Dynamic Analysis Specifications

bika/lims/adapters/configure.zcml

@@ -5,6 +5,14 @@
     xmlns:monkey="http://namespaces.plone.org/monkey"
     i18n_domain="senaite.core">
 
+    <!-- Dynamic Results Range Adapter
+         Looked up in `abstractroutineanalysis.getResultsRange` -->
+    <adapter
+      for="bika.lims.interfaces.IRoutineAnalysis"
+      factory=".dynamicresultsrange.DynamicResultsRange"
+      provides="bika.lims.interfaces.IDynamicResultsRange"
+      />
+
     <adapter
       for="zope.interface.Interface
            zope.publisher.interfaces.browser.IBrowserRequest"

bika/lims/adapters/dynamicresultsrange.py

@@ -0,0 +1,138 @@
+# -*- coding: utf-8 -*-
+
+from bika.lims import api
+from bika.lims.interfaces import IDynamicResultsRange
+from zope.interface import implementer
+
+marker = object()
+
+DEFAULT_RANGE_KEYS = [
+    "min",
+    "warn_min",
+    "min_operator",
+    "minpanic",
+    "max",
+    "warn_max",
+    "max",
+    "maxpanic",
+    "error",
+]
+
+
+@implementer(IDynamicResultsRange)
+class DynamicResultsRange(object):
+    """Default Dynamic Results Range Adapter
+    """
+
+    def __init__(self, analysis):
+        self.analysis = analysis
+        self.analysisrequest = analysis.getRequest()
+        self.specification = self.analysisrequest.getSpecification()
+        self.dynamicspec = None
+        if self.specification:
+            self.dynamicspec = self.specification.getDynamicAnalysisSpec()
+
+    @property
+    def keyword(self):
+        """Analysis Keyword
+        """
+        return self.analysis.getKeyword()
+
+    @property
+    def range_keys(self):
+        """The keys of the result range dict
+        """
+        if not self.specification:
+            return DEFAULT_RANGE_KEYS
+        # return the subfields of the specification
+        return self.specification.getField("ResultsRange").subfields
+
+    def convert(self, value):
+        # convert referenced UIDs to the Title
+        if api.is_uid(value):
+            obj = api.get_object_by_uid(value)
+            return api.get_title(obj)
+        return value
+
+    def get_match_data(self):
+        """Returns a fieldname -> value mapping of context data
+
+        The fieldnames are selected from the column names of the dynamic
+        specifications file. E.g. the column "Method" of teh specifications
+        file will lookup the value (title) of the Analysis and added to the
+        mapping like this: `{"Method": "Method-1"}`.
+
+        :returns: fieldname -> value mapping
+        :rtype: dict
+        """
+        data = {}
+
+        # Lookup the column names on the Analysis and the Analysis Request
+        for column in self.dynamicspec.get_header():
+            an_value = getattr(self.analysis, column, marker)
+            ar_value = getattr(self.analysisrequest, column, marker)
+            if an_value is not marker:
+                data[column] = self.convert(an_value)
+            elif ar_value is not marker:
+                data[column] = self.convert(ar_value)
+
+        return data
+
+    def get_results_range(self):
+        """Return the dynamic results range
+
+        The returning dicitionary should containe at least the `min` and `max`
+        values to override the ResultsRangeDict data.
+
+        :returns: An `IResultsRangeDict` compatible dict
+        :rtype: dict
+        """
+        if self.dynamicspec is None:
+            return {}
+        # A matching Analysis Keyword is mandatory for any further matches
+        keyword = self.analysis.getKeyword()
+        by_keyword = self.dynamicspec.get_by_keyword()
+        # Get all specs (rows) from the Excel with the same Keyword
+        specs = by_keyword.get(keyword)
+        if not specs:
+            return {}
+
+        # Generate a match data object, which match both the column names and
+        # the field names of the Analysis.
+        match_data = self.get_match_data()
+
+        rr = {}
+
+        # Iterate over the rows and return the first where **all** values match
+        # with the analysis' values
+        for spec in specs:
+            skip = False
+
+            for k, v in match_data.items():
+                # break if the values do not match
+                if v != spec[k]:
+                    skip = True
+                    break
+
+            # skip the whole specification row
+            if skip:
+                continue
+
+            # at this point we have a match, update the results range dict
+            for key in self.range_keys:
+                value = spec.get(key, marker)
+                # skip if the range key is not set in the Excel
+                if value is marker:
+                    continue
+                # skip if the value is not floatable
+                if not api.is_floatable(value):
+                    continue
+                # set the range value
+                rr[key] = value
+            # return the updated result range
+            return rr
+
+        return rr
+
+    def __call__(self):
+        return self.get_results_range()

bika/lims/browser/configure.zcml

@@ -20,6 +20,7 @@
   <include file="calcs.zcml"/>
   <include file="clientfolder.zcml"/>
   <include file="contact.zcml"/>
+  <include file="dynamic_analysisspec.zcml"/>
   <include file="instrument.zcml"/>
   <include file="instrumentlocation.zcml"/>
   <include file="instrumenttype.zcml"/>

bika/lims/browser/dynamic_analysisspec.py

@@ -0,0 +1,72 @@
+# -*- coding: utf-8 -*-
+
+import collections
+
+from bika.lims import _
+from bika.lims import api
+from senaite.core.listing.view import ListingView
+
+
+class DynamicAnalysisSpecView(ListingView):
+    """A listing view that shows the contents of the Excel
+    """
+    def __init__(self, context, request):
+        super(DynamicAnalysisSpecView, self).__init__(context, request)
+
+        self.pagesize = 50
+        self.context_actions = {}
+        self.title = api.get_title(self.context)
+        self.description = api.get_description(self.context)
+        self.show_search = False
+        self.show_column_toggles = False
+
+        if self.context.specs_file:
+            filename = self.context.specs_file.filename
+            self.description = _("Contents of the file {}".format(filename))
+
+        self.specs = self.context.get_specs()
+        self.total = len(self.specs)
+
+        self.columns = collections.OrderedDict()
+        for title in self.context.get_header():
+            self.columns[title] = {
+                "title": title,
+                "toggle": True}
+
+        self.review_states = [
+            {
+                "id": "default",
+                "title": _("All"),
+                "contentFilter": {},
+                "transitions": [],
+                "custom_transitions": [],
+                "columns": self.columns.keys()
+            }
+        ]
+
+    def update(self):
+        super(DynamicAnalysisSpecView, self).update()
+
+    def before_render(self):
+        super(DynamicAnalysisSpecView, self).before_render()
+
+    def make_empty_item(self, **kw):
+        """Create a new empty item
+        """
+        item = {
+            "uid": None,
+            "before": {},
+            "after": {},
+            "replace": {},
+            "allow_edit": [],
+            "disabled": False,
+            "state_class": "state-active",
+        }
+        item.update(**kw)
+        return item
+
+    def folderitems(self):
+        items = []
+        for record in self.specs:
+            items.append(self.make_empty_item(**record))
+        return items

bika/lims/browser/dynamic_analysisspec.zcml

@@ -0,0 +1,17 @@
+<configure
+    xmlns="http://namespaces.zope.org/zope"
+    xmlns:browser="http://namespaces.zope.org/browser"
+    i18n_domain="senaite.core">
+
+  <!-- Needed for cmf.AddPortalContent permission -->
+  <include package="Products.CMFCore" file="permissions.zcml" />
+
+  <browser:page
+      name="view"
+      for="bika.lims.content.dynamic_analysisspec.IDynamicAnalysisSpec"
+      class=".dynamic_analysisspec.DynamicAnalysisSpecView"
+      permission="zope2.View"
+      layer="bika.lims.interfaces.IBikaLIMS"
+      />
+
+</configure>

bika/lims/browser/viewlets/configure.zcml

@@ -245,4 +245,18 @@
       layer="bika.lims.interfaces.IBikaLIMS"
       />
 
+  <!-- Dynamic Specifications viewlet. Displays an informative message when the
+    specification has a dynamic specification assigned, so ranges might be
+    overriden by the ranges provided in the xls file from the Dynamic
+    Specification -->
+  <browser:viewlet
+    for="bika.lims.interfaces.IAnalysisSpec"
+    name="bika.lims.dynamic_spec_viewlet"
+    class=".dynamic_specs.DynamicSpecsViewlet"
+    manager="plone.app.layout.viewlets.interfaces.IAboveContent"
+    template="templates/dynamic_specs_viewlet.pt"
+    permission="zope2.View"
+    layer="bika.lims.interfaces.IBikaLIMS"
+  />
+
 </configure>

bika/lims/browser/viewlets/dynamic_specs.py

@@ -0,0 +1,30 @@
+# -*- coding: utf-8 -*-
+#
+# This file is part of SENAITE.CORE.
+#
+# SENAITE.CORE is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, version 2.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program; if not, write to the Free Software Foundation, Inc., 51
+# Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# Copyright 2018-2020 by it's authors.
+# Some rights reserved, see README and LICENSE.
+
+from Products.Five.browser.pagetemplatefile import ViewPageTemplateFile
+from plone.app.layout.viewlets import ViewletBase
+
+
+class DynamicSpecsViewlet(ViewletBase):
+    """ Displays an informative message when the specification has a dynamic
+    specification assigned, so ranges might be overriden by the ranges provided
+    in the xls file from the Dynamic Specification
+    """
+    template = ViewPageTemplateFile("templates/dynamic_specs_viewlet.pt")

bika/lims/browser/viewlets/templates/dynamic_specs_viewlet.pt

@@ -0,0 +1,25 @@
+<div tal:omit-tag=""
+     tal:define="dynamic_spec python:context.getDynamicAnalysisSpec()"
+     tal:condition="python:dynamic_spec"
+     i18n:domain="senaite.core">
+
+  <div class="visualClear"></div>
+
+  <div id="portal-alert">
+    <div class="portlet-alert-item alert alert-warning alert-dismissible">
+      <button type="button" class="close" data-dismiss="alert" aria-label="Close">
+        <span aria-hidden="true">&times;</span>
+      </button>
+      <strong i18n:translate="">
+        This Analysis Specification has a Dynamic Specification assigned
+      </strong>
+      <p class="title">
+        <span i18n:translate="">
+          Be aware that the ranges provided in the spreadsheet file from the
+          dynamic specification might override the ranges defined in the
+          Specifications list below.
+        </span>
+      </p>
+    </div>
+  </div>
+</div>