Curating submitted alleles.

kjolley · Jun 23, 2015 · 1cc8e82 · 1cc8e82
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diff --git a/curate_submissions.rst b/curate_submissions.rst
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+#######################
+Curating submitted data
+#######################
+Data may be submitted by users using the automated submission system if it has
+been enabled for a specific database.  As a curator, you will be notified of
+pending submissions when you log in to the curator's interface or if you access
+the 'Manage submissions' links from the standard contents page.  Additionally,
+if your user account has the 'submission_emails' flag set in the users' table 
+you will also receive E-mail notification of new submissions for which you have
+sufficient privileges to curate.
+
+.. image:: /images/curate_submissions/curate_submissions1.png
+
+Any submissions for which you have sufficient privileges to curate will be
+shown.
+
+.. image:: /images/curate_submissions/curate_submissions2.png
+
+*******
+Alleles
+*******
+Click the link to the appropriate submission on the 'Manage submissions' page.
+
+.. image:: /images/curate_submissions/curate_submissions3.png
+
+You will see a summary section that describes details about how the sequences
+were obtained.  There should also be link here to download all the sequences
+in FASTA format.
+
+.. image:: /images/curate_submissions/curate_submissions4.png
+
+There will also be a table summarizing the sequences in the submission and
+their current submission status.
+
+.. image:: /images/curate_submissions/curate_submissions5.png
+
+Individual allele curation
+==========================
+Individual sequences can be curated singly by clicking the 'Curate' links next
+to the sequence in the table.  If you have supporting data attached to the
+submission, e.g. Sanger trace files then you may need to assess the submission 
+based on the policy of the database.
+
+.. image:: /images/curate_submissions/curate_submissions6.png
+
+Clicking this link takes you to the curation interface 
+:ref:`single sequence upload page<single_allele_upload>`.  The upload form will
+be filled with details from the submission.  You will need to manually set the
+status from the dropdown list of values.
+
+.. image:: /images/curate_submissions/curate_submissions7.png
+
+Clicking 'Submit' from this form will define the new allele and add it to the
+database.  A link on the confirmation page will take you back to the submission
+management page.
+
+.. image:: /images/curate_submissions/curate_submissions8.png
+
+You will find that the status of the newly assigned sequence has changed in the
+summary table.  The assigned value and status are determined on display and
+should always reflect the live database values.
+
+.. image:: /images/curate_submissions/curate_submissions9.png
+
+Batch allele curation
+=====================
+Often, you will want to batch upload submitted sequences.  This can be done by
+clicking the 'Batch curate' button.
+
+.. image:: /images/curate_submissions/curate_submissions10.png
+
+This takes you to the 
+:ref:`batch FASTA upload page<batch_allele_fasta_upload>` in the curators' 
+interface.
+
+The upload form will be filled with details from the submission.  You will need
+to manually set the status from the dropdown list of values.
+
+.. image:: /images/curate_submissions/curate_submissions11.png
+
+Click 'Check' on this form will perform some standard checks before allowing
+you to upload the sequences.
+
+.. image:: /images/curate_submissions/curate_submissions12.png
+
+A link on the confirmation page will take you back to the submission
+management page.
+
+.. image:: /images/curate_submissions/curate_submissions13.png
+
+The status of the sequences should reflect their newly assigned status.
+
+.. image:: /images/curate_submissions/curate_submissions14.png
+
+Rejecting sequences
+===================
+Sometimes you may need to reject all, or some of, the sequences in a submission.
+You can do this by changing the value in the status dropdown box next to each
+sequence.  Click 'Update' to make the change. 
+
+.. image:: /images/curate_submissions/curate_submissions15.png
+
+Closing the submission
+======================
+You can add a message to the submitter by entering it in the message box and 
+clicking 'Add message'.  Once sequences have all been either assigned or 
+rejected, the 'Close submission button' will be displayed.  Click this to close
+the submission.  The submitter will be notified of their submission status.
+
+.. image:: /images/curate_submissions/curate_submissions16.png
+
+********
+Profiles
+********
+
+********
+Isolates
+********
diff --git a/curator_guide.rst b/curator_guide.rst
@@ -38,6 +38,8 @@ relevant for users with a status of 'user' or 'submitter'.
 Adding new allele sequence definitions
 **************************************
 
+.. _single_allele_upload:
+
 Single allele
 =============
 To add a single new allele, click the sequences (all loci) add (+) link on the
@@ -113,6 +115,8 @@ If there are any problems with the submission, these should be indicated at this
 
 .. image:: /images/curation/add_alleles7.png
 
+.. _batch_allele_fasta_upload:
+
 Upload using a FASTA file
 -------------------------
 Uploading new alleles from a FASTA file is usually more straightforward than generating an Excel sheet.

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diff --git a/index.rst b/index.rst
@@ -18,6 +18,7 @@ The software has been released under the GNU General Public Licence version 3.
    dbase_setup
    administration
    curator_guide
+   curate_submissions
    offline_tools
    data_downloads
    data_records