Upgrade script from 1.3.1 to 1.4.0

baobab/lims/profiles/default/metadata.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <metadata>
-  <version>1.3.1</version>
+  <version>1.4.0</version>
   <dependencies>
       <dependency>profile-bika.lims:default</dependency>
   </dependencies>

baobab/lims/upgrade/configure.zcml

@@ -3,7 +3,7 @@
     xmlns:genericsetup="http://namespaces.zope.org/genericsetup"
     i18n_domain="bika">
 
- <genericsetup:upgradeStep
+  <genericsetup:upgradeStep
         title="Client contact security access to projects"
         description="Change Project content type catalog to portal catalog"
         source="1300"
@@ -12,5 +12,12 @@
         sortkey="1"
         profile="baobab.lims:default"/>
 
-
-</configure>
+  <genericsetup:upgradeStep
+        title="Batch samples, donors and disease ontology"
+        description="New modules added"
+        source="1310"
+        destination="1400"
+        handler="baobab.lims.upgrade.to1400.upgrade"
+        sortkey="2"
+        profile="baobab.lims:default"/>
+</configure>

baobab/lims/upgrade/to1400.py

@@ -0,0 +1,112 @@
+from Acquisition import aq_inner
+from Acquisition import aq_parent
+from Products.CMFCore.utils import getToolByName
+from zExceptions import BadRequest
+from Products.CMFCore import permissions
+
+
+def upgrade(tool):
+    portal = aq_parent(aq_inner(tool))
+
+    at = getToolByName(portal, 'archetype_tool')
+    bsc = getToolByName(portal, 'bika_setup_catalog')
+    pc = getToolByName(portal, 'portal_catalog')
+    portal = aq_parent(aq_inner(tool))
+    setup = portal.portal_setup
+    types_tool = getToolByName(portal, 'portal_types')
+    # wf = getToolByName(portal, 'portal_workflow')
+
+    # Update all tools in which changes have been made
+    setup.runImportStepFromProfile('profile-baobab.lims:default', 'propertiestool')
+    setup.runImportStepFromProfile('profile-baobab.lims:default', 'typeinfo')
+    setup.runImportStepFromProfile('profile-baobab.lims:default', 'repositorytool')
+    setup.runImportStepFromProfile('profile-baobab.lims:default', 'workflow')
+    setup.runImportStepFromProfile('profile-baobab.lims:default', 'workflow-csv')
+    setup.runImportStepFromProfile('profile-baobab.lims:default', 'factorytool')
+    setup.runImportStepFromProfile('profile-baobab.lims:default', 'jsregistry')
+    setup.runImportStepFromProfile('profile-baobab.lims:default', 'portlets', run_dependencies=False)
+    setup.runImportStepFromProfile('profile-baobab.lims:default', 'viewlets')
+    setup.runImportStepFromProfile('profile-plone.app.jquery:default', 'jsregistry')
+
+    # Add the SampleBatches /samplebatches
+    try:
+        types_tool.constructContent(type_name="SampleBatches",
+                                   container=portal,
+                                   id='samplebatches',
+                                   title='Batch Samples')
+        obj = portal['samplebatches']
+        obj.unmarkCreationFlag()
+        obj.reindexObject()
+    except BadRequest:
+        # folder already exists
+        pass
+
+    # /samplebatches folder permissions
+    mp = portal.samplebatches.manage_permission
+    mp(permissions.ListFolderContents, ['Manager', 'LabManager', 'Analyst', ], 0)
+    mp(permissions.View, ['Manager', 'LabManager', 'Analyst'], 0)
+    mp(permissions.ModifyPortalContent, ['Manager', 'LabManager', 'Analyst', 'Owner'], 0)
+    mp('Access contents information', ['Manager', 'LabManager', 'Analyst', 'Owner'], 0)
+    portal.supplyorders.reindexObject()
+
+    # Add the SampleDonors /donors
+    try:
+        types_tool.constructContent(type_name="SampleDonors",
+                                    container=portal,
+                                    id='donors',
+                                    title='Sample Donors')
+        obj = portal['donors']
+        obj.unmarkCreationFlag()
+        obj.reindexObject()
+    except BadRequest:
+        # folder already exists
+        pass
+
+    # /donors folder permissions
+    mp = portal.donors.manage_permission
+    mp(permissions.ListFolderContents, ['Manager', 'LabManager', 'Analyst', ], 0)
+    mp(permissions.View, ['Manager', 'LabManager', 'Analyst'], 0)
+    mp(permissions.ModifyPortalContent, ['Manager', 'LabManager', 'Analyst', 'Owner'], 0)
+    mp('Access contents information', ['Manager', 'LabManager', 'Analyst', 'Owner'], 0)
+    portal.supplyorders.reindexObject()
+
+    # Add the DiseaseOntologies /disease_ontologies
+    try:
+        types_tool.constructContent(type_name="DiseaseOntologies",
+                                    container=portal,
+                                    id='disease_ontologies',
+                                    title='Disease Ontology')
+        obj = portal['disease_ontologies']
+        obj.unmarkCreationFlag()
+        obj.reindexObject()
+    except BadRequest:
+        # folder already exists
+        pass
+
+    # Set catalogs for SampleBatch, SampleDonor and DiseaseOntology
+    at.setCatalogsByType('SampleBatch', ['bika_catalog', 'portal_catalog'])
+    at.setCatalogsByType('SampleDonor', ['bika_catalog', 'portal_catalog'])
+    at.setCatalogsByType('DiseaseOntology', ['bika_catalog', 'portal_catalog'])
+
+    # Set to None; Batch, Donor and DiseaseOntology to all Sample objects
+    proxies = pc(portal_type="Sample")
+    samples = (proxy.getObject() for proxy in proxies)
+    for sample in samples:
+        sample.getField('Batch').set(sample, None)
+        sample.getField('Donor').set(sample, None)
+        sample.getField('DiseaseOntology').set(sample, None)
+
+    # change objects catalog from bsc to pc
+    at.setCatalogsByType('ManagedStorage', ['portal_catalog', ])
+    at.setCatalogsByType('UnmanagedStorage', ['portal_catalog', ])
+    at.setCatalogsByType('StorageUnit', ['portal_catalog', ])
+    at.setCatalogsByType('StoragePosition', ['portal_catalog', ])
+
+    for content_type in ['ManagedStorage', 'UnmanagedStorage', 'StorageUnit', 'StoragePosition']:
+        proxies = bsc(portal_type=content_type)
+        storages = (proxy.getObject() for proxy in proxies)
+        for storage in storages:
+            storage.unmarkCreationFlag()
+            storage.reindexObject()
+
+    return True