Merge branch 'main' of github.com:ucphhpc/migrid-user-docs

Author: SebastianPrehn

docs/_static/custom.css

@@ -1,5 +1,3 @@
-
-
 a {
 	color: #679c5b;
 }
@@ -8,6 +6,11 @@ body {
 }
 /* Custom theming for screens width 1100px and up */
 @media screen and (min-width: 1100px) {
+     .rst-content img.with-border {
+          border-color: lightgrey;
+          border-width: 2px;
+          border-style: solid;
+     }
 		.rst-content .note .admonition-title, 
 		.rst-content .note .wy-alert-title, 
 		.rst-content .seealso .admonition-title,
@@ -17,61 +20,61 @@ body {
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-        .rst-content .wy-alert-info.hint .admonition-title, 
-        .rst-content .wy-alert-info.hint .wy-alert-title, 
-        .rst-content .wy-alert-info.tip .admonition-title, 
-        .rst-content .wy-alert-info.tip .wy-alert-title,  
-        .wy-alert.wy-alert-info .rst-content .admonition-title 
-        {
+    .rst-content .wy-alert-info.hint .admonition-title, 
+    .rst-content .wy-alert-info.hint .wy-alert-title, 
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+    .rst-content .wy-alert-info.tip .wy-alert-title,  
+    .wy-alert.wy-alert-info .rst-content .admonition-title 
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 		.rst-content .wy-alert-info.attention .admonition-title, 
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-        .rst-content .wy-alert-info.error .admonition-title, 
-        .rst-content .wy-alert-info.error .wy-alert-title, 
+    .rst-content .wy-alert-info.attention .wy-alert-title, 
+    .rst-content .wy-alert-info.caution .admonition-title, 
+    .rst-content .wy-alert-info.caution .wy-alert-title, 
+    .rst-content .wy-alert-info.danger .admonition-title, 
+    .rst-content .wy-alert-info.danger .wy-alert-title, 
+    .rst-content .wy-alert-info.error .admonition-title, 
+    .rst-content .wy-alert-info.error .wy-alert-title, 
 		.rst-content .important .admonition-title, 
-        .rst-content .wy-alert-info.important .admonition-title, 
-        .rst-content .wy-alert-info.important .wy-alert-title, 
-        .rst-content .wy-alert-info.warning .admonition-title, 
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-        .rst-content .wy-alert.wy-alert-info .admonition-title, 
-        .wy-alert.wy-alert-info .wy-alert-title
-        {
+    .rst-content .wy-alert-info.important .admonition-title, 
+    .rst-content .wy-alert-info.important .wy-alert-title, 
+    .rst-content .wy-alert-info.warning .admonition-title, 
+    .rst-content .wy-alert-info.warning .wy-alert-title, 
+    .rst-content .wy-alert.wy-alert-info .admonition-title, 
+    .wy-alert.wy-alert-info .wy-alert-title
+    {
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 		.rst-content .wy-alert-info.admonition, 
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-        .rst-content .important, 
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-        .rst-content .wy-alert-info.hint, 
-        .wy-alert.wy-alert-info, 
-        .rst-content .tip
-        {
+    .rst-content .wy-alert-info.attention, 
+    .rst-content .important, 
+    .rst-content .wy-alert-info.tip, 
+    .rst-content .wy-alert-info.hint, 
+    .wy-alert.wy-alert-info, 
+    .rst-content .tip
+    {
        		background: #fff;
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-        .rst-content .wy-alert-info.caution, 
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-        .rst-content .wy-alert-info.error, 
-        .rst-content .wy-alert-info.important, 
-        .rst-content .wy-alert-info.warning
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+    .rst-content .wy-alert-info.caution, 
+    .rst-content .wy-alert-info.danger, 
+    .rst-content .wy-alert-info.error, 
+    .rst-content .wy-alert-info.important, 
+    .rst-content .wy-alert-info.warning
+    {
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 	  		border: 1px solid #901A1E; 
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     	.wy-nav-side, .wy-grid-for-nav {
         	margin-left: calc(((100vw - 1100px) / 2));
-        }
-	   	.wy-menu-vertical header, .wy-menu-vertical p.caption {
+    }
+	  .wy-menu-vertical header, .wy-menu-vertical p.caption {
    			color: #000;
    			font-size: 95%;
-   		}
+   	}
 		.wy-grid-for-nav nav {
 			background: white
 		}

docs/images/archives/archives-create-freezearchive.png

@@ -1,6 +1,13 @@
+.. _index-start:
+
 ERDA/SIF: User Guides
 =====================
 
+.. toctree::
+   :hidden:
+   
+   HOME <self>
+
 .. toctree::
    :maxdepth: 2
    :hidden:
@@ -19,8 +26,9 @@ ERDA/SIF: User Guides
    sections/erda/jupyter/index
    sections/erda/networkdrive/index
    sections/erda/seafile/index
+   sections/erda/archiving/index
 
-.. Note::
+.. danger::
    This documentation is WIP! We are currently focused on updating our ERDA-related resources.
 
 Welcome to the documentation site for ERDA and SIF! `ERDA <https://erda.ku.dk/>`_ and `SIF <https://sif.ku.dk/>`_ simplifies storing, sharing, analyzing and archiving research data for KU/UCPH employees, their collaboration partners, and KU/UCPH students.

docs/images/archives/archives-createnew.png

@@ -0,0 +1,110 @@
+.. _erda-archiving-start:
+
+================
+Archives in ERDA
+================
+
+The Archives page provides a method to archive or freeze a snapshot of one or more files.
+
+This is required, for example, in relation to handing in PhD dissertations and, in certain cases, required or convenient when
+submitting a paper to a conference or journal.
+
+There are two kinds of archives in ERDA:
+
+ * **Backup archives** - Allows for one-time or recurring backups, and manual recovery of data.
+ * **Frozen archives** - Provides a snapshot of a dataset, frozen in time. Two subtypes:
+  * *Private, frozen archives* - Snapshots are held in private archives.
+  * *Public, frozen archives* - Extra secure, long-term storage guaranteed + DOI for public data.
+
+.. Note:: Archiving does not remove the files you may have selected from ERDA, but only saves a snapshot of the current contents. That is, you are free to keep working on such files afterwards and without causing changes to the archived version.
+   
+Overview of Frozen Archives
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Initially your archives list is empty, but after adding a
+few different archives, it could look like the example below.
+
+.. image:: /images/archives/archives-frozenarchives.png
+   :alt: Frozen Archives screenshot with example archives.
+   :class: with-border
+   :width: 90%  
+	   
+You can inspect a frozen archive with the green info icon IKON, edit unfinished archives with the green
+wrench icon IKON , and, if the system is configured to allow deletion of archives, you can remove them
+again with the red remove icon IKON.
+
+|
+
+Creating an archive
+^^^^^^^^^^^^^^^^^^^
+**Step 1: Create**
+
+New archives can be created with the **Create a new frozen archive** link at the bottom of the page.
+
+As an example, we could create a new archive called "Article Data ..." by filling out the resulting form
+like this:
+
+.. image:: /images/archives/archives-createnew.png
+   :alt: Creating a new archive screenshot
+   :class: with-border
+   :width: 90% 
+   
+**Step 2: Add files/directories**
+
+Existing private or shared ERDA files can be added with the **Add file/directory** button, and new
+files can be uploaded directly to the archive with the **Add upload** button. The former button brings
+up a file select dialog in which you can select from your ERDA files: double-click individual files
+or right-click and choose select to pick entire folders. The latter button opens an upload dialog like
+the one from **Files**. When you are done adding files and have marked if you want the archive files to
+be published, you can click **Save and Preview** to inspect the current contents.
+
+.. image:: /images/archives/archives-create-freezearchive.png
+   :alt: Creating a new archive screenshot
+   :class: with-border
+   :width: 90%
+	   
+|	   
+
+**Step 3: Preview & Finalise**
+
+If you selected Make Dataset Publicly available you can use the Preview publishing button to see
+a draft of the published archive. At this point, you can continue modifying the archive contents like
+above through the Edit archive button, until at last you click Finalize archive to actually
+permanently freeze it and thereby mark it ready for additional tape archiving. This is necessary to
+get the extra data safety and guarantee that it will remain available for at least 10 years.
+
+
+.. image:: /images/archives/archives-finalizearchive.png
+   :alt: Screenshot of page which allows user to modify, preview, and finalize creation of public archive
+   :class: with-border
+   :width: 90%	   
+
+|
+
+**Step 4: View the resulting archive**
+	   
+After finalizing you can use the "View details" button to see all the details registered about it on the
+view archive page and use the links to access the associated files.
+
+.. image:: /images/archives/archives-show-freezearchive-details.png
+   :alt: Screenshot of the page View details, which shows the finalized archive
+   :class: with-border
+   :width: 90%	   
+
+|
+
+DOI for public archives
+^^^^^^^^^^^^^^^^^^^^^^
+For archives with publish enabled, we also integrate access to request a Digital Object Identifier
+(DOI) after finalizing the archive. From view archive you click "Register Archive DOI" at the
+bottom to reach the central UCPH DOI registration portal. Typically, this involves clicking through a
+standard UCPH login and small DOI intro dialogue to get to the actual DOI metadata schema shown.
+
+.. image:: /images/archives/archives-register-doi.png
+   :alt: Screenshot of Digital Object Identifier registration form
+   :class: with-border
+   :width: 90%	   
+
+Once filled and submitted the request is sent through the UCPH validation procedure and if
+everything is okay you receive a permanent https://dx.doi.org/XYZ URL alias for your published
+archive data. From then on you can e.g. use it as a reference in research papers or provide it to
+research colleagues interested in re-using your published data.

docs/images/archives/archives-finalizearchive.png

@@ -16,6 +16,7 @@ sensitive private data.
    which 'Datatilsynet' and other authorities define as a suitable algorithm for strong encryption.
 
 .. _erda-seafile-gettingstarted:
+
 Getting Started with Seafile
 ============================
 
@@ -32,6 +33,7 @@ Once on the Seafile login page, you just need to enter your email address and yo
 
 
 .. _erda-seafile-about:
+
 About libraries
 ===============
 
@@ -43,6 +45,7 @@ You can also install the Seafile client and use it to enter data automatically f
 
 
 .. _erda-seafile-install:
+
 Seafile Client
 ==============
 
@@ -59,6 +62,7 @@ On a standard UCPH computer (B machine), you have access to installing programs
 
 
 .. _erda-seafile-setup:
+
 Set up Seafile Client
 ---------------------
 
@@ -70,6 +74,7 @@ Once the client has been installed, you will find a small Seafile icon in your s
 
 
 .. _erda-seafile-synch:
+
 Synchronize Files
 -----------------
 
@@ -81,11 +86,12 @@ Right-click your Seafile client in the library you want to synchronize. In the e
 
 You may be prompted to select which path on your hard drive to synchronize to. Choose this before clicking "OK".
 
-.. INFO::
+.. NOTE::
    When the synchronization of a library is initiated, the cloud icon will change to show the progress, and the cloud will turn green once the process is complete. This is also visible from within the Seafile client.
 
 
 .. _erda-seafile-share:
+
 Exchange or share data with others
 ==================================
 
@@ -113,6 +119,7 @@ An email will be sent to the selected recipients containing a link to the select
 
 
 .. _erda-seafile-sharecollab:
+
 Share data with collaboration partners
 --------------------------------------
 
@@ -157,6 +164,7 @@ Under "Shared with groups", your collaboration partners can see what you have sh
 
 
 .. _erda-seafile-creategroup:
+
 Create group
 ^^^^^^^^^^^^
 
@@ -180,6 +188,7 @@ You can share a link to a file internally within a group which already have acce
 
 
 .. _erda-seafile-receive:
+
 Receive data from others with "Upload link"
 -------------------------------------------
 
@@ -195,6 +204,7 @@ You will see a Upload Link, and if you click "Send", you will be prompted to wri
 
 
 .. _erda-seafile-tips:
+
 Tips
 ====
 
@@ -218,4 +228,4 @@ View library history
 
 Open your library and click on the clock icon "History"
 
-.. image:: /images/seafile-seafile-libraryhistory.png
+.. image:: /images/seafile/seafile-libraryhistory.png