6 releases
0.3.1 | Apr 23, 2020 |
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0.3.0 | Apr 22, 2020 |
0.2.1 | Apr 21, 2020 |
0.1.1 | Apr 17, 2020 |
#18 in #variety
440KB
726 lines
gnverify
Takes a name or a list of names and verifies them against a variety of biodiversity Data Sources
Features
- Small and fast app to verify scientific names against many biodiversity databases.
- Has 4 different match levels:
- Exact: complete match with a canonical form or full name-string from a data source.
- Fuzzy: if exact match did not happen, it tries to match name-strings assuming spelling errors.
- Partial: strips middle or last epithets from bi- or multi-nomial names and tries to match what is left.
- PartialFuzzy: the same as Partial but assuming spelling mistakes.
- Taxonomic resolution. If a database contains taxonomic information, returns currently accepted name for a name-string, if it is different from the matched name.
- Best match is returned according to the match score. Data sources with some manual curation have priority over auto-curated and uncurated datasets. For example Catalogue of Life or WoRMS are considered curated, GBIF auto-curated, uBio not curated.
- It is possible to map any name-strings checklist to any of registered Data Sources.
- If a Data Source provides classification for a name, it will be returned in the output.
- Works for checking just one name-string, or multiple ones written in a file.
- Supports feeding data vie pips of an operating system. This feature allows to chain the program together with other tools.
Installation
MS Windows
Download the latest release from github, unzip.
One possible way would be to create a default folder for executables and place
gnveriry
there.
Use Windows+R
keys
combination and type "cmd
". In the appeared terminal window type:
mkdir C:\Users\your_username\bin
copy path_to\gnverify.exe C:\Users\your_username\bin
Add C:\Users\your_username\bin
directory to your PATH
environment variable.
Another, simpler way, would be to use cd C:\Users\your_username\bin
command
in cmd
terminal window. The gnverify
program then will be automatically
found by Windows operating system when you run its commands from that
directory.
You can also read more a detailed guide for Windows users in a PDF document.
Linux and Mac
Download the latest release from github, untar, and install binary somewhere in your path.
tar xvf gnverify-linux-0.2.0.tar.xz
# or tar xvf gnverify-mac-0.2.0.tar.gz
sudo mv gnverify /usr/local/bin
Compile from source
Install Rust according to their installation instructions
cargo install gnverify
Usage
gnverify
takes one name-string or a tab-delimited file with many
name-strings as an argument, sends a query with these data to remote
gnindex
server to match the name-strigs against many different
biodiversity databases and returns results to STDOUT either in JSON or CSV
format.
One name-string
gnverify "Monohamus galloprovincialis"
Many name-strings in a file
gnverify /path/to/names.tsv
The app assumes that a file either contains a simple list of names, one per line,
of a tab-separated list where the first column is an id
associated with a
name_string, and the second is the name-string itself. You can find examples
of such files in the project's test directory.
It is also possible to feed data via STDIN:
cat /path/to/names.txt | gnverify
Options and flags
According to POSIX standard flags and options can be given either before or after name-string or file name.
help
gnverify -h
# or
gnverify --help
# or
gnverify
version
gnverify -V
# or
gnverify --version
name_field
If the name-string's ScientificName field is not the first in your data,
the name-field
flag is very important. Set it to the position of
the name-string field.
For example, if your file has the following fields:
"ID", "Taxon_ID", "Name", "Reference", "Notes"
and the "Name" field contains the names you want to verify, use
gnverify -n 3
# or
gnverify --name-field=3
format
Allows to pick a format for output. Supported format are
- compact: one-liner JSON.
- pretty: prettified JSON with new lines and tabs for easier reading.
- csv: (DEFAULT) returns CSV representation.
gnverify -f compact file.txt
# or
gnverify --format="pretty" file.csv
Note that a separate JSON "document" is returned for each separate record, instead of returning one big JSON document for all records. For large lists it significantly speeds up parsin of the JSON on the user side.
sources
By default gnverify
returns only one "best" result of a match. If a user
has a particular interest in a data set, s/he can set it with this option, and
all matches that exist for this source will be returned as well. You need to
provide a data source id for a dataset. Ids can be found at the following
url. Some of them are provided in the gnverify
help
output as well.
Data from such sources will be returned in preferred_results section of JSON output, or with CSV rows that start with "PreferredMatch" string.
gnverify file.csv -s "1,11,172"
# or
gnverify file.tsv --sources="12"
# or
cat file.txt | gnverify -s '1,12'
preferred_only
Sometimes all users wants is to map one list of names to a DataSource. They
are not interested if name matched anywhere else. In such case you can use
the preferred_only
flag.
gnverify -p -s '12' file.txt
# or
gnverify --preferred_only --sources='1,12' file.tsv
Copyright
Authors: Dmitry Mozzherin
Copyright (c) 2020 Dmitry Mozzherin. See LICENSE for further details.
Dependencies
~22–33MB
~548K SLoC