Merge branch 'hotfix/3.1.1'

bikalims · Jul 11, 2014 · 32795e9 · 32795e9
2 parents 1ac8ea3 + e9d2930
commit 32795e9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
@@ -0,0 +1,36 @@
+3.1.1
+------------------
+
+HEALTH-122: Client contact cannot open Client page/AR page blank
+HEALTH-92: Display Patients tab inside Referral Institution (Client)
+HEALTH-109: Manually adding symptoms saving but remaining on the same page
+HEALTH-124: Client contact can access doctors and patients of other clients
+HEALTH-121: Client contact gets Insufficient Privileges upon login
+HEALTH-133: Case creation: Basal body temperature fields accepting values way out of range
+HEALTH-106: Mimetype text/plain is not allowed in Drug edit view
+HEALTH-73: Current and Historic results in PDF sorted in the same order
+HEALTH-61: Sort Symptoms table on gender
+HEALTH-23: No drugs listed in Drugs folder
+Hyperlinks to Analysis Requests in Patient's Historic Results
+
+
+3.1 Naringenin (2014-06-04)
+------------------
+
+- Inherits all features from Bika LIMS release/3.1
+- Customisations towards CLIA compliance
+- Incorrect published results invalidation workflow
+- Regulatory Inspector role
+- Tighter Patient privacy restrictions
+- Life Threat Alert
+- Public Results specifications
+- Results reports inclusion of relevant QC results
+- Patient results history graphs
+- Simplified Clinical Case sections for Signs and Symptoms, Patient Condition
+- Stream-lined anonymous Patient workflow
+
+
+0.1 - 2012-12-31
+------------------
+
+- Create separate product from the Bika-LIMS/health branch.
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-Bika Health 3.1 (Naringenin)
+Bika Health 3.1.1 (Naringenin)
 ================
 
 Bika Laboratory Information Management System customised for use in Health laboratories.
@@ -7,8 +7,9 @@ Bika Laboratory Information Management System customised for use in Health labor
 
 Installation instructions:
 
-https://github.com/bikalabs/bika.health/wiki/Installing-Bika-Health-Extension
-
+1. Read https://plone.org/documentation/manual/installing-plone
+2. Read https://plone.org/documentation/kb/installing-add-ons-quick-how-to
+3. Install Plone and the "bika.health" package
 
 If you have questions, please post to one of our mailing lists:
 
@@ -17,11 +18,14 @@ If you have questions, please post to one of our mailing lists:
 * LIMS design: https://groups.google.com/forum/?hl=en#%21forum/bika-design
 * Developers: http://lists.sourceforge.net/lists/listinfo/bika-developers
 
-Please log issues, feature requests, or bug reports in the public issue
-tracker at Github: https://github.com/bikalabs/bika.health/issues
+Please log issues, feature requests, or bug reports in the [issue tracker](http://jira.bikalabs.com/)
 
-Bika Lab Systems
 
-info@bikalabs.com
 
+Bika Lab Systems
+info@bikalabs.com
 http://www.bikalabs.com
+
+Naralabs
+info@naralabs.com
+http://www.naralabs.com
diff --git a/bika/health/__init__.py b/bika/health/__init__.py
@@ -53,6 +53,7 @@ def initialize(context):
 
     from controlpanel.bika_aetiologicagents import AetiologicAgents
     from controlpanel.bika_caseoutcomes import CaseOutcomes
+    from controlpanel.bika_casesyndromicclassifications import CaseSyndromicClassifications
     from controlpanel.bika_casestatuses import CaseStatuses
     from controlpanel.bika_diseases import Diseases
     from controlpanel.bika_drugprohibitions import DrugProhibitions

diff --git a/bika/health/browser/analysisrequest/publish.py b/bika/health/browser/analysisrequest/publish.py
@@ -167,3 +167,13 @@ def get_historicresults(self, patient):
         dates, data = historic(patient)
         return {'dates': dates,
                 'results': data}
+
+    def sortDictTitles(self, analyses_dict):
+        sorted_t_list = list()
+        sorted_list = list()
+        for analysis in analyses_dict:
+            sorted_t_list.append((analyses_dict[analysis]['title'],analysis))
+        sorted_t_list.sort()
+        for tanalysis,nanalysis in sorted_t_list:
+            sorted_list.append(nanalysis)
+        return sorted_list
diff --git a/bika/health/browser/analysisrequest/report_results.pt b/bika/health/browser/analysisrequest/report_results.pt
@@ -573,16 +573,20 @@
                         tal:content="python:row['object'].Title()"
                         style='font-weight:bold;text-align:left;padding-top:8px;'></th>
                 </tr>
-                <tal:analyses repeat="analysis python:row['analyses'].itervalues()">
-                <tr tal:attributes="cat python:row['object'].Title()">
-                    <td style='text-align:left;' tal:content="python:analysis['title']"></td>
-                    <tal:rowdates repeat="date dates">
-                    <td tal:content="python:analysis.get(date,{}).get('formattedresult', '')" class='center'></td>
-                    </tal:rowdates>
-                    <td tal:content="python:analysis['units']"></td>
-                    <td tal:content="python:analysis['specs'].get('rangecomment','')"></td>
-                </tr>
-                </tal:analyses>
+		<tal:analyses define="analyses_dict python:row['analyses'];
+				      analyses_sorted_list python: view.sortDictTitles(analyses_dict);">
+		  <tal:analysis repeat="analysis analyses_sorted_list">
+                    <tr tal:attributes="cat python:row['object'].Title()">
+                      <td style='text-align:left;' tal:content="python:analyses_dict[analysis]['title']"></td>
+                      <tal:rowdates repeat="date dates">
+			<td tal:content="python:analyses_dict[analysis].get(date,{}).get('formattedresult', '')" class='center'></td>
+                      </tal:rowdates>
+                      <td tal:content="python:analyses_dict[analysis]['units']"></td>
+                      <td tal:content="python:analyses_dict[analysis]['specs'].get('rangecomment','')"></td>
+                    </tr>
+		  </tal:analysis>
+		</tal:analyses>
+
                 </tal:sampletypes>
             </tbody>
         </table>

diff --git a/bika/health/browser/client/overrides.zcml b/bika/health/browser/client/overrides.zcml
@@ -8,26 +8,26 @@
       for="bika.lims.interfaces.IClient"
       name="batches"
       class="bika.health.browser.client.batches.BatchesView"
-      permission="bika.lims.ManageClients"
+      permission="zope2.View"
       layer="bika.lims.interfaces.IBikaLIMS"
     />
-    
+
     <browser:page
       for="bika.lims.interfaces.IClient"
       name="samples"
       class="bika.health.browser.client.samples.ClientSamplesView"
-      permission="bika.lims.ManageClients"
+      permission="zope2.View"
       layer="bika.lims.interfaces.IBikaLIMS"
     />
-    
+
     <browser:page
       for="bika.lims.interfaces.IClient"
       name="base_view"
       class="bika.health.browser.client.analysisrequests.AnalysisRequestsView"
-      permission="bika.lims.ManageClients"
+      permission="zope2.View"
       layer="bika.lims.interfaces.IBikaLIMS"
     />
-    
+
     <browser:page
       for="bika.lims.interfaces.IClient"
       name="workflow_action"

diff --git a/bika/health/browser/patient/historicresults.pt b/bika/health/browser/patient/historicresults.pt
@@ -233,7 +233,13 @@
                             <span style="font-size:0.8em;color:#333;" tal:content="python:' ('+analysis['keyword']+')'"/>
                         </td>
                         <tal:rowdates repeat="date dates">
-                        <td tal:content="python:analysis.get(date,{}).get('formattedresult', '')" class='center'></td>
+			<td tal:condition="python:analysis.get(date,None)"> 
+			  <span tal:content="python:analysis.get(date,{}).get('formattedresult', '')" class='center'/> - 
+			  <a href="" tal:attributes="href python:analysis.get(date,{}).get('object','').aq_parent.absolute_url()">
+			    <span tal:content="python:analysis.get(date,{}).get('object','').aq_parent.id" class='center'/> 
+			  </a>
+			</td>
+			<td tal:condition="python:not analysis.get(date,None)"></td>
                         </tal:rowdates>
                         <td tal:content="python:analysis['units']"></td>
                         <td tal:content="python:analysis['specs'].get('rangecomment','')"></td>

diff --git a/bika/health/content/drug.py b/bika/health/content/drug.py
@@ -20,8 +20,8 @@
     ),
 
     TextField('Indications',
-        default_content_type = 'text/x-web-intelligent',
-        allowable_content_types = ('text/x-web-intelligent',),
+        default_content_type = 'text/plain',
+        allowable_content_types = ('text/plain',),
         default_output_type="text/plain",
         widget = TextAreaWidget(
             label = _("Drug indications",
@@ -31,8 +31,8 @@
     ),
 
     TextField('Posology',
-        default_content_type = 'text/x-web-intelligent',
-        allowable_content_types = ('text/x-web-intelligent',),
+        default_content_type = 'text/plain',
+        allowable_content_types = ('text/plain',),
         default_output_type="text/plain",
         widget = TextAreaWidget(
             label = _("Drug posology",
@@ -42,8 +42,8 @@
     ),
 
     TextField('SideEffects',
-        default_content_type = 'text/x-web-intelligent',
-        allowable_content_types = ('text/x-web-intelligent',),
+        default_content_type = 'text/plain',
+        allowable_content_types = ('text/plain',),
         default_output_type="text/plain",
         widget = TextAreaWidget(
             label = _("Drug side effects",
@@ -53,8 +53,8 @@
     ),
 
     TextField('Preservation',
-        default_content_type = 'text/x-web-intelligent',
-        allowable_content_types = ('text/x-web-intelligent',),
+        default_content_type = 'text/plain',
+        allowable_content_types = ('text/plain',),
         default_output_type="text/plain",
         widget = TextAreaWidget(
             label = _("Drug preservation",

diff --git a/bika/health/controlpanel/bika_symptoms.py b/bika/health/controlpanel/bika_symptoms.py
@@ -41,7 +41,7 @@ def __init__(self,context,request):
                             'index': 'description',
                             'toggle': True},
             'Gender': {'title': _('Gender'),
-                            'index': 'gender',
+                            'index': 'getGender',
                             'toggle': True},
         }
 

diff --git a/bika/health/profiles/default/metadata.xml b/bika/health/profiles/default/metadata.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <metadata>
-  <version>3002</version>
+  <version>3004</version>
   <dependencies>
     <dependency>profile-bika.lims:default</dependency>
   </dependencies>

diff --git a/bika/health/profiles/default/types/CaseSyndromicClassification.xml b/bika/health/profiles/default/types/CaseSyndromicClassification.xml
@@ -3,7 +3,7 @@
         meta_type="Factory-based Type Information with dynamic views"
         xmlns:i18n="http://xml.zope.org/namespaces/i18n"
         i18n:domain="plone">
- <property name="title" i18n:translate="">Case SyndromicClassification</property>
+ <property name="title" i18n:translate="">Case Syndromic Classification</property>
  <property name="description"></property>
  <property name="content_icon">++resource++bika.health.images/casesyndromicclassification.png</property>
  <property name="content_meta_type">CaseSyndromicClassification</property>

diff --git a/bika/health/setuphandlers.py b/bika/health/setuphandlers.py
@@ -292,13 +292,16 @@ def addColumn(cat, col):
     at.setCatalogsByType('AetiologicAgent', ['bika_setup_catalog', ])
     at.setCatalogsByType('Treatment', ['bika_setup_catalog'])
     at.setCatalogsByType('Symptom', ['bika_setup_catalog'])
+    at.setCatalogsByType('Drug', ['bika_setup_catalog'])
     at.setCatalogsByType('DrugProhibition', ['bika_setup_catalog'])
     at.setCatalogsByType('VaccinationCenter', ['bika_setup_catalog', ])
     at.setCatalogsByType('Immunization', ['bika_setup_catalog', ])
     at.setCatalogsByType('CaseStatus', ['bika_setup_catalog', ])
     at.setCatalogsByType('CaseOutcome', ['bika_setup_catalog', ])
     at.setCatalogsByType('EpidemiologicalYear', ['bika_setup_catalog', ])
     at.setCatalogsByType('IdentifierType', ['bika_setup_catalog', ])
+    addIndex(bsc,'getGender', 'FieldIndex')
+    addColumn(bsc,'getGender')
 
     # bika_patient_catalog
     bpc = getToolByName(portal, 'bika_patient_catalog', None)

diff --git a/bika/health/skins/bika_health/validate_integrity.cpy b/bika/health/skins/bika_health/validate_integrity.cpy
@@ -25,44 +25,25 @@ else:
     stat = 'created'
 
     # Redirection after saving edition forms
-    if context.portal_type == 'AetiologicAgent':
-    	state.setNextAction('redirect_to:string:${portal_url}/bika_setup/bika_aetiologicagents')
-
-    elif context.portal_type == 'BatchLabel':
-    	state.setNextAction('redirect_to:string:${portal_url}/bika_setup/bika_batchlabels')
-
-    elif context.portal_type == 'CaseOutcome':
-    	state.setNextAction('redirect_to:string:${portal_url}/bika_setup/bika_caseoutcomes')
-
-    elif context.portal_type == 'CaseStatus':
-    	state.setNextAction('redirect_to:string:${portal_url}/bika_setup/bika_casestatuses')
-
-    elif context.portal_type == 'Disease':
-    	state.setNextAction('redirect_to:string:${portal_url}/bika_setup/bika_diseases')
-
-    elif context.portal_type == 'Drug':
-    	state.setNextAction('redirect_to:string:${portal_url}/bika_setup/bika_drugs')
-
-    elif context.portal_type == 'DrugProhibition':
-    	state.setNextAction('redirect_to:string:${portal_url}/bika_setup/bika_drugprohibitions')
-
-    elif context.portal_type == 'Immunization':
-    	state.setNextAction('redirect_to:string:${portal_url}/bika_setup/bika_immunizations')
-
-    elif context.portal_type == 'Treatment':
-    	state.setNextAction('redirect_to:string:${portal_url}/bika_setup/bika_treatments')
-
-    elif context.portal_type == 'VaccionationCenter':
-    	state.setNextAction('redirect_to:string:${portal_url}/bika_setup/bika_vaccionationcenters')
-
-    elif context.portal_type == 'EpidemiologicalYear':
-    	state.setNextAction('redirect_to:string:${portal_url}/bika_setup/bika_epidemiologicalyears')
-
-    elif context.portal_type == 'IdentifierType':
-    	state.setNextAction('redirect_to:string:${portal_url}/bika_setup/bika_identifiertypes')
-
+    redirects = {'AetiologicAgent' : '/bika_setup/bika_aetiologicagents',
+                 'BatchLabel' : '/bika_setup/bika_batchlabels',
+                 'CaseOutcome': '/bika_setup/bika_caseoutcomes',
+                 'CaseStatus': '/bika_setup/bika_casestatuses',
+                 'Disease': '/bika_setup/bika_diseases',
+                 'Drug': '/bika_setup/bika_drugs',
+                 'DrugProhibition': '/bika_setup/bika_drugprohibitions',
+                 'Immunization': '/bika_setup/bika_immunizations',
+                 'Treatment': '/bika_setup/bika_treatments',
+                 'VaccionationCenter': '/bika_setup/bika_vaccionationcenters',
+                 'EpidemiologicalYear': '/bika_setup/bika_epidemiologicalyears',
+                 'IdentifierType': '/bika_setup/bika_identifiertypes',
+                 'Symptom': '/bika_setup/bika_symptoms' }
+
+    if context.portal_type in redirects:
+        redirect = 'redirect_to:string:${portal_url}' + redirects[context.portal_type]
+        state.setNextAction(redirect)
     else:
-    	stat = 'success'
+        stat = 'success'
 
-	addStatusMessage(request, message)
+    addStatusMessage(request, message)
     return state.set(status=stat)
diff --git a/bika/health/static/js/bika.health.batch_edit.js b/bika/health/static/js/bika.health.batch_edit.js
@@ -178,6 +178,9 @@ function BatchEditView() {
         fillPatientAgeAtCaseOnsetDate();
         toggleMenstrualStatus();
         toggleSymptoms();
+
+	// Advertismen for too hight/low Basal body temperature
+	basalBodyTemperatureControl();
     }
 
     /**
@@ -678,4 +681,20 @@ function BatchEditView() {
         }
         return editdoctor_overlay;
     }
+
+    function basalBodyTemperatureControl() {
+	$( "[id^='BasalBodyTemperature-Day']" ).change(function() {
+	    if ( parseInt($(this).val()) > 41 ) {
+		$(this).next().remove(".warning");
+		$(this).parent().append("<span class = 'warning'><img title='Very high temperature' src='http://localhost:8080/Plone/++resource++bika.lims.images/warning.png'></span>");
+	    }
+	    else if ( parseInt($(this).val()) < 32 ) {
+		$(this).next().remove(".warning");
+		$(this).parent().append("<span class = 'warning'><img title='Very low temperature' src='http://localhost:8080/Plone/++resource++bika.lims.images/warning.png'></span>");
+	    }
+	    else {
+		$(this).next().remove(".warning");
+	    }
+	});
+    }
 }