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= GenoEx- PSE – User's Manual =
This document describes the procedures for the upload and download of the data for the [[https://genoex.org/|GenoEx-PSE]] service. The PSE Code of Practice you can find [[https://interbull.org/ib/pse_cop|here]] 

The User Manual describes in detail the required file formats, login process and usage of the service itself both for data upload and data download.

Please note that !GenoEx service is under regular improvement and thus new functionalities may be introduced. It is therefore important to always use the latest version of this manual.

== Login ==
After you have signed the User’s Agreement and joined the service, you will receive login details from Interbull Center for the users you have requested access for. From this moment you are entitled to use the !GenoEx-PSE service via [[https://genoex.org/|genoex.org]].

The '''login''' tab can be found on the top right corner of the front page. If you have lost or forgotten your password, a new password can be requested from the '''Lost Password''' page, which can be accessed both under the login tab and from the login page.  Once you log in you can change your password by pressing the '''Change password''' under your username tab in the top right corner. We highly recommend that you change the password from the one provided to you, at the very first login.

Under the '''About''' tab, you will find links to all documentation relevant for the !GenoEx-services.

Under the '''Contact''' tab you will find information needed to contact Interbull Center should you have any questions, comments or concerns regarding the platform or the service.

On the '''System Data''' page, four tables are presented: ''SNP Arrays'', ''Laboratories'', ''Breeds'', and ''Countries''. All of the tables have clickable headers, and a search field to ease the looking up of information. The information in these tables represent the only allowed values for the information regarding SNP array, genotyping laboratory, breed and country in the files to be uploaded. See the section for file format for more information

The '''History''' tab directs you to the history page, where you find a table showing all the uploads or downloads done by any user of your organization. The history table as well as downloads and uploads, found under the PSE-tab, will be described in the following sections.

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== Data Upload ==
To access the '''Upload''' page, go to the '''PSE''' tab and click Upload. The data to be uploaded must be presented in a .zip-file as described in section 1 of the Users Manual. Details of the file format you can find [[https://interbull.org/ib/pse_file_formats|HERE]].  Click the '''Browse '''button, find and select the file to be uploaded, and then click UPLOAD.

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After pressing the UPLOAD button, you will be redirected to a status-page showing the job-id, job type, current status and the date and time, as shown in the pictures below.

An uploading process can have four different statuses: ''Initiated'', ''Processing'', ''Finished ''or ''Failed''. At the initial re-direction from the upload page, the current status will be shown as ''Initiated''.    The duration of the upload process depends on the size of your file. To follow the progress of your upload, you can either refresh the status page as shown in the three following pictures, or go to the History table. When the Processing is complete, and the upload is either successful or failed, you will receive a notificiation via e-mail to the e-mail address connected to your GenoEx user account.

{{attachment:3a_statusUpload_initating.JPG||height="297",width="901"}}

{{attachment:3b_statusUpload_processing.JPG||height="285",width="901"}}

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=== Failed upload ===
In the case where the upload is unsuccessful, the job status will be displayed as ''Failed''. The number of errors and the cause of the failed upload will be shown. In the case presented in the image below, the upload failed as the animal-ID used in the snps.csv-file did not correspond to the animal-ID used in the meta.csv-file.

{{attachment:3d_statusUpload_failed.JPG||height="318",width="900"}}

== Data extraction ==
To access the download page, go to the '''PSE'''-tab and click '''Download'''.

In the download page, query the desired data by sex, breed and country. A selection  must be done in all three fields for the extraction to be initiated. In  order to select more than one criteria use CTRL+click.

The data can be extracted either in TOP-format or in AB-format, independently of the format that it was submitted in.

In cases where animals is represented with more than one genotype, the '''Best only''' will give you the genotype with the highest call rate. By selecting '''All''' you will be provided with all the genotypes your organization have access to.

Specific  time periods of when data has been uploaded can be select, to for  example only download data that has become available since your latest  download. The dates provided by default gives you all data uploaded to  the database that your organization has access to.

When all the extraction criteria are selected, click CREATE EXTRACTION.

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After clicking CREATE EXTRACTION, you will be redirected to a status-page showing the  job-id, job type, current status and the date and time, as shown in the  pictures below. 

A downloading process can have two different statuses: ''Processing'' or ''Finished''. At the initial re-direction from the upload page, the current status will be shown as ''Processing''. The duration of the download process depends on the amount of data that is extracted.  To follow the progress of your download, you can either refresh the  status page as shown in the two following pictures, or go to the  History table. When the Processing is complete, and the download is Finished, you will receive a notificiation via e-mail to  the e-mail address connected to your !GenoEx user account.

When the extraction is completed, you can fetch the extracted file by clicking on ''Download extracted file'' on the jobs status page. The downloaded file can be fetched either directly, or at a later time and date. The data will be presented in a zipped folder containing the files snps.csv and meta.csv, following the file format as described in section 1. '''Note''' that the download files has an extra column compared to the uploaded files, as they contain a unique identifier in order to separate several genotypes for the same animal.

{{attachment:6a_statusDownload_processing.JPG||height="414",width="901"}}

{{attachment:6b_statusDownload_finished.JPG||height="346",width="901"}}

== History Table ==
The progress of both uploads and downloads can also be followed in the history table.

The table is by default sorted by date, with the most recent job shown first, but all headers can be pressed to change the sorting as you choose. The search field can be used to easier find specific jobs you may search for.

By clicking on the job-ID  of the job of your interest, you will be re-directed to the status-page for that upload or download.

{{attachment:7_history_extraction.JPG||height="302",width="901"}}

<<Include(public/PSE_file_formats)>>

== More information about allowed values in PSE-files can also be found here: ==
 * [[https://interbull.org/ib/pse_file_formats|PSE File Formats]]
 * [[https://interbull.org/ib/icarbreedcodes|Breed codes]]
 * [[https://www.iso.org/obp/ui/#search|ISO country codes]]
 * [[https://genoex.org/display#arrays|Platform arrays]]
 * [[https://genoex.org/display#labs|Laboratories]]
 * [[http://interbull.org/ib/pse_parentage_verification_snps|Parentage verification SNP]]
 * [[http://interbull.org/ib/pse_parentage_discovery_snps|Parentage discovery SNP]]