anchor.diff:  = [.ebi-color]#How to bulk upload samples to BioSamples using the new drag'n'drop uploader#
   :last-update-label!:
   
  -== User requirements
  +== Who should read this guide?
   
  -I am a non programmatic submitter and I want to store my samples in BioSamples using a easy route without having to go through the technical challenges of using the API's
  +Anyone who wants to create a number of samples in BioSamples, using a easy route without having to go through the technical challenges of using an API.
  +If you have set of samples to create as a one off upload, or expect to submit rarely, we recommend using this system.
  +If you want to create a sustainable process for syncing samples programmatically, refer to the link:../references/api/submit[BioSamples JSON API]
   
   == Requirements
   
  -- You need an AAP account or a WEBIN submission account to proceed with this recipe Please refer our link:../guides/authentication[AUTHENTICATION GUIDE] for more information
  +You need an AAP account or a WEBIN submission account to proceed with this recipe Please refer our link:../guides/authentication[AUTHENTICATION GUIDE] for more information
  +
  +== Steps to upload
  +
  +=== Login Page
  +
  +1. Click on the upload menu to open the uploader login page
  +2. Select the radio button, if you wish to use your AAP credentials please select AAP, else select WEBIN
  +3. Enter the credentials you have setup in the authentication system selected in step 2
  +4. Click on the button Sign in to Upload
  +
  +=== Upload Page
  +
  +1. If you have logged in using your AAP credentials then select your AAP domain that you want to use for the submission from the "Select AAP domain" dropdown.
  +This is not required for submissions using WEBIN authentication.
  +The dropdown is pre-populated with domains you have access to
  +2. Select a checklist that you want to validate the samples against from the "Select checklist for validation" dropdown.
  +If you don't have a specific checklist to validate against, please select biosamples-minimal.
  +Compliance to biosamples-minimal is a basic system requirement of BioSamples database and this checklist checks if the sample has a valid organism attribute
  +3. Drag'n'drop the files you want to upload.
  +*Please note* you can upload a maximum of 5 files at once
  +4. Click on Upload files button
  +5. If your upload is successful you will receive a file which will contain all the samples persisted in BioSamples with the accessions.
  +The file is exactly the same as your uploaded file but contains the accessions against each sample.
  +*Please note* the downloaded file has a receipt section at the end which is a summary of the submission
  +6. If your upload fails you will still receive a file which will contain the reason of the failure.
  +Please contact the BioSamples team at EBI at mailto:biosamples@ebi.ac.uk[biosamples@ebi.ac.uk]
  +and we will look into it
   
   == Important information related to the file format
   
  -- The file format for uploading sample metadata to BioSamples is ISA-Tab (https://isa-specs.readthedocs.io/en/latest/isatab.html).
  +1. The file format for uploading sample metadata to BioSamples is ISA-Tab (https://isa-specs.readthedocs.io/en/latest/isatab.html).
   Although ISA-Tab is specifically for Investigation, Study and Assay data, we have tried to use the sample table format specified in the ISA-Tab specification
  -- The ISA-Tab file format is a tab delimited format (TSV)
  +2. The ISA-Tab file format is a tab delimited format (TSV)
   
   == Data format
   
   .TSV file Columns
  -[width="100%",cols=">s,^m,e",frame="topbot",options="header"]
  +[width="50%",cols="3,^2,^2,10",frame="topbot",options="header"]
   |===
  -|Columns |Description | Mandatory/Optional
  +|Columns |Description |Mandatory/Optional (column of table)| Mandatory/Optional
  +(value in table row while adding sample metadata)
   
   |Source Name | Source Name can be the name/ID of your investigation, study, assay,
   project or even sample. It can be the ID of the donor as well.
  -Source Name is specifically added as a column to comply with ISA-Tab standards.
  -If you don't have a source name then you can keep it blank or add any dummy value.
  -The entered value is eventually ignored.
  -Remember
  -not to miss the tab delimiter even if you are keeping Source Name as blank | Optional
  +BioSamples doesnt require a source, so ignores this column,
  +although you need to include it as a column in the file as
  +this is a required column in the ISA-TAB.
  +Remember while filling in metadata to the file, adding a value for this column is completely
  +optional
  +| Mandatory
  +| Optional
   
   |Sample Name | The name of the sample, mandatory, and expected to be unique
  -for all samples | Mandatory
  +for all samples in the TSV file being uploaded
  +| Mandatory
  +| Mandatory
   
  -|Release date | The release date of the sample | Mandatory
  +|Release date | The release date of the sample
  +| Mandatory
  +| Mandatory
   
   |Characteristics [characteristics name] | Your sample attributes are represented by
   Characteristics, you can have any number of characteristics
  
positive.code: 5.If you are looking to update existing samples that has been uploaded, you can use the file that was returned to you after your submission.
  Please remember to remove the receipt section
  
  == Steps to upload
  
  === Login Page
  
  1. Click on the upload menu to open the uploader login page
  2. Select the radio button, if you wish to use your AAP credentials please select AAP, else select WEBIN
  3. Enter the credentials you have setup in the authentication system selected in step 2
  4. Click on the button Sign in to Upload
  
  === Upload Page
  
  1. If you have logged in using your AAP credentials then select your AAP domain that you want to use for the submission from the "Select AAP domain" dropdown.
  This is not required for submissions using WEBIN authentication.
  The dropdown is pre-populated with domains you have access to
  2. Select a checklist that you want to validate the samples against from the "Select checklist for validation" dropdown.
  If you don't have a specific checklist to validate against, please select biosamples-minimal.
  Compliance to biosamples-minimal is a basic system requirement of BioSamples database and this checklist checks if the sample has a valid organism attribute
  3. Drag'n'drop the files you want to upload.
  *Please note* you can upload a maximum of 5 files at once
  4. Click on Upload files button
  5. If your upload is successful you will receive a file which will contain all the samples persisted in BioSamples with the accessions.
  The file is exactly the same as your uploaded file but contains the accessions against each sample.
  *Please note* The downloaded file has a receipt section at the end which is a summary of the submission.
  
  == Next steps
  
  This is the first release of our BioSamples drag'n'drop uploader.
  
negative.code: name in the file. If you wish to establish a relationship with a sample that is already in BioSamples
  you need to mention the accession of the sample
  | Optional
  | Optional
  
  |Comment[external DB REF] | The reference to this sample in any other database
  | Optional
  | Optional
  
  |Comment[submission_contact:email] | The email address of the submitter
  | Optional
  | Optional
  
  |Sample Identifier | The ID/ accession of the sample. In case of new sample submission it
  is optional, mandatory if you are looking to update existing samples
  | Optional (for new submissions)
  / mandatory (for sample updates)
  | Optional (for new submissions)
  / mandatory (for sample updates)
  |===
  
  == Example file
  
  [width="100%" %header,format=tsv]
  |===
  include::files/isa-example.tsv[]
  |===
  