SSR Database User Manual

SSR Database User Manual

Properties Version Date Title Project Author

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0.2 20/09/2010 User Manual SSR Database Evoltree Audrey JACQUES-GUSTAVE

Table of contents I.

Organization and technical information.......................................................................................3 1.

Technical information..............................................................................................................3

2.

SSR Database organization ......................................................................................................3

II.

a.

Authentication page ............................................................................................................3

b.

Home page ..........................................................................................................................3

c.

Importation, Viewer, Logout ................................................................................................4

Functionalities.............................................................................................................................4 1.

View data ................................................................................................................................4

2.

Exportation .............................................................................................................................5

3.

Data insertion..........................................................................................................................5

III.

FAQ .........................................................................................................................................7

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I.

Organization and technical information

1. Technical information The web interface of the SSR Database has been developed in Ruby on Rails and tested on Mozilla Firefox. The database system management used is PostgreSQL (8.1.x).

2. SSR Database organization a. Authentication page You must be connected to access to the database. Login and password are delivered by the database administrator on demand ([email protected]).

Figure 1 : login page

b. Home page The home page contains an abstract on the Evoltree Project, which involves the SSR database. A frame on the right announces the last modifications concerning the database. A link is also proposed to contact the database administrator in case.

Figure 2: home page

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c. Importation, Viewer, Logout Those functions are accessible from the navigation bar.

II.

Functionalities

1. View data

Figure 3 : The "Viewer"

The data displaying is accessible from the navigation bar. On this page (see Figure 3), the user can display all markers contained in an assembly which has been inserted by himself: those assemblies are listed in a table.

Figure 5: assemblies display Figure 4: Search form

The user can search on the entire database, in the existing assemblies with a search form. The following fields must be completed: -

Referenced species: the species on which the marker was developed Tested species: the species of interest. The search can be done for one species or for all the species. 4

-

Assembly version: Assembly name. Repeat class: can be mono, di, tri, tetra, penta or hexanucleotides. Motif class: Motif can be compound, perfect or imperfect.

The display of the search results or of all markers of an assembly is the same: the markers are listed in a table with all disposable information.

Figure 6: marker's display

2. Exportation The export is made at the level of the data’s display. When the search result is displayed, a button “export” appears under the table (Figure 7). By clicking on it, you will be redirected to a page with a link to download the file (Figure 8).

Figure 7: export button

Figure 8: link to download

3. Data insertion Data are imported in the database with an importation file in a CSV format (separator “;”). The access to the importation function is done by clicking on Import Data in the navigation bar. An excel template is disposable to downloading. It’s important to save the importation file in the CSV format. The importation is done with a form. The name of the assembly must be filled in the field Assembly version.

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Warning: this name is unique. To insert markers in an existing assembly, it’s important to respect the spelling and the case. An automatic completion helps to fill this field.

Figure 9: Importation form

Then the file (CSV FILE!!) to import is selected, and it can be validated or not before importation by ticking the option: “validate the file”. This validation is fully recommended before the importation. Anyway, if the file is incorrect, the importation won’t be done and this will be notified by a warning message (Figure 11).

Figure 10: correct file

Figure 11: incorrect file

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Figure 12: importation complete

Figure 13: aborted importation

III.

FAQ

The exportation failed while my files were validated: -

Check if you filled the “species_ref” column If you filled the “publication_author” column, the “publication_title” must be filled too The column separator is “;” The file must be a CSV file The first line of the template describes the columns; don’t keep it in your CSV file.

Informations concerning tested populations have not been inserted: -

Check if you filled the “population_ident” and the “population_type” columns.

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