Changes between Version 13 and Version 14 of SoftWare/ProjectMeta


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Timestamp:
Jun 16, 2018, 3:46:07 PM (6 years ago)
Author:
sommeria
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  • SoftWare/ProjectMeta

    v13 v14  
    11= SoftWare / !ProjectMeta - Meta project for open data management =
     2== Aim ==
     3Project-Meta is a software to help you to manage your open data, using the protocol OpenDAP. The initiative is supported by the European Commission as part of the project Hydralab+ of the Horizon 2020 programme. This programme  requests that research data are open access, that is providing online access free of charge to the end-user and reusable. Furthermore access must allow the right to copy, distribute, search, link, crawl and mine the data. In addition to these general requests, we aim at achieving the following goals:
    24
    3 == Aim ==
     5 1. Allow the end user to scan and visualise the data without downloading.
     6 1. Integrate the process in the data analysis procedure, with minimal additional work.
    47
    5 Project-Meta is a software to help you to manage your open data, using the protocol OpenDAP.
    6 The initiative is supported by the European Commission as part of the project Hydralab+ of the Horizon 2020 programme.
    7 This programme  requests that research data are open access, that is providing online access free of charge to the end-user and reusable.
    8 Furthermore access must allow the right to copy, distribute, search, link, crawl and mine the data.
    9 In addition to these general requests, we aim at achieving the following goals:
    10  1. Allow the end user to scan and visualise the data without downloading.
    11  2. Integrate the process in the data analysis procedure, with minimal additional work.
    12 
     8The attached document [[OpenDAP_GM.pdf]] describes the wider motivation of the project.
    139
    1410== OPeNDAP ==
     11The protocol OPeNDAP (Open-source Project for a Network Data Access Protocol). This includes standards for encapsulating structured data, annotating the data with attributes and adding semantics that describe the data. OPeNDAP is widely used by governmental agencies such as NASA and NOAA to serve satellite, weather and other observed earth science data.
    1512
    16 The protocol OPeNDAP (Open-source Project for a Network Data Access Protocol).
    17 This includes standards for encapsulating structured data, annotating the data with attributes and adding semantics that describe the data.
    18 OPeNDAP is widely used by governmental agencies such as NASA and NOAA to serve satellite, weather and other observed earth science data.
    19 
    20 The protocol is based on http, so that data can be scanned with an ordinary web browser.
    21 However added functionality of data visualization is provided by graphics programs (like Matlab, GrADS, Ferret or ncBrowse).
    22 Compared to ordinary file transfer protocols (e.g. FTP) a major advantage using OPeNDAP is the ability to retrieve subsets of files,
    23 so it is possible to work remotely without downloading whole data files.
    24 Although any file format can be use, data are often in HDF or NetCDF formats.
    25 The older NetCDF format is limited to arrays of numbers, while HDF provides wider possibilities of data structures (and it contains NetCDF as a particular case).
    26 We choose the NetCDF format which is sufficient for most experimental data and can be more easily read with a variety of software.
    27 
     13The protocol is based on http, so that data can be scanned with an ordinary web browser. However added functionality of data visualization is provided by graphics programs (like Matlab, GrADS, Ferret or ncBrowse). Compared to ordinary file transfer protocols (e.g. FTP) a major advantage using OPeNDAP is the ability to retrieve subsets of files, so it is possible to work remotely without downloading whole data files. Although any file format can be use, data are often in HDF or NetCDF formats. The older NetCDF format is limited to arrays of numbers, while HDF provides wider possibilities of data structures (and it contains NetCDF as a particular case). We choose the NetCDF format which is sufficient for most experimental data and can be more easily read with a variety of software.
    2814
    2915== Description ==
     16The creation of the OpenDAP repository is done by the script [http://servforge.legi.grenoble-inp.fr/pub/soft-trokata/project-meta/project-meta.html project-meta] using UNIX commands, scripts in Perl and C++.
    3017
    31 The creation of the OpenDAP repository is done by the script
    32 [http://servforge.legi.grenoble-inp.fr/pub/soft-trokata/project-meta/project-meta.html project-meta]
    33 using UNIX commands, scripts in Perl and C++.
    34 
    35 The first step is to make a list of the data folders to display.
    36 This list needs to be introduced in a text file, complemented by some information about the authors of the work and about related publications.
    37 This text file must be put in your current folder with the name `PROJECT-META.yml`.
    38 The text structure must follow some simple rules consisting in the YAML format.
    39 An example could be found in the Project-Meta repository or online
    40 [http://servforge.legi.grenoble-inp.fr/pub/soft-trokata/project-meta/PROJECT-META.sample.yml PROJECT-META.sample.yml].
     18The first step is to make a list of the data folders to display. This list needs to be introduced in a text file, complemented by some information about the authors of the work and about related publications. This text file must be put in your current folder with the name `PROJECT-META.yml`. The text structure must follow some simple rules consisting in the YAML format. An example could be found in the Project-Meta repository or online [http://servforge.legi.grenoble-inp.fr/pub/soft-trokata/project-meta/PROJECT-META.sample.yml PROJECT-META.sample.yml].
    4119
    4220{{{
    … …  
    4422man project-meta
    4523}}}
     24== `PROJECT-META.yml` meta file ==
     25This file is at the core of the procedure. A first task is to list the data folder to publish. For that purpose a good practice is to organise the data and the procedures of analysis such that the final data to publish are contained in folders named with specific extensions. Then search tools can be used to list all the selected folders. For instance the following unix command lists all the folders with extension '`*.mproj*`' and append it to the file `PROJECT-META.yml` (and creates the file if it does not exist yet):
    4626
    47 == `PROJECT-META.yml` meta file ==
    48 
    49 This file is at the core of the procedure. A first task is to list the data folder to publish.
    50 For that purpose a good practice is to organise the data and the procedures of analysis such that the final data to publish are contained in folders named with specific extensions.
    51 Then search tools can be used to list all the selected folders.
    52 For instance the following unix command lists all the folders with extension '`*.mproj*`' and append it to the file `PROJECT-META.yml`
    53 (and creates the file if it does not exist yet):
    5427{{{
    5528find . -name '*.mproj*' -a -type d | sed 's/^/    - /;' >> PROJECT-META.yml
    … …  
    5730The `find` command only search the folders with the right extension (recursively)  under the current one (.) and the `sed` command add 4 spaces and the dash at the beginning of each line in order to respect the YAML format.
    5831
    59 The YAML file has to be complemented by general information about the authors and the related publications,
    60 following the template  [http://servforge.legi.grenoble-inp.fr/pub/soft-trokata/project-meta/PROJECT-META.sample.yml PROJECT-META.sample.yml].
    61 
     32The YAML file has to be complemented by general information about the authors and the related publications, following the template  [http://servforge.legi.grenoble-inp.fr/pub/soft-trokata/project-meta/PROJECT-META.sample.yml PROJECT-META.sample.yml].
    6233
    6334== Debian package ==
    64 
    65 Debian is a GNU/Linux distribution.
    66 Debian (and certainly Ubuntu) package for amd64 arch could be download on: http://servforge.legi.grenoble-inp.fr/pub/soft-trokata/project-meta/download.
     35Debian is a GNU/Linux distribution. Debian (and certainly Ubuntu) package for amd64 arch could be download on: http://servforge.legi.grenoble-inp.fr/pub/soft-trokata/project-meta/download.
    6736
    6837You can then install it with
     38
    6939{{{
    7040sudo dpkg -i project-meta_*_amd64.deb
    … …  
    7242(just replace * with the version you have donwloaded).
    7343
    74 
    7544== Software repository ==
    76 
    7745All code is under '''free license'''. Scripts in `bash` are under GPL version 3 or later (http://www.gnu.org/licenses/gpl.html), `C++` sources are under GPL version 2 or newer, the `perl` scripts are under the same license as `perl` itself ie the double license GPL and Artistic License (http://dev.perl.org/licenses/artistic.html).
    7846