Merge branch '2.x' into sample-batch-reference-show-title-or-id

CHANGES.rst

@@ -5,6 +5,9 @@ Changelog
 ------------------
 
 - #2654 Show Batch title or ID in Sample reference field
+- #2657 Methods from analyses are not updated on instrument change in worksheet
+- #2656 Fix AnalysisProfile keyword validator fail with non-ascii value 
+- #2646 Add SelectOtherField and SelectOtherWidget
 - #2649 Fix event subscribers are not triggered on analysis initialization
 - #2650 Fix AttributeError on analysis update with interim values via jsonapi
 - #2648 Increase the default width for field labels to min 150px

src/bika/lims/content/instrument.py

@@ -66,6 +66,7 @@
 from senaite.core.catalog import SETUP_CATALOG
 from senaite.core.exportimport import instruments
 from senaite.core.p3compat import cmp
+from zope.deprecation import deprecate
 from zope.interface import implements
 
 schema = BikaFolderSchema.copy() + BikaSchema.copy() + Schema((
@@ -160,15 +161,21 @@
     ),
 
     UIDReferenceField(
-        'Methods',
-        vocabulary='_getAvailableMethods',
-        allowed_types=('Method',),
-        relationship='InstrumentMethods',
+        "Methods",
+        vocabulary="_getAvailableMethods",
+        allowed_types=("Method",),
+        relationship="InstrumentMethods",
         required=0,
         multiValued=1,
         widget=PicklistWidget(
             size=10,
-            label=_("Methods"),
+            label=_(u"label_instrument_methods",
+                    default=u"Supported methods"),
+            description=_(
+                u"description_instrument_methods",
+                default=u"Methods that are supported by this analytical "
+                        u"instrument"
+            )
         ),
     ),
 
@@ -414,11 +421,16 @@ def getMaintenanceTypesList(self):
     def getCalibrationAgentsList(self):
         return getCalibrationAgents(self)
 
+    def getRawMethods(self):
+        """Returns the UIDs of the methods supported by this instrument
+
+        :returns: Method UIDs
+        """
+        return self.getField("Methods").getRaw(self)
+
+    @deprecate("Use getRawMethods instead")
     def getMethodUIDs(self):
-        uids = []
-        if self.getMethods():
-            uids = [m.UID() for m in self.getMethods()]
-        return uids
+        return self.getRawMethods()
 
     def _getAvailableMethods(self):
         """ Returns the available (active) methods.

src/bika/lims/content/worksheet.py

@@ -1194,36 +1194,47 @@ def getNumberOfRegularSamples(self):
         return len(set(samples))
 
     def setInstrument(self, instrument, override_analyses=False):
-        """ Sets the specified instrument to the Analysis from the
-            Worksheet. Only sets the instrument if the Analysis
-            allows it, according to its Analysis Service and Method.
-            If an analysis has already assigned an instrument, it won't
-            be overriden.
-            The Analyses that don't allow the instrument specified will
-            not be modified.
-            Returns the number of analyses affected
+        """Assigns the specified analytical instrument to the analyses in this
+        worksheet that are compatible with the instrument. The system will
+        attempt to assign the first method supported by the instrument that is
+        also compatible with each analysis.
+
+        By default, the instrument and method assigned to the analysis won't be
+        replaced unless the analysis does not have an instrument assigned yet
+        or the parameter override_analyses is set to True. Analyses that are
+        incompatible with the specified instrument will remain unchanged.
         """
-        analyses = [an for an in self.getAnalyses()
-                    if (not an.getInstrument() or override_analyses) and
-                    an.isInstrumentAllowed(instrument)]
+        analyses = self.getAnalyses()
+        instrument = api.get_object(instrument, default=None)
+
+        # find out the methods supported by the instrument, if any
+        supported_methods = instrument.getRawMethods() if instrument else []
+
         total = 0
         for an in analyses:
-            # An analysis can be done using differents Methods.
-            # Un method can be supported by more than one Instrument,
-            # but not all instruments support one method.
-            # We must force to set the instrument's method too. Otherwise,
-            # the WS manage results view will display the an's default
-            # method and its instruments displaying, only the instruments
-            # for the default method in the picklist.
-            instr_methods = instrument.getMethods()
-            meth = instr_methods[0] if instr_methods else None
-            if meth and an.isMethodAllowed(meth):
-                if an.getMethod() not in instr_methods:
-                    an.setMethod(meth)
 
+            if not override_analyses and an.getRawInstrument():
+                # skip, no overwrite analysis if an instrument is set
+                continue
+
+            if not an.isInstrumentAllowed(instrument):
+                # skip, instrument cannot run this analysis
+                continue
+
+            # assign the instrument
             an.setInstrument(instrument)
             total += 1
 
+            if an.getRawMethod() in supported_methods:
+                # the analysis method is supported by this instrument
+                continue
+
+            # reset and try to assign the first supported method
+            allowed = an.getRawAllowedMethods()
+            methods = list(filter(lambda m: m in allowed, supported_methods))
+            method = methods[0] if methods else None
+            an.setMethod(method)
+
         self.getField('Instrument').set(self, instrument)
         return total
 

src/senaite/core/browser/widgets/__init__.py

@@ -23,3 +23,4 @@
 from .queryselect import QuerySelectWidget  # noqa F401
 from .recordswidget import RecordsWidget  # noqa F401
 from .referencewidget import ReferenceWidget  # noqa F401
+from .selectotherwidget import SelectOtherWidget  # noqa F401

src/senaite/core/browser/widgets/selectotherwidget.py

@@ -0,0 +1,92 @@
+# -*- coding: utf-8 -*-
+
+import json
+from bika.lims import _
+from Products.Archetypes.Registry import registerWidget
+from Products.Archetypes.Widget import StringWidget
+from senaite.core.i18n import translate as t
+from senaite.core.z3cform.widgets.selectother.widget import OTHER_OPTION_VALUE
+
+
+class SelectOtherWidget(StringWidget):
+    """Select Other Widget for AT fields
+    """
+    # CSS class that is picked up by the ReactJS component
+    klass = u"senaite-selectother-widget-input"
+
+    _properties = StringWidget._properties.copy()
+    _properties.update({
+        "macro": "senaite_widgets/selectotherwidget",
+    })
+
+    def process_form(self, instance, field, form, empty_marker=None,
+                     emptyReturnsMarker=False, validating=True):
+        value = form.get(field.getName(), "")
+        if isinstance(value, list):
+            if value[0] == OTHER_OPTION_VALUE:
+                return value[1], {}
+            value = value[0]
+
+        return value, {}
+
+    def get_input_widget_attributes(self, context, field, value):
+        """Return input widget attributes for the ReactJS component
+
+        This method get called from the page template to populate the
+        attributes that are used by the ReactJS widget component.
+
+        :param context: The current context of the field
+        :param field: The current field of the widget
+        :param value: The current field value
+        """
+        option = ""
+        other = ""
+
+        # find out if the value is a predefined option
+        choices = self.get_choices(context, field)
+        options = dict(choices).keys()
+        if value in options:
+            option = value
+        elif value:
+            option = OTHER_OPTION_VALUE
+            other = value
+
+        attributes = {
+            "data-id": field.getName(),
+            "data-name": field.getName(),
+            "data-choices": choices,
+            "data-option": option,
+            "data-option_other": OTHER_OPTION_VALUE,
+            "data-other": other,
+        }
+
+        # convert all attributes to JSON
+        for key, value in attributes.items():
+            attributes[key] = json.dumps(value)
+
+        return attributes
+
+    def get_vocabulary(self, context, field):
+        func = getattr(field, "Vocabulary", None)
+        if callable(func):
+            return func(context)
+        return None
+
+    def get_choices(self, context, field):
+        """Returns the predefined options for this field
+        """
+        # generate a list of tuples (value, text) from vocabulary
+        vocabulary = self.get_vocabulary(context, field)
+        choices = list(vocabulary.items()) if vocabulary else []
+
+        # insert the empty option
+        choices.insert(0, ("", ""))
+
+        # append the "Other..." choice
+        other = (OTHER_OPTION_VALUE, t(_("Other...")))
+        choices.append(other)
+
+        return choices
+
+
+registerWidget(SelectOtherWidget, title="Select Other Widget")

src/senaite/core/content/analysisprofile.py

@@ -209,7 +209,7 @@ def validate_profile_key(data):
             return
         query = {
             "portal_type": "AnalysisProfile",
-            "profile_key": profile_key,
+            "profile_key": api.to_utf8(profile_key),
         }
         results = api.search(query, catalog=SETUP_CATALOG)
         if len(results) > 0:

src/senaite/core/schema/__init__.py

@@ -38,6 +38,8 @@
 from .phonefield import IPhoneField
 from .phonefield import PhoneField
 from .richtextfield import RichTextField
+from .selectotherfield import ISelectOtherField
+from .selectotherfield import SelectOtherField
 from .uidreferencefield import IUIDReferenceField
 from .uidreferencefield import UIDReferenceField
 
@@ -49,4 +51,5 @@
 classImplementsFirst(IntField, IIntField)
 classImplementsFirst(PhoneField, IPhoneField)
 classImplementsFirst(RichTextField, IRichTextField)
+classImplementsFirst(SelectOtherField, ISelectOtherField)
 classImplementsFirst(UIDReferenceField, IUIDReferenceField)

src/senaite/core/schema/interfaces.py

@@ -87,3 +87,8 @@ class IDurationField(ITimedelta):
 class IGPSCoordinatesField(IDict):
     """Senaite GPS Coordinated field
     """
+
+
+class ISelectOtherField(INativeString):
+    """Senaite SelectOther field
+    """

src/senaite/core/schema/selectotherfield.py

@@ -0,0 +1,14 @@
+# -*- coding: utf-8 -*-
+
+from senaite.core.schema.fields import BaseField
+from senaite.core.schema.interfaces import ISelectOtherField
+from zope.interface import implementer
+from zope.schema import Choice
+
+
+@implementer(ISelectOtherField)
+class SelectOtherField(Choice, BaseField):
+    """A field that handles a value from a predefined vocabulary or custom
+    """
+    def _validate(self, value):
+        super(SelectOtherField, self)._validate(value)

src/senaite/core/skins/senaite_templates/senaite_widgets/selectotherwidget.pt

@@ -0,0 +1,61 @@
+<html xmlns="http://www.w3.org/1999/xhtml"
+      xmlns:tal="http://xml.zope.org/namespaces/tal"
+      xmlns:metal="http://xml.zope.org/namespaces/metal"
+      xmlns:i18n="http://xml.zope.org/namespaces/i18n"
+      metal:use-macro="here/main_template/macros/master"
+      i18n:domain="senaite.core">
+<body>
+
+  <!-- VIEW MACRO -->
+  <metal:view_macro define-macro="view">
+  </metal:view_macro>
+
+  <!-- EDIT MACRO -->
+  <metal:edit_macro define-macro="edit">
+    <tal:values define="value python:field.getEditAccessor(here)() or [];
+                        session_value python:here.session_restore_value(fieldName, value);
+                        cached_value python:request.get(fieldName, session_value);
+                        value python:cached_value or value;
+                        required field/required|nothing;
+                        required python: required and 'required' or None;
+                        error_id python:errors.get(fieldName);
+                        i18n_domain field/widget/i18n_domain|context/i18n_domain|string:plone;">
+
+      <tal:ifLabel tal:condition="not: widget/render_own_label | nothing">
+        <label class="formQuestion"
+               tal:attributes="for python:fieldName">
+              <span tal:replace="python:widget.Label(here)"
+                    i18n:translate=""></span>
+          <span class="required"
+                tal:condition="field/required"
+                title="Required"
+                i18n:attributes="title title_required;">&nbsp;</span>
+          <span class="formHelp"
+                tal:define="description python:widget.Description(here)"
+                tal:content="structure description"
+                tal:attributes="id string:${fieldName}_help"
+                i18n:translate="">
+                Help
+              </span>
+        </label>
+      </tal:ifLabel>
+
+      <div tal:define="widget_attrs python:field.widget.get_input_widget_attributes(context, field, value);"
+           tal:attributes="id python:fieldName;
+                           class python: test(error_id, 'field error ' + 'Archetypes' + widget.getName(), 'field ' + 'Archetypes' + widget.getName()) + ' ' + widget.klass;
+                           data-required python:required and '1' or '0';
+                           python:widget_attrs;">
+        <!-- ReactJS controlled component -->
+      </div>
+
+      <div class="fieldErrorBox" tal:condition="required"></div>
+      <div class="fieldErrorBox" tal:content="error_id" i18n:translate=""></div>
+    </tal:values>
+
+  </metal:edit_macro>
+
+  <metal:search_macro define-macro="search">
+    <div metal:use-macro="context/widgets/string/macros/edit"></div>
+  </metal:search_macro>
+
+</body>

src/senaite/core/z3cform/interfaces.py

@@ -81,3 +81,9 @@ class IDurationWidget(IWidget):
 class IListingWidget(IWidget):
     """Listing view widget
     """
+
+
+class ISelectOtherWidget(IWidget):
+    """Allows to select a pre-populated option from a select element along with
+    manual introduction when the built-in option 'Other' is selected
+    """

src/senaite/core/z3cform/widgets/configure.zcml

@@ -9,6 +9,7 @@
   <include package=".gpscoordinates" />
   <include package=".listing" />
   <include package=".queryselect" />
+  <include package=".selectother" />
   <include package=".uidreference" />
 
   <include file="address.zcml" />

src/senaite/core/z3cform/widgets/selectother/__init__.py

@@ -0,0 +1 @@
+# -*- coding: utf-8 -*-