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services
README.md
check.sh
checkall.sh
export.sh
formats.sh
functions.sh
import.sh
mdz
medusa.conf.example
meta.rnc
mimetypes.txt
prepare.sh
receive.sh
send.sh

README.md

Medusa: A metadata-enriched distributed universal storage

This is a rough implementation of a generic data store and associated services. It was developed based on the need for a structured way to manage molecular data, data with a variety of file formats and analyses, and where a rapidly advancing technology ensures that new formats keep coming.

Basic structure

The repository is organized as a content adressable storage, where objects are indexed by their SHA-1 checksum. There is in principle no limitation on content.

Each data set consists of a set of data objects, and a separate metadata object, conforming to the meta.rnc schema. The metadata object describes the dataset, its relationship to other datasets, and contains a list of data objects.

The 'medusa' directory

This directory contains the bulk of the implementation, mostly in the form of shell scripts.

  • mdz - The main driver script that sets up the environment and calls other commands
  • medusa.conf.example - Example config file, copy to $HOME/.medusa.conf and edit as appropriate.

Supporting files and basic infrastructure (the shell scripts correspond to mdz commands):

  • meta.rnc - RelaxNG schema for metadata XML files
  • mimetypes.txt - a list of known file types. Note that this is not exhaustive, and unknown file type is not an error.
  • check.sh - checks the data sets given as command-line parameters for consistency and correctness
  • checkall.sh - checks all data sets using check.sh, and outputs a summary
  • prepare.sh - builds a skeleton metadata file for the given dataset, trying to automatically determine file types
  • import.sh - calculates SHA-1 hashes, performs some further checks, and prompts the user before importing data into the repository
  • export.sh - calculates SHA-1 hashes, performs some further checks, and prompts the user before importing data into the repository

Services are contained in their own subdirectories in the services directory. Each subdir contains a script of the same name (plus a ".sh" extension) and optionally supporting or configuration files.

  • xapian-index - builds a generic search index using xapian and omega
  • viroblast - builds a Viroblast sequence search service
  • website - builds a website with metadata presented as web pages with links to data and index pages.

Required software

The scripts rely heavily on xmlstarlet to extract information from the metadata files. This is availabe through most Linux distributions, or the link above. Unfortunately, xmlstarlet cannot read RNC schemas directly, and we need trang to convert to RNG. In addition, [xsltproc] is needed to process XSLT stylesheets.

Some of the services require special software, e.g. the viroblast service requires viroblast, and the xapian-index search service uses xapian and its omega web interface.

Setting up

Get the necessary software, on Debian or Ubuntu, something like this should do the trick:

apt-get install xapian-omega xsltproc trang xmlstarlet libapache2-mod-php5

Copy and edit the medusa.conf.example, and store it as .medusa.config in your home directory.

Take ownership of the default directory for the web server - for a more complex setup, you will probably want to set up this as a separate Apache service:

sudo chown $USER /var/www/html
sudo rm /var/www/html/index.html

Download Viroblast and unpack it in the /var/www/html (or whatever directory MDZ_WEBSITE_DIR or MDZ_VIROBLAST_DIR points to). Note that you need to ensure that the viroblast/data directory is writable by the webserver user. Viroblast ships with 32-bit versions of the BLAST+ suite, so on a 64bit system, you also need to get some compatibility stuff:

sudo apt-get install libc6-i386 libstdc++6:i386 zlib1g:i386 bzip2:i386

Xapian is by default installed in the /usr/lib/cgi-bin directory, but you may need to link mods-available/cgi.load to mods-enabled in the Apache config directory. See also the README file in the services/xapian-index directory.

Adding a dataset

To add a data set, make a new subdirectory, and populate it with the files that constitute the dataset. Then run mdz prepare.

mkdir DataSet
mv [....] DataSet/
mdz prepare DataSet

You should now have a meta.xml file in DataSet. Now, edit the metadata file, and fill in details. When everything is satisfactory, you can run mdz import, and if everything goes well, the data set is imported into the repository.

When mdz prepare is run, two metadata sections are generated with empty (that is, just an ellipsis) contents. The <description> section should contain a text describing what the data set is, while the <provenance> section should describe how the data set came about (usually corresponding to 'methods'). Plain text is fine, and can be used by many services, e.g. it will be indexed and searched by the xapian/omega service. But in order to be more directly useful, one might want to add more structure to the text. Currently, the following tags are defined to help with this:

Species

A reference to a species can be wrapped with a <species> tag. The contents is just free text, but the tag has a required attribute, tsn, and an optional one sciname. Typically, it would look something like:

<species tsn="89113" sciname="Lepeophtheirus salmonis">Atlantic salmon louse</species>

Currently, this will be indexed by xapain (so you can search for e.g. species:salmon), and the website service builds a table linking datasets to species.

Dataset

Often it is useful to refer to other datasets. Again, the contents is plain text, but a required attribute must point to the dataset ID (i.e. its directory name), and an optional attribute describes the kind of relationship. For example:

...replaces the <dataset id="1234567890abcdef" rel="obsoletes">454 libraries</dataset>...

The possible values for rel are defined in the schema file meta.rnc.

Person and location

Currently plain text fields, this is likely to change as more structure is added in the future.