README
¶
JDH - Joseph Dalton Hooker
Jdh (named after botanist and biogeographer Joseph Dalton Hooker, is an open source software for management of taxonomic and biogeographic data.
It is implemented in Go.
Motivation
The main objective of JDH is to provide a simple and flexible platform to manipulate taxonomic and biogeographic data, in a way that will be possible to interact with biodiversity databases (e.g. GBIF), and allowing an easy use of that data in biogeographic studies.
Code organization
The code is separated in two parts, a libary (pkg directory) with several Go packages aimed to store and manipulate biogeographic data. The second part is the source for jdh binary executables (cmd directory), whereas the code is fully functional, the main objective is to be an example of the usage of the jdh packages.
To see main code documentation use godoc.
Architecture
JDH is a server-client model. A server is used to store the database that is typically accessed by a net connection. The program include a default server (implemented in pkg/native and pkg/server, default port is :16917), that is assumed by each command, but it is possible to use other servers, this is implemented through database drivers (implemented in pkg/driver), so it is possible to use the jdh commands to consult remote databases (such as GBIF) in the same way as the local database.
A jdh dataset is a based on text, so it can be easily maintained using git.
Quick startup guide
The command structure of jdh is as a set of hosted commands (as in go command and git command. Usually the command starts with an acronym that indicate the kind of expected data.
To startup the server, navigate to the database directory. It can be any directory, if database files are present in the directory, they will be used by the server. Then, it is recommended to create a new directory for each dataset you want to use. Once you are in the database directory type 'jdh init':
$ jdh init
As the server must be open through the whole season of jdh, you can open it in an independent command line season, or in the background, redirecting the loging file. In Linux:
$ jdh init > log.txt &
And in Windows:
> start /b jdh init > log.txt
Once the server is open, by default any jdh command will be using the data in the database file as the data for the command.
Once you finish a session, you must close the server. To do this type 'jdh close':
$ jdh close
And the server will be closed.
In standard jdh commands, modifications in the database will be immediately committed (saved to hard drive). If you are using some customised application, this might be not the case, so you can call jdh close with the option '--commit' to make sure the database will be saved to hard drive.
$ jdh close --commit
Funding
This project is made thanks to the financial support from a doctoral grant awarded by CONICET (to J. Salvador Arias), and the GBIF Student Award (2012, to J. Salvador Arias). Material facilities are provided by INSUE at the Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Tucumán (Argentina).
Authorship and license
Copyright (c) 2014, J. Salvador Arias [email protected] All rights reserved. Distributed under BSD2 license that can be found in the LICENSE file.
Directories
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| Path | Synopsis |
|---|---|
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cmd
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jdh
Joseph Dalton Hooker.
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Joseph Dalton Hooker. |
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jdh.gui
Joseph Dalton Hooker GUI.
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Joseph Dalton Hooker GUI. |
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pkg
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driver/gbif
Package gbif implements a jdh driver for gbif.
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Package gbif implements a jdh driver for gbif. |
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driver/inat
Package inat implements a jdh driver for i-Naturalist.
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Package inat implements a jdh driver for i-Naturalist. |
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driver/native
Package native implements the driver of native jdh databases.
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Package native implements the driver of native jdh databases. |
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driver/ncbi
Package ncbi implements a jdh driver for genbank using ncbi and embl.
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Package ncbi implements a jdh driver for genbank using ncbi and embl. |
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geography
Package geography implements some geographic utilities.
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Package geography implements some geographic utilities. |
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geography/geolocate
Package geolocate implements the geolocate gazetteer service.
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Package geolocate implements the geolocate gazetteer service. |
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jdh
Package jdh defines the database used by a jdh client application.
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Package jdh defines the database used by a jdh client application. |
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native
Package native implements the jdh native database.
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Package native implements the jdh native database. |
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raster
Package raster implements a different taxon distribution raster kinds and their operations.
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Package raster implements a different taxon distribution raster kinds and their operations. |
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server
Package server implements the native jdh database server.
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Package server implements the native jdh database server. |