Merge pull request #3855 from BirkbeckCTP/b_1_5_1

Merge of 1.5.1-RC-4

requirements.txt

@@ -40,6 +40,7 @@ maxminddb==1.5.4
 mock
 mozilla-django-oidc==1.2.4
 orcid==1.0.3
+packaging==23.2
 pdfkit==1.0.0
 pdfminer.six
 psycopg2-binary~=2.8.6
@@ -52,7 +53,6 @@ python-dateutil==2.8.1
 python-docx==0.8.11
 python-magic==0.4.13
 requests==2.31.0
-semver==3.0.0
 six==1.14.0
 sqlparse==0.4.4
 swapper==1.3.0

src/core/janeway_global_settings.py

@@ -518,7 +518,7 @@ def filter(self, record):
 
 # New XML galleys will be associated with this stylesheet by default when they
 # are first uploaded
-DEFAULT_XSL_FILE_LABEL = 'Janeway default (1.4.3)'
+DEFAULT_XSL_FILE_LABEL = 'Janeway default (1.5.1)'
 
 # Skip migrations by default on sqlite for faster execution
 if (

src/core/plugin_loader.py

@@ -9,12 +9,12 @@
 from django.conf import settings
 from django.core.exceptions import ImproperlyConfigured
 from django.db.utils import OperationalError, ProgrammingError
-from semver import Version
+from packaging import version
 
 from core.workflow import ELEMENT_STAGES, STAGES_ELEMENTS
+from janeway import __version__ as janeway_version
 from submission.models import PLUGIN_WORKFLOW_STAGES
 from utils import models
-from utils.logic import get_janeway_version
 
 
 def get_dirs(directory):
@@ -88,12 +88,12 @@ def load(directory="plugins", prefix="plugins", permissive=False):
 def validate_plugin_version(plugin_settings):
     valid = None
     try:
-        wants_version = Version.parse(plugin_settings.JANEWAY_VERSION)
+        wants_version = version.parse(plugin_settings.JANEWAY_VERSION)
     except AttributeError:
         # No MIN version pinned by plugin
         return
 
-    current_version = get_janeway_version()
+    current_version = version.parse(janeway_version.base_version)
     valid = current_version >= wants_version
 
     if not valid:

src/janeway/__init__.py

@@ -1,2 +1,2 @@
-from semver import Version
-__version__ = Version.parse("1.5.1-RC-1")
+from packaging import version
+__version__ = version.parse("1.5.1-RC-4")

src/journal/views.py

@@ -2624,10 +2624,10 @@ def get_facet_queryset(self):
 
     def get_order_by_choices(self):
         return [
-            ('title', _('Titles A-Z')),
-            ('-title', _('Titles Z-A')),
             ('-date_published', _('Newest')),
             ('date_published', _('Oldest')),
+            ('title', _('Titles A-Z')),
+            ('-title', _('Titles Z-A')),
             ('correspondence_author__last_name', _('Author Name')),
             ('primary_issue__volume', _('Volume')),
         ]

src/press/migrations/0032_auto_20231116_1057.py

@@ -2,14 +2,23 @@
 
 from django.db import migrations, models
 
+def set_constraints_immediately(apps, schema_editor):
+    """Circumvents psql not allowing transactions with DDL operations"""
+    if schema_editor.connection.vendor.startswith("postgresql"):
+        schema_editor.execute("SET CONSTRAINTS ALL IMMEDIATE")
+
+def set_constraints_deferred(apps, schema_editor):
+    if schema_editor.connection.vendor.startswith("postgresql"):
+        schema_editor.execute("SET CONSTRAINTS ALL DEFERRED")
+
 
 class Migration(migrations.Migration):
 
     dependencies = [
         ('press', '0031_press_journal_footer_text'),
     ]
-
     operations = [
+        migrations.RunPython(set_constraints_immediately, reverse_code=set_constraints_deferred),
         migrations.AlterField(
             model_name='press',
             name='description',
@@ -28,4 +37,5 @@ class Migration(migrations.Migration):
             field=models.TextField(blank=True, default='', help_text='Text that will appear in the footer of every journal, to display publisher address or other essential info. ', verbose_name='Journal footer text'),
             preserve_default=False,
         ),
+        migrations.RunPython(set_constraints_deferred, reverse_code=set_constraints_immediately),
     ]

src/static/common/css/common.css

@@ -266,7 +266,7 @@ article .list-romanupper {
   color: #fff;
 }
 .no-list-type {
-    list-style-type: none;
+    list-style-type: none !important;
 }
 .no-list-type:first-child p {
     display: inline;
@@ -297,4 +297,4 @@ article .list-romanupper {
     background: #f0f0f0;
     padding: 15px;
     margin-top: 15px;
-}
+}

src/submission/forms.py

@@ -234,10 +234,11 @@ class EditorArticleInfoSubmit(ArticleInfo):
 
     def __init__(self, *args, **kwargs):
         super(EditorArticleInfoSubmit, self).__init__(*args, **kwargs)
-        self.fields['section'].label_from_instance = lambda obj: obj.display_name_public_submission
-        self.fields['section'].help_text = "As an editor you will see all " \
-                                           "sections even if they are  " \
-                                           "closed for public submission"
+        if self.fields.get('section'):
+            self.fields['section'].label_from_instance = lambda obj: obj.display_name_public_submission
+            self.fields['section'].help_text = "As an editor you will see all " \
+                                               "sections even if they are  " \
+                                               "closed for public submission"
 
 
 class AuthorForm(forms.ModelForm):

src/templates/common/elements/journal/social_meta.html

@@ -1,13 +1,13 @@
     <meta name="twitter:card" content="summary">
     {% if journal_settings.general.twitter_handle %}<meta name="twitter:site" content="{{ journal_settings.general.twitter_handle }}">{% endif %}
     <meta name="twitter:title" content="{{ article.title }}">
-    <meta name="twitter:description" content="{{ article.abstract }}">
+    <meta name="twitter:description" content="{{ article.abstract|striptags }}">
     {% if article.correspondence_author.twitter_handle %}<meta name="twitter:creator" content="{{ article.correspondence_author.twitter_handle }}">{% endif %}
     <meta name="twitter:image" content="{{ article.get_meta_image_path }}">
 
     <meta property="og:title" content="{{ article.title }}" />
     <meta property="og:type" content="article" />
     <meta property="og:url" content="{{ article.url }}" />
     <meta property="og:image" content="{{ article.get_meta_image_path }}" />
-    <meta property="og:description" content="{{ article.abstract }}" />
+    <meta property="og:description" content="{{ article.abstract|striptags }}" />
     <meta property="og:site_name" content="{{ request.journal.name }}" />

src/themes/material/assets/mat.css

@@ -1,3 +1,10 @@
+html {
+  line-height: 1.5;
+  font-family: "Roboto", sans-serif;
+  font-weight: normal;
+  color: rgba(0,0,0,0.87);
+}
+
 .container {
   margin: 0 auto;
   max-width: 1500px;

src/themes/material/templates/core/base.html

@@ -27,6 +27,7 @@
         <link rel="icon" href="{{ request.repository.favicon.url }}" type="image/vnd.microsoft.icon"/>
     {% endif %}
     <link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
+    <link href="https://fonts.googleapis.com/icon?family=Roboto" rel="stylesheet">
     <link
         rel="stylesheet"
         href="https://cdn.jsdelivr.net/npm/@materializecss/[email protected]/dist/css/materialize.min.css">

src/transform/xsl/default.xsl

@@ -445,6 +445,12 @@
         </ol>
     </xsl:template>
 
+    <xsl:template match="table-wrap-foot/fn-group">
+      <ol class="table-footnotes">
+        <xsl:apply-templates/>
+      </ol>
+    </xsl:template>
+
     <xsl:template match="fn-group/fn">
       <xsl:call-template name="referenced-footnote" />
     </xsl:template>
@@ -850,6 +856,8 @@
             <xsl:apply-templates select="*[name()!='sec'] | node()"/>
         </div>
     </xsl:template>
+
+  <xsl:template match="sec/label"/>
 
     <xsl:template match="sec[not(@sec-type='datasets')]/title | boxed-text/caption/title">
         <xsl:if test="node() != ''">
@@ -3547,6 +3555,15 @@
                             <xsl:attribute name="class">
                                 <xsl:value-of select="'list-romanlower'"/>
                             </xsl:attribute>
+                            <xsl:if test="@continued-from">
+                                <xsl:variable name="continued-from-id" select="@continued-from"/>
+                                <xsl:variable name="count-list-items">
+                                  <xsl:number count="list-item[ancestor::list[@id=$continued-from-id]]"  level="any"/>
+                                </xsl:variable>
+                                <xsl:attribute name="start">
+                                  <xsl:value-of select="$count-list-items + 1"/>
+                                </xsl:attribute>
+                            </xsl:if>
                             <xsl:apply-templates/>
                         </ol>
                     </xsl:when>
@@ -3555,6 +3572,15 @@
                             <xsl:attribute name="class">
                                 <xsl:value-of select="'list-romanupper'"/>
                             </xsl:attribute>
+                            <xsl:if test="@continued-from">
+                                <xsl:variable name="continued-from-id" select="@continued-from"/>
+                                <xsl:variable name="count-list-items">
+                                  <xsl:number count="list-item[ancestor::list[@id=$continued-from-id]]"  level="any"/>
+                                </xsl:variable>
+                                <xsl:attribute name="start">
+                                  <xsl:value-of select="$count-list-items + 1"/>
+                                </xsl:attribute>
+                            </xsl:if>
                             <xsl:apply-templates/>
                         </ol>
                     </xsl:when>
@@ -3563,6 +3589,15 @@
                             <xsl:attribute name="class">
                                 <xsl:value-of select="'list-alphalower'"/>
                             </xsl:attribute>
+                          <xsl:if test="@continued-from">
+                            <xsl:variable name="continued-from-id" select="@continued-from"/>
+                            <xsl:variable name="count-list-items">
+                              <xsl:number count="list-item[ancestor::list[@id=$continued-from-id]]"  level="any"/>
+                            </xsl:variable>
+                            <xsl:attribute name="start">
+                              <xsl:value-of select="$count-list-items + 1"/>
+                            </xsl:attribute>
+                          </xsl:if>
                             <xsl:apply-templates/>
                         </ol>
                     </xsl:when>
@@ -3571,9 +3606,23 @@
                             <xsl:attribute name="class">
                                 <xsl:value-of select="'list-alphaupper'"/>
                             </xsl:attribute>
+                          <xsl:if test="@continued-from">
+                            <xsl:variable name="continued-from-id" select="@continued-from"/>
+                            <xsl:variable name="count-list-items">
+                              <xsl:number count="list-item[ancestor::list[@id=$continued-from-id]]"  level="any"/>
+                            </xsl:variable>
+                            <xsl:attribute name="start">
+                              <xsl:value-of select="$count-list-items + 1"/>
+                            </xsl:attribute>
+                          </xsl:if>
                             <xsl:apply-templates/>
                         </ol>
                     </xsl:when>
+                    <xsl:otherwise>
+                      <ul>
+                        <xsl:apply-templates/>
+                      </ul>
+                    </xsl:otherwise>
                 </xsl:choose>
             </xsl:otherwise>
         </xsl:choose>
@@ -3584,10 +3633,10 @@
     <xsl:template match="list-item">
         <xsl:choose>
             <xsl:when test="not(parent::list[@list-type='gloss']) and not(parent::list[@list-type='sentence-gloss'])">
-                <!-- Target list-items that have a title so we can use the title as the list-item-type -->
-                <!-- See also match="title" where we handle wrapping the title in a span -->
+                <!-- Target list-items that have a label so we can use the title as the list-item-type -->
+                <!-- See also match="label" where we handle wrapping the label in a span -->
                 <xsl:choose>
-                    <xsl:when test="name(*[1]) = 'title'">
+                    <xsl:when test="name(*[1]) = 'label'">
                         <li class="no-list-type">
                             <xsl:apply-templates/>
                         </li>
@@ -3689,18 +3738,15 @@
       </xsl:template>
 
     <xsl:template match="title">
-        <xsl:choose>
-            <xsl:when test="name(parent::*) = 'list-item'">
-                <span class="jats-list-type">
-                    <xsl:value-of select="node()" />
-                </span>
-            </xsl:when>
-            <xsl:otherwise>
-                <strong>
-                    <xsl:apply-templates/>
-                </strong>
-            </xsl:otherwise>
-        </xsl:choose>
+      <strong>
+          <xsl:apply-templates/>
+      </strong>
+    </xsl:template>
+
+    <xsl:template match="list-item/label">
+      <span class="jats-list-type">
+          <xsl:value-of select="node()" />
+      </span>
     </xsl:template>
 
     <xsl:template match="disp-quote">