Merge branch 'hotfix/next'. Version 3.1.6

CHANGELOG.txt

@@ -1,3 +1,43 @@
+3.1.6 (2014-12-17)
+------------------
+
+LIMS-1530: Scrambled Analysis Category order in Published Results
+LIMS-1529: Error while inserting an AR with container-based partitioning is required
+LIMS-1460: Additional field in AR for comments or results interpretation
+LIMS-1441: An error message related to partitions unit is shown when selecting analysis during AR creation
+LIMS-1470: AS Setup. File attachment field tag is missing
+LIMS-1422: Results doesn't display yes/no once verified but 1 or 0
+LIMS-1486: Typos in instrument messages
+LIMS-1498: Published Results not Showing for Logged Clients
+LIMS-1445: Scientific names should be written in italics in published reports
+LIMS-1389: Units in results publishing should allow super(sub)script format, for example in cm2 or m3
+LIMS-1500: Alere Pima's Instrument Interfice
+LIMS-1457: Exponential notation in published AR pdf should be formatted like a×10^b instead of ae^+b
+LIMS-1334: Calculate result precision from Uncertainty value
+LIMS-1446: After retracting a published AR the Sample gets cancelled
+LIMS-1390: More workflow for Batches
+LIMS-1378: Bulking up Batches
+LIMS-1479: new-version and upgrade-steps should be python viewlets
+LIMS-1362: File attachment uploads to Batches
+LIMS-1404: New Batch attributes (and their integration with existing ones on Batch views)
+LIMS-1467: Sample Point Lookup doesn't work on AR modify
+LIMS-1363: Batches per Client
+LIMS-1405: New Sample and AR attributes
+LIMS-1085: Allow Clients to add Attachments to ARs
+LIMS-1444: In AR published report accredited analysis services are not marked as accredited
+LIMS-1443: In published reports the publishing date is not shown in the pdf
+LIMS-1420: Status filter is not kept after moving to next page
+LIMS-1442: Sample Type is not filtred by Sample Point
+LIMS-1448: Reports: when you click on "Analysis turnaround time" displays others
+LIMS-1440: Error when trying to publish with analysis from different categories
+LIMS-1459: Error when checking instrument validity in manage_results
+LIMS-1430: Create an AR from batch allows you to introduce a non existent Client and Contacts don't work properly
+
+- After modifying analysis Category, reindex category name and UID for all subordinate analyses
+- Setup data import improvements and fixes
+- Simplify installation with a custom Plone overview and add site
+
+
 3.1.5 (2014-10-06)
 ------------------
 

README.rst

@@ -11,7 +11,7 @@ language of the world's first people.
 Installation
 ------------
 
-* `Installing Bika LIMS <https://github.com/bikalabs/Bika-LIMS/blob/13c8e4e/INSTALL.rst>`_
+* `Installing Bika LIMS <https://github.com/bikalabs/Bika-LIMS/blob/0c606e0/INSTALL.rst>`_
 
 Documentation
 -------------

bika/lims/browser/__init__.py

@@ -138,21 +138,3 @@ def time_format(self):
         if fmt == "time_format":
             fmt = "%I:%M %p"
         return fmt
-
-
-class ajaxGetProductVersion(BrowserView):
-    def __call__(self):
-        plone.protect.CheckAuthenticator(self.request)
-        vers = {}
-        if self.context.bika_setup.getShowNewReleasesInfo() == True:
-            pl = self.context
-            qi = pl.get('portal_quickinstaller')
-            for key in qi.keys():
-                vers[key] = qi.getProductVersion(key);
-        return json.dumps(vers)
-
-
-class ajaxHideNewReleasesInfo(BrowserView):
-    def __call__(self):
-        plone.protect.CheckAuthenticator(self.request)
-        return self.context.bika_setup.setShowNewReleasesInfo(False);

bika/lims/browser/admin.py

@@ -0,0 +1,16 @@
+from Products.CMFPlone.browser.admin import Overview as OverviewBase
+from Products.Five.browser.pagetemplatefile import ViewPageTemplateFile
+
+
+
+class Overview(OverviewBase):
+    """ Customized plone overview. """
+
+    index = ViewPageTemplateFile('templates/plone-overview.pt')
+
+    def __call__(self):
+        """ Redirect to bika.lims instance if single instance is found. """
+        sites = self.sites()
+        if len(sites) == 1 and not self.outdated(sites[0]):
+            return self.request.response.redirect(sites[0].absolute_url())
+        return self.index()

bika/lims/browser/analyses.py

@@ -2,7 +2,8 @@
 from AccessControl import getSecurityManager
 from Products.CMFPlone.utils import safe_unicode
 from bika.lims import bikaMessageFactory as _
-from bika.lims.utils import t, dicts_to_dict
+from bika.lims.utils import t, dicts_to_dict, format_supsub
+from bika.lims.utils.analysis import format_uncertainty
 from bika.lims.browser import BrowserView
 from bika.lims.browser.bika_listing import BikaListingView
 from bika.lims.config import QCANALYSIS_TYPES
@@ -332,7 +333,7 @@ def folderitems(self):
             items[i]['service_uid'] = service.UID()
             items[i]['Service'] = service.Title()
             items[i]['Keyword'] = keyword
-            items[i]['Unit'] = unit and unit or ''
+            items[i]['Unit'] = format_supsub(unit) if unit else ''
             items[i]['Result'] = ''
             items[i]['formatted_result'] = ''
             items[i]['interim_fields'] = interim_fields
@@ -605,8 +606,10 @@ def folderitems(self):
             # permission, otherwise just put an icon in Result column.
             if can_view_result:
                 items[i]['Result'] = result
-                items[i]['formatted_result'] = obj.getFormattedResult()
-                items[i]['Uncertainty'] = obj.getUncertainty(result)
+                scinot = self.context.bika_setup.getScientificNotationResults()
+                dmk = self.context.bika_setup.getResultsDecimalMark()
+                items[i]['formatted_result'] = obj.getFormattedResult(sciformat=int(scinot),decimalmark=dmk)
+                items[i]['Uncertainty'] = format_uncertainty(obj, result, decimalmark=dmk, sciformat=int(scinot))
 
             else:
                 items[i]['Specification'] = ""

bika/lims/browser/analysis.py

@@ -1,10 +1,12 @@
 # coding=utf-8
 from Products.CMFCore.utils import getToolByName
+from bika.lims.jsonapi import get_include_fields
 from bika.lims import bikaMessageFactory as _
 from bika.lims.utils import t, dicts_to_dict
-from bika.lims.interfaces import IAnalysis, IResultOutOfRange
+from bika.lims.interfaces import IAnalysis, IResultOutOfRange, IJSONReadExtender
 from bika.lims.interfaces import IFieldIcons
 from bika.lims.utils import to_utf8
+from bika.lims.utils import dicts_to_dict
 from zope.component import adapts, getAdapters
 from zope.interface import implements
 
@@ -165,5 +167,29 @@ def isOutOfRange(self, result, Min, Max, error):
         if self.isOutOfShoulderRange(result, Min, Max, error):
             return True, True
         return True, False
+
+class JSONReadExtender(object):
+
+    """- Adds the specification from Analysis Request to Analysis in JSON response
+    """
+
+    implements(IJSONReadExtender)
+    adapts(IAnalysis)
+
+    def __init__(self, context):
+        self.context = context
+
+    def analysis_specification(self):
+        ar = self.context.aq_parent
+        rr = dicts_to_dict(ar.getResultsRange(),'keyword')
+
+        return rr[self.context.getService().getKeyword()]
+
+    def __call__(self, request, data):
+        self.request = request
+        self.include_fields = get_include_fields(request)
+        if not self.include_fields or "specification" in self.include_fields:
+            data['specification'] = self.analysis_specification()
+        return data
 
 

bika/lims/browser/analysis.zcml

@@ -21,5 +21,9 @@
       for="bika.lims.interfaces.IAnalysis"
       factory="bika.lims.adapters.priorityicons.PriorityIcons"
     />
+
+    <adapter 
+    factory="bika.lims.browser.analysis.JSONReadExtender"
+    provides="bika.lims.interfaces.IJSONReadExtender" />
 
 </configure>

bika/lims/browser/analysisrequest/__init__.py

@@ -2,6 +2,7 @@
 from bika.lims.jsonapi import get_include_fields
 from bika.lims.jsonapi import load_brain_metadata
 from bika.lims.jsonapi import load_field_values
+from bika.lims.utils import dicts_to_dict
 from bika.lims.interfaces import IAnalysisRequest
 from bika.lims.interfaces import IFieldIcons
 from bika.lims.interfaces import IJSONReadExtender
@@ -150,7 +151,6 @@ def __call__(self, request, data):
         self.include_fields = get_include_fields(request)
         if not self.include_fields or "Analyses" in self.include_fields:
             data['Analyses'] = self.ar_analysis_values()
-        return data
 
 class mailto_link_from_contacts:
 

bika/lims/browser/analysisrequest/manage_results.py

@@ -1,4 +1,5 @@
 from AccessControl import getSecurityManager
+from Products.CMFPlone.utils import safe_unicode
 from bika.lims import bikaMessageFactory as _
 from bika.lims.utils import t
 from bika.lims.browser.analyses import AnalysesView
@@ -77,7 +78,7 @@ def checkInstrumentsValidity(self):
         for an in ans:
             valid = an.isInstrumentValid()
             if not valid:
-                inv = '%s (%s)' % (an.Title(), an.getInstrument().Title())
+                inv = '%s (%s)' % (safe_unicode(an.Title()), safe_unicode(an.getInstrument().Title()))
                 if inv not in invalid:
                     invalid.append(inv)
         if len(invalid) > 0:

bika/lims/browser/analysisrequest/publish.py

@@ -1,6 +1,7 @@
 from smtplib import SMTPServerDisconnected, SMTPRecipientsRefused
 from bika.lims import bikaMessageFactory as _, t
-from bika.lims.utils import to_utf8, formatDecimalMark
+from bika.lims.utils import to_utf8, formatDecimalMark, format_supsub
+from bika.lims.utils.analysis import format_uncertainty
 from bika.lims import logger
 from bika.lims.browser import BrowserView
 from bika.lims.config import POINTS_OF_CAPTURE
@@ -172,7 +173,7 @@ def _ar_data(self, ar, excludearuids=[]):
                 'remarks': ar.getRemarks(),
                 'member_discount': ar.getMemberDiscount(),
                 'date_sampled': self.ulocalized_time(ar.getDateSampled(), long_format=1),
-                'date_published': self.ulocalized_time(ar.getDatePublished(), long_format=1),
+                'date_published': self.ulocalized_time(DateTime(), long_format=1),
                 'invoiced': ar.getInvoiced(),
                 'late': ar.getLate(),
                 'subtotal': ar.getSubtotal(),
@@ -184,7 +185,8 @@ def _ar_data(self, ar, excludearuids=[]):
                 'footer': to_utf8(self.context.bika_setup.getResultFooter()),
                 'prepublish': False,
                 'child_analysisrequest': None,
-                'parent_analysisrequest': None}
+                'parent_analysisrequest': None,
+                'resultsinterpretation':ar.getResultsInterpretation()}
 
         # Sub-objects
         excludearuids.append(ar.UID())
@@ -428,11 +430,13 @@ def _analysis_data(self, analysis, decimalmark=None):
                   'id': analysis.id,
                   'title': analysis.Title(),
                   'keyword': keyword,
+                  'scientific_name': service.getScientificName(),
                   'accredited': service.getAccredited(),
                   'point_of_capture': to_utf8(POINTS_OF_CAPTURE.getValue(service.getPointOfCapture())),
                   'category': to_utf8(service.getCategoryTitle()),
                   'result': analysis.getResult(),
                   'unit': to_utf8(service.getUnit()),
+                  'formatted_unit': format_supsub(to_utf8(service.getUnit())),
                   'capture_date': analysis.getResultCaptureDate(),
                   'request_id': analysis.aq_parent.getId(),
                   'formatted_result': '',
@@ -480,7 +484,8 @@ def _analysis_data(self, analysis, decimalmark=None):
                     if specs else {}
 
         andict['specs'] = specs
-        andict['formatted_result'] = analysis.getFormattedResult(specs, decimalmark)
+        scinot = self.context.bika_setup.getScientificNotationReport()
+        andict['formatted_result'] = analysis.getFormattedResult(specs=specs, sciformat=int(scinot), decimalmark=decimalmark)
 
         fs = ''
         if specs.get('min', None) and specs.get('max', None):
@@ -490,7 +495,7 @@ def _analysis_data(self, analysis, decimalmark=None):
         elif specs.get('max', None):
             fs = '< %s' % specs['max']
         andict['formatted_specs'] = formatDecimalMark(fs, decimalmark)
-        andict['formatted_uncertainty'] = formatDecimalMark(str(analysis.getUncertainty()), decimalmark)
+        andict['formatted_uncertainty'] = format_uncertainty(analysis, analysis.getResult(), decimalmark=decimalmark, sciformat=int(scinot))
 
         # Out of range?
         if specs:

bika/lims/browser/analysisrequest/published_results.py

@@ -96,7 +96,8 @@ def folderitems(self):
         member = pm.getAuthenticatedMember()
         roles = member.getRoles()
         if 'Manager' not in roles \
-            and 'LabManager' not in roles:
+            and 'LabManager' not in roles \
+            and 'Client' not in roles:
             return []
         for x in range(len(items)):
             if 'obj' in items[x]:

bika/lims/browser/analysisrequest/templates/analysisrequest_view.pt

@@ -32,21 +32,25 @@
 <metal:content-description fill-slot="content-description">
 </metal:content-description>
 
-    <metal:content-core fill-slot="content-core" tal:define="
-        portal context/@@plone_portal_state/portal;
-        specification python:request.get('specification', view.getDefaultSpec());
-        sample here/getSample;
-        colspan python:10;
-        ar_attach_allowed here/bika_setup/getARAttachmentsPermitted;
-        review_state python:context.portal_workflow.getInfoFor(context, 'review_state');
-        inactive_state python:context.portal_workflow.getInfoFor(context, 'inactive_state', 'asdf');
-        analysis_attach_allowed here/bika_setup/getAnalysisAttachmentsPermitted;
-        attachments_allowed here/bika_setup/getAttachmentsPermitted;
-        attachments here/getAttachment | nothing;
-        update_attachments python:context.portal_membership.checkPermission('EditResults', context) or
-                                  context.portal_membership.checkPermission('EditFieldResults', context);
-        add_attachments python:context.portal_membership.checkPermission('BIKA: Add Attachment', context);
-        delete_attachments python:(add_attachments and not user.allowed(context, ['Client'])) or update_attachments;">
+<metal:content-core fill-slot="content-core" tal:define="
+    portal context/@@plone_portal_state/portal;
+    specification python:request.get('specification', view.getDefaultSpec());
+    sample here/getSample;
+    colspan python:10;
+    ar_attach_allowed here/bika_setup/getARAttachmentsPermitted;
+    review_state python:context.portal_workflow.getInfoFor(context, 'review_state');
+    inactive_state python:context.portal_workflow.getInfoFor(context, 'inactive_state', 'asdf');
+    analysis_attach_allowed here/bika_setup/getAnalysisAttachmentsPermitted;
+    attachments_allowed here/bika_setup/getAttachmentsPermitted;
+    attachments here/getAttachment | nothing;
+    update_attachments python:context.portal_membership.checkPermission('EditResults', context) or
+                              context.portal_membership.checkPermission('EditFieldResults', context);
+    add_attachments python:context.portal_membership.checkPermission('BIKA: Add Attachment', context);
+    delete_attachments python:(add_attachments and not user.allowed(context, ['Client'])) or update_attachments;">
+
+    <input type="hidden" id="bika_setup"
+            tal:attributes="bika_samplepoints python: context.bika_setup.bika_samplepoints.UID()">
+
     <div
         tal:condition="python:update_attachments or add_attachments"
         tal:define="ar_review_state review_state">

bika/lims/browser/analysisrequest/templates/reports/default.css

@@ -34,7 +34,12 @@ h2 {
     color:#777;
     font-weight:normal;
     font-style:italic;
+}
+.units sub,
+.units sup {
+    color:#777;
     font-size:10px;
+    font-style:italic;
 }
 
 table tr td,
@@ -216,6 +221,11 @@ div#section-info table {
     width: 100%;
 }
 
+img.accredited-ico {
+    vertical-align:bottom;
+    padding-right:5px;
+}
+
 @media print {
     * {
         font: 9pt Arial, Verdana, serif;