, 2011
Authors: {Beaulieu}, J. -P.; et al.
bibcode: 2011ApJ...731...16B
ADS url: https://ui.adsabs.harvard.edu/abs/2011ApJ...731...16B
arXiv url: http://arxiv.org/abs/1007.0324
key: BeaulieuEtal2011apjGJ436b
Note
There might be cases when one does not want to ADS-update an
entry. To prevent this to happen, the user can set the freeze
meta-parameter through the bibm edit
command (see edit).
References