upgrade to altamisa v0.3.0 (#2033)

bihealth · Oct 29, 2024 · db08fc0 · db08fc0
1 parent dc19d61
commit db08fc0
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Showing 4 changed files with 8 additions and 1 deletion.
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -30,6 +30,7 @@ Added
     - Missing assay plugin ``__init__.py`` files (#2014)
     - Study plugin override via ISA-Tab comments (#1885)
     - Token auth support in study plugin IGV XML serving views (#1999, #2021)
+    - Support for newlines in altamISA error messages (#2033)
 - **Taskflowbackend**
     - ``TaskflowAPI.raise_submit_api_exception()`` helper (#1847)
 
@@ -44,6 +45,7 @@ Changed
     - Update ``Dockerfile`` for v1.0 upgrades (#2003, #2004)
     - Upgrade to iRODS v4.3.3 in CI (#1815)
     - Upgrade to python-irodsclient v2.2.0 (#2007, #2023)
+    - Upgrade to altamisa v0.3.0 (#2033)
     - Upgrade minimum supported iRODS version to v4.3.3 (#1815, #2007)
     - Use constants for timeline event status types (#2010)
 - **Irodsbackend**

diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
@@ -25,6 +25,7 @@ Release for SODAR Core v1.0 upgrade, iRODS v4.3 upgrade and feature updates.
 - Update lock requiring REST API views to return 503 if project is locked
 - Upgrade to Postgres v16
 - Upgrade to python-irodsclient v2.2.0
+- Upgrade to altamISA v0.3.0
 - Upgrade to SODAR Core v1.0.2
 - SODAR Core v1.0 updates: OIDC auth support, new REST API versioning,
   owner/delegate remote sync controls, etc

diff --git a/requirements/base.txt b/requirements/base.txt
@@ -87,7 +87,7 @@ celery==5.3.6
 ####################
 
 # CUBI AltamISA parser
-altamisa==0.2.9
+altamisa==0.3.0
 # -e git+https://github.com/bihealth/altamisa.git@f6de23aa6073d446f7c49ede0af7fa8729992209#egg=altamisa
 
 # Python iRODS client

diff --git a/samplesheets/views.py b/samplesheets/views.py
@@ -130,6 +130,7 @@
 SYNC_FAIL_INVALID_URL = 'Invalid API URL'
 SYNC_FAIL_STATUS_CODE = 'Source API responded with status code'
 CUBI_TPL_DICT = {t.name: t for t in CUBI_TEMPLATES}
+ISA_ERROR_REPLACE_ARGS = ['\\n', '<br />']
 
 EMAIL_DELETE_REQUEST_ACCEPT = r'''
 Your delete request has been accepted.
@@ -329,13 +330,16 @@ def _add_crits(legend, warnings, eh):
                     ex_msg = _add_crits(k, v, ex_msg)
                 ex_msg += '</ul>'
             if ui_mode:
+                ex_msg = ex_msg.replace(*ISA_ERROR_REPLACE_ARGS)
                 messages.error(self.request, mark_safe(ex_msg))
 
         else:
             ex_msg = 'ISA-Tab import failed: {}'.format(ex)
             extra_data = None
             logger.error(ex_msg)
             if ui_mode:
+                if '\\n' in ex_msg:
+                    ex_msg = mark_safe(ex_msg.replace(*ISA_ERROR_REPLACE_ARGS))
                 messages.error(self.request, ex_msg)
 
         if tl_event and self.timeline: