.. _faq-sample-managers:

Sample managers
---------------

.. tip::

   To read the entire answer to a :abbr:`FAQ (Frequently Asked Question)`,
   click the arrow icon
   (|collapsible-item-arrow|) below any question to expand or collapse it.

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  <hr>

Who can be assigned as a sample manager?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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      <br>

   * Make a request to the :email:`COPO team <ei.copo@earlham.ac.uk>`
     indicating the type of profile group that you would like to be assigned
     as a sample manager.

   * The permission will be granted after the request has been approved.

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   <br>

Am I assigned as a sample manager?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. collapse:: Click to view answer

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      <br>

   You can check if you are assigned as a sample manager by either of the
   following methods:

   * The |accept-reject-samples-navigation-button| button will be displayed on
     the page.

   * The **Accept or Reject Samples** page will be displayed once the button is
     clicked.

   * Alternatively, if you can navigate to the `Accept or Reject Samples page
     <https://copo-project.org/copo/dtol_submission/accept_reject_sample>`__
     with an **Unauthorisation** error page being displayed then, you are not a
     sample manager.

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   <br>

How do I search for a profile or sample on the Accept or Reject page?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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      <br>

   See :ref:`accept-reject-samples-query-profiles-and-samples` section for
   guidelines on querying profiles and sample records on the
   **Accept or Reject Samples** page.

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   <br>

How do I accept or reject submitted samples?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. collapse:: Click to view answer

   .. note::

      See :ref:`accessing-accept-reject-samples-page` section for guidelines
      on accessing the **Accept or Reject Samples** page.


   See :ref:`accept-reject-samples` section for more information.

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   <br>

How can I download submitted sample manifests from providers or submitters?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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      <br>

  See :ref:`Downloading submitted sample manifest
  <samples-submission-download-sample-manifest-sample-managers>` section for
  more information.

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   <br>

Can I download user-uploaded permits?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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      <br>

   Yes, on the **Accept or Reject Samples** page, permits can be downloaded by
   selecting the desired sample record(s) then, clicking the
   |download-permits-button2| button on the page.

   See :ref:`Downloading permits
   <permits-submission-download-permits-sample-managers>` section for more
   information.

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   <br>

How can I view user-uploaded images?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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      <br>

   Yes, on the **Accept or Reject Samples** page, images can be viewed by
   selecting the desired sample record(s) then, clicking the
   |view-images-button2| button on the page.

   See :ref:`Viewing images <image-submission-view-images-sample-managers>`
   section for more information.

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  <br>

.. _faq-sample-managers-within-several-manifest-groups:

How can I view or accept samples from multiple sample manager manifest groups?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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      <br>

   .. note::

      * The manifest dropdown menu will only be displayed on the
        **Accept or Reject samples** page if you as a sample manager, belongs
        to more than one sample manager manifest group.

      * If the *dtol* sample manager group dropdown menu option is selected,
        both Aquatic Symbiosis Genomics (ASG) profiles and  Darwin Tree of
        Life (DToL) profiles will be displayed in the **All profiles** tab
        and/or **Profiles for My Sequencing Centre** the
        **Accept or Reject samples** page will be displayed (if any exists).

   * Choose desired sample manager group from the manifest group dropdown menu.

   * Click the |accept-reject-samples-navigation-button| button to accept or
     reject samples.

     .. figure:: /assets/images/profiles/modals/profile-new-user-add-email-address-dialogue.png
        :alt: Add email address dialogue
        :align: center
        :target: https://raw.githubusercontent.com/EarlhamInst/COPO-documentation/main/assets/images/profiles/modals/profile-new-user-add-email-address-dialogue.png
        :class: with-shadow with-border

        **Accept or Reject samples: Email address prompt shown when a user
        logs into COPO for the first time**


   See :ref:`Viewing images <image-submission-view-images-sample-managers>`
   section for more information.

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  <br>

.. _faq-sample-managers-samples-awaiting-another-review:

How can I check if sample records are awaiting review by another manager?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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      <br>

   If samples require more than one sample manager to accept or reject them,
   the samples will be displayed in the **Pending Samples** tab until
   **all** sample managers have accepted them. Once all sample managers have
   accepted the samples, the samples will be displayed in the
   **Accepted Samples** tab.

   As shown in the image below, sample records that are awaiting another
   acceptance will be highlighted **yellow** or **amber** and the date when
   the records have been accepted will be displayed in the **Approval Date**
   column in the samples data table.

   Refer to the **Associated TOL (Tree of life) Project** column to view the
   associated project(s) that the sample record belongs to. See the image
   below for an illustration.

   .. figure:: /assets/images/samples/accept-reject-samples/ui/samples-accept-reject-awaiting-another-acceptance1.png
      :alt: Sample record awaiting another acceptance
      :align: center
      :target: https://raw.githubusercontent.com/EarlhamInst/COPO-documentation/main/assets/images/samples/accept-reject-samples/ui/samples-accept-reject-awaiting-another-acceptance1.png
      :class: with-shadow with-border

      **Sample record highlighted in yellow awaiting another acceptance**

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      <br>

   .. figure:: /assets/images/samples/accept-reject-samples/ui/samples-accept-reject-awaiting-another-acceptance2.png
      :alt: Sample record awaiting another acceptance
      :align: center
      :target: https://raw.githubusercontent.com/EarlhamInst/COPO-documentation/main/assets/images/samples/accept-reject-samples/ui/samples-accept-reject-awaiting-another-acceptance2.png
      :class: with-shadow with-border

      **Approval date displayed in the 'Approval Date' column of the samples
      data table**

   In the example above, the sample record is associated with both
   :abbr:`BGE (Biodiversity Genomics Europe)` and
   SANGER (Sanger Institute) (associated) project types. A
   :abbr:`BGE (Biodiversity Genomics Europe)` sample manager
   has accepted the sample record, which is reflected in the
   **Approval Date** column in the data table. The record is highlighted in
   yellow to indicate that it is still awaiting acceptance from another
   sample manager.

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      <br>

   .. hint::

      * The **Approval Date** column displays the date when the sample
        record was accepted by the sample manager as well as the associated
        project that the sample manager belongs to.

      * The **Associated TOL (Tree of life) Project** column displays the
        associated project that the sample record belongs to.

   After the sample record has been accepted by all sample managers, the
   sample record will be displayed in the **Accepted Samples** tab as shown
   in the image below.

   .. figure:: /assets/images/samples/accept-reject-samples/ui/samples-accept-reject-after-all-accepted1.png
      :alt: Sample record after all sample managers have accepted it
      :align: center
      :target: https://raw.githubusercontent.com/EarlhamInst/COPO-documentation/main/assets/images/samples/accept-reject-samples/ui/samples-accept-reject-after-all-accepted1.png
      :class: with-shadow with-border

      **Sample record after all sample managers have accepted it**

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      <br>

   .. figure:: /assets/images/samples/accept-reject-samples/ui/samples-accept-reject-after-all-accepted2.png
      :alt: Updated approval date in the 'Approval Date' column of the
            samples data table
      :align: center
      :target: https://raw.githubusercontent.com/EarlhamInst/COPO-documentation/main/assets/images/samples/accept-reject-samples/ui/samples-accept-reject-after-all-accepted2.png
      :class: with-shadow with-border

      **Approval date updated in the 'Approval Date' column of the samples
      data table**

   In the example above, the sample record is associated with two projects:
   :abbr:`BGE (Biodiversity Genomics Europe)` and SANGER (Sanger Institute),
   as shown in the **Associated TOL (Tree of Life) Project** column.
   The sample managers assigned to both associated project types have
   approved the sample record and the **Approval Date** column has been
   updated in the samples data table.

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  <br>

How can a sample manager check the status of accepted or rejected samples?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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      <br>

   **Option 1**: Accepted samples can be viewed in the **Accepted Samples**
   tab while rejected samples can be found in the **Rejected Samples** tab on
   the **Accept or Reject Samples** page.

   **Option 2**: The **Status** column in the samples data table will display
   the status of the sample record.

   **Option 3**: The **Error** column in the samples data table will display
   an error message if the sample record has been rejected or if there are
   any errors associated with the sample record.

   **Option 4**: The **Status** log will display a chronological list of the
   status of the sample record as shown in the images below. It is located on
   the right of the **Accept or Reject Samples** page below the top navigation
   bar.

   .. figure:: /assets/images/samples/accept-reject-samples/ui/samples-accept-reject-status-log-collapsed.png
      :alt: Sample record status log collapsed
      :align: center
      :target: https://raw.githubusercontent.com/EarlhamInst/COPO-documentation/main/assets/images/samples/accept-reject-samples/ui/samples-accept-reject-status-log-collapsed.png
      :class: with-shadow with-border
      :height: 200px

      **Sample record status log collapsed**

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      <br>

   .. figure:: /assets/images/samples/accept-reject-samples/ui/samples-accept-reject-status-log-expanded.png
      :alt: Sample record status log expanded
      :align: center
      :target: https://raw.githubusercontent.com/EarlhamInst/COPO-documentation/main/assets/images/samples/accept-reject-samples/ui/samples-accept-reject-status-log-expanded.png
      :class: with-shadow with-border
      :height: 600px

      **Sample record status log expanded on hover**

   .. hint::

      If you hover over the **Status** log, it will expand to display more
      information about the status of the sample record.

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  <br>

How to view sample details clearer on the Accept or Reject Samples page?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. collapse::   Click to view answer

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      <br>

   Click the |show-profile-panel-button| button to toggle the profile panel
   visibility on the **Accept or Reject Samples** page to either hide the
   profile panel and view more sample records or show the profile panel to
   view more profiles.

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   <hr>

..
    Images declaration
..

.. |accept-reject-samples-navigation-button| image:: /assets/images/samples/accept-reject-samples/buttons/samples-accept-reject-navigation-button.png
   :height: 4ex
   :class: no-scaled-link

.. |collapsible-item-arrow| image:: /assets/images/icons/arrow-right.png
   :height: 2ex
   :class: no-scaled-link

.. |download-permits-button2| image:: /assets/images/buttons/permits-download-button2.png
   :height: 4ex
   :class: no-scaled-link

.. |show-profile-panel-button| image:: /assets/images/samples/accept-reject-samples/buttons/show-profile-panel-button.png
   :height: 4ex
   :class: no-scaled-link

.. |view-images-button2| image:: /assets/images/buttons/images-view-button2.png
   :height: 4ex
   :class: no-scaled-link