add zip warning, add syncmodifyapi note (#1689)

docs_manual/source/_include/sheets_zip_warning.rst

@@ -0,0 +1,6 @@
+.. warning::
+
+    When using Microsoft Windows, please note that the built-in Zip archiver
+    will fail to properly handle ISA-Tab files due to naming conventions. We
+    recommend `NanaZip <https://apps.microsoft.com/store/detail/nanazip/9N8G7TSCL18R>`_
+    for working with ISA-Tab Zip archives under Windows.

docs_manual/source/admin_commands.rst

@@ -31,8 +31,8 @@ These commands originate in SODAR Core. More information can be found in the
 ``syncgroups``
     Synchronize user groups.
 ``syncmodifyapi``
-    Submit missing project metadata to iRODS. Generally should only be used in
-    development.
+    Synchronize project metadata and user access in iRODS. Generally should only
+    be used in development.
 ``syncremote``
     Synchronize project and user data from a remote site if remote project sync
     is enabled.

docs_manual/source/app_samplesheets_create.rst

@@ -35,23 +35,26 @@ upload them at once.
 .. note::
 
     When uploading multiple files instead of a zip archive, all files for the
-    investigation must be present or the import will fail!
+    investigation must be present and in the same directory or the import will
+    fail.
+
+.. note::
+
+    Importing ISA-Tab files with empty study or assay tables is not allowed.
+    Study tables must also contain source and sample materials.
+
+.. include:: _include/sheets_zip_warning.rst
 
 .. figure:: _static/app_samplesheets/sheet_import.png
     :align: center
     :scale: 70%
 
     ISA-Tab import form
 
-In case of a successful import, you will be redirected to the main sample sheets
+After a successful import, you will be redirected to the main sample sheets
 view, where you should see the study and assay tables for your imported sample
 sheets.
 
-.. note::
-
-    Importing ISA-Tab files with empty study or assay tables is not allowed.
-    Study tables must also contain source and sample materials.
-
 Parser Warnings
 ---------------
 

docs_manual/source/app_samplesheets_export.rst

@@ -19,6 +19,8 @@ archive containing all the ISA-Tab files as tab separated values (TSV). The
 export is fully ISA-Tab compatible and can be used with other software
 supporting the model.
 
+.. include:: _include/sheets_zip_warning.rst
+
 
 Export Excel Table
 ==================

docs_manual/source/metadata_recording.rst

@@ -380,15 +380,22 @@ with appropriate ontology identifier and sources.
 4. Uploading
 ============
 
-The upload/integration of metadata into a SODAR project can be facilitated by
-CUBI (e.g. after validation) or any project member with appropriate rights
-(owner, delegate, contributor).
+Uploading metadata into a SODAR project can be facilitated by CUBI (e.g. after
+validation) or any project member with appropriate role (owner, delegate, or
+contributor).
 
-All related ISA-Tab files need be bundled as a one-file zip archive. Then, in
-the corresponding SODAR project go to **Sample Sheets**, **Sheet Operations**,
-and **Add/Replace ISA-Tab** to upload the metadata.
+To upload sample sheets into SODAR, first navigate into the **Sample Sheets**
+application within the corresponding project. In the
+:guilabel:`Sheet Operations` dropdown, select :guilabel:`Import ISA-Tab`. If you
+are replacing existing sheets in the project, this option will appear as
+:guilabel:`Replace ISA-Tab`.
 
-After uploading, it is recommended to compare/validate the number of
-study/assay rows between the SODAR project and ISA-Tab files to exclude
+In the import form, the ISA-Tab TSV files can either be imported as separate
+files, or a Zip archive containing all of the files in the same directory.
+
+.. include:: _include/sheets_zip_warning.rst
+
+After uploading, it is recommended to compare and validate the number of
+study and assay rows between the SODAR project and ISA-Tab files to exclude
 mistakes in metadata recording, in particular with respect to splitting and
 pooling.

docs_manual/source/sodar_release_notes.rst

@@ -21,6 +21,13 @@ Major feature update.
 - Contract sample sheet table height to fit content in browsing mode
 - Upgrade to SODAR Core v0.13.0
 
+Migration Guide
+---------------
+
+Upon deploying this release on an existing instance, admins must run the
+``syncmodifyapi`` management command. This will update project user access in
+iRODS according to the role inheritance update introduced in SODAR Core v0.13.
+
 
 v0.13.4 (2023-05-15)
 ====================