Catalog mapping for Samples and Analyses

CHANGES.rst

@@ -5,6 +5,7 @@ Changelog
 2.3.0 (unreleased)
 ------------------
 
+- #2130 Catalog mapping for Samples and Analyses
 - #2131 Allow to edit the analysis service sort keys in the services listing
 - #2133 Filter Contact and CCContact by Client on first click
 - #2134 Render unit after result and interim fields

src/senaite/core/setuphandlers.py

@@ -33,7 +33,14 @@
 from senaite.core.api.catalog import get_columns
 from senaite.core.api.catalog import get_indexes
 from senaite.core.api.catalog import reindex_index
+from senaite.core.catalog import ANALYSIS_CATALOG
 from senaite.core.catalog import AUDITLOG_CATALOG
+from senaite.core.catalog import AUTOIMPORTLOG_CATALOG
+from senaite.core.catalog import REPORT_CATALOG
+from senaite.core.catalog import SAMPLE_CATALOG
+from senaite.core.catalog import SENAITE_CATALOG
+from senaite.core.catalog import SETUP_CATALOG
+from senaite.core.catalog import WORKSHEET_CATALOG
 from senaite.core.catalog import AnalysisCatalog
 from senaite.core.catalog import AuditlogCatalog
 from senaite.core.catalog import AutoImportLogCatalog
@@ -57,6 +64,8 @@
     class INonInstallable(Interface):
         pass
 
+PORTAL_CATALOG = "portal_catalog"
+
 
 @implementer(INonInstallable)
 class HiddenProfiles(object):
@@ -105,62 +114,82 @@ def getNonInstallableProfiles(self):
 
 INDEXES = (
     # catalog, id, indexed attribute, type
-    ("portal_catalog", "Analyst", "", "FieldIndex"),
-    ("portal_catalog", "analysisRequestTemplates", "", "FieldIndex"),
-    ("portal_catalog", "getFullname", "", "FieldIndex"),
-    ("portal_catalog", "getName", "", "FieldIndex"),
-    ("portal_catalog", "getParentUID", "", "FieldIndex"),
-    ("portal_catalog", "getUsername", "", "FieldIndex"),
-    ("portal_catalog", "is_active", "", "BooleanIndex"),
-    ("portal_catalog", "path", "getPhysicalPath", "ExtendedPathIndex"),
-    ("portal_catalog", "review_state", "", "FieldIndex"),
-    ("portal_catalog", "sample_uid", "", "KeywordIndex"),
-    ("portal_catalog", "title", "", "FieldIndex"),
+    (PORTAL_CATALOG, "Analyst", "", "FieldIndex"),
+    (PORTAL_CATALOG, "analysisRequestTemplates", "", "FieldIndex"),
+    (PORTAL_CATALOG, "getFullname", "", "FieldIndex"),
+    (PORTAL_CATALOG, "getName", "", "FieldIndex"),
+    (PORTAL_CATALOG, "getParentUID", "", "FieldIndex"),
+    (PORTAL_CATALOG, "getUsername", "", "FieldIndex"),
+    (PORTAL_CATALOG, "is_active", "", "BooleanIndex"),
+    (PORTAL_CATALOG, "path", "getPhysicalPath", "ExtendedPathIndex"),
+    (PORTAL_CATALOG, "review_state", "", "FieldIndex"),
+    (PORTAL_CATALOG, "sample_uid", "", "KeywordIndex"),
+    (PORTAL_CATALOG, "title", "", "FieldIndex"),
 )
 
 COLUMNS = (
     # catalog, column name
-    ("portal_catalog", "analysisRequestTemplates"),
-    ("portal_catalog", "review_state"),
-    ("portal_catalog", "getClientID"),
-    ("portal_catalog", "Analyst"),
+    (PORTAL_CATALOG, "analysisRequestTemplates"),
+    (PORTAL_CATALOG, "review_state"),
+    (PORTAL_CATALOG, "getClientID"),
+    (PORTAL_CATALOG, "Analyst"),
 )
 
 CATALOG_MAPPINGS = (
     # portal_type, catalog_ids
-    ("ARReport", ["senaite_catalog_report", "portal_catalog"]),
-    ("ARTemplate", ["senaite_catalog_setup", "portal_catalog"]),
-    ("AnalysisCategory", ["senaite_catalog_setup", "portal_catalog"]),
-    ("AnalysisProfile", ["senaite_catalog_setup", "portal_catalog"]),
-    ("AnalysisService", ["senaite_catalog_setup", "portal_catalog"]),
-    ("AnalysisSpec", ["senaite_catalog_setup", "portal_catalog"]),
-    ("Attachment", ["senaite_catalog", "portal_catalog"]),
-    ("AttachmentType", ["senaite_catalog_setup", "portal_catalog"]),
-    ("Batch", ["senaite_catalog", "portal_catalog"]),
-    ("BatchLabel", ["senaite_catalog_setup", "portal_catalog"]),
-    ("Calculation", ["senaite_catalog_setup", "portal_catalog"]),
-    ("Container", ["senaite_catalog_setup", "portal_catalog"]),
-    ("ContainerType", ["senaite_catalog_setup", "portal_catalog"]),
-    ("Department", ["senaite_catalog_setup", "portal_catalog"]),
-    ("Instrument", ["senaite_catalog_setup", "portal_catalog"]),
-    ("InstrumentType", ["senaite_catalog_setup", "portal_catalog"]),
-    ("LabContact", ["senaite_catalog_setup", "portal_catalog"]),
-    ("LabProduct", ["senaite_catalog_setup", "portal_catalog"]),
-    ("Manufacturer", ["senaite_catalog_setup", "portal_catalog"]),
-    ("Method", ["senaite_catalog_setup", "portal_catalog"]),
-    ("Multifile", ["senaite_catalog_setup", "portal_catalog"]),
-    ("Preservation", ["senaite_catalog_setup", "portal_catalog"]),
-    ("ReferenceDefinition", ["senaite_catalog_setup", "portal_catalog"]),
-    ("ReferenceSample", ["senaite_catalog", "portal_catalog"]),
-    ("SampleCondition", ["senaite_catalog_setup", "portal_catalog"]),
-    ("SampleMatrix", ["senaite_catalog_setup", "portal_catalog"]),
-    ("SamplePoint", ["senaite_catalog_setup", "portal_catalog"]),
-    ("SampleType", ["senaite_catalog_setup", "portal_catalog"]),
-    ("SamplingDeviation", ["senaite_catalog_setup", "portal_catalog"]),
-    ("StorageLocation", ["senaite_catalog_setup", "portal_catalog"]),
-    ("SubGroup", ["senaite_catalog_setup", "portal_catalog"]),
-    ("Supplier", ["senaite_catalog_setup", "portal_catalog"]),
-    ("WorksheetTemplate", ["senaite_catalog_setup", "portal_catalog"]),
+    ("ARReport", [REPORT_CATALOG, PORTAL_CATALOG]),
+    ("ARTemplate", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Analysis", [ANALYSIS_CATALOG]),
+    ("AnalysisCategory", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("AnalysisProfile", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("AnalysisRequest", [SAMPLE_CATALOG]),
+    ("AnalysisService", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("AnalysisSpec", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Attachment", [SENAITE_CATALOG, PORTAL_CATALOG]),
+    ("AttachmentType", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("AutoImportLog", [AUTOIMPORTLOG_CATALOG, PORTAL_CATALOG]),
+    ("Batch", [SENAITE_CATALOG, PORTAL_CATALOG]),
+    ("BatchLabel", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Calculation", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Client", [PORTAL_CATALOG]),
+    ("Contact", [PORTAL_CATALOG]),
+    ("Container", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("ContainerType", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Department", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("DuplicateAnalysis", [ANALYSIS_CATALOG, PORTAL_CATALOG]),
+    ("Instrument", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("InstrumentCalibration", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("InstrumentCertification", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("InstrumentLocation", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("InstrumentMaintenanceTask", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("InstrumentScheduledTask", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("InstrumentType", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("InstrumentValidation", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Invoice", [SENAITE_CATALOG, PORTAL_CATALOG]),
+    ("LabContact", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("LabProduct", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Laboratory", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Manufacturer", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Method", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Multifile", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Preservation", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Pricelist", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("ReferenceAnalysis", [ANALYSIS_CATALOG, PORTAL_CATALOG]),
+    ("ReferenceDefinition", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("ReferenceSample", [SENAITE_CATALOG, PORTAL_CATALOG]),
+    ("RejectAnalysis", [ANALYSIS_CATALOG, PORTAL_CATALOG]),
+    ("Report", [REPORT_CATALOG, PORTAL_CATALOG]),
+    ("SampleCondition", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("SampleMatrix", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("SamplePoint", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("SampleType", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("SamplingDeviation", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("StorageLocation", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("SubGroup", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Supplier", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("SupplierContact", [SETUP_CATALOG, PORTAL_CATALOG]),
+    ("Worksheet", [WORKSHEET_CATALOG, PORTAL_CATALOG]),
+    ("WorksheetTemplate", [SETUP_CATALOG, PORTAL_CATALOG]),
 )
 
 

src/senaite/core/tests/doctests/Catalogs.rst

@@ -0,0 +1,80 @@
+Catalogs
+--------
+
+SENAITE comes with several catalogs to index specific objects.
+For Archetype objects, the catalog mapping is done in `archetype_tool`.
+
+
+Running this test from the buildout directory::
+
+    bin/test test_textual_doctests -t Catalogs
+
+
+Test Setup
+..........
+
+Needed Imports::
+
+    >>> from bika.lims import api
+
+    >>> from senaite.core.catalog import ANALYSIS_CATALOG
+    >>> from senaite.core.catalog import AUDITLOG_CATALOG
+    >>> from senaite.core.catalog import SAMPLE_CATALOG
+    >>> from senaite.core.setuphandlers import CATALOG_MAPPINGS
+
+
+Variables::
+
+    >>> portal = self.portal
+    >>> request = self.request
+    >>> archetype_tool = api.get_tool("archetype_tool")
+
+
+Catalog Mappings
+................
+
+Catalogs should be mapped according to the catalog mappings:
+
+    >>> passed = {}
+
+    >>> for mapping in CATALOG_MAPPINGS:
+    ...     portal_type, catalogs = mapping
+    ...     mapped = archetype_tool.catalog_map.get(portal_type)
+    ...     passed[portal_type] = set(catalogs).issubset(mapped)
+
+    >>> all(passed.values())
+    True
+
+
+Sample Catalog
+..............
+
+Samples should be registered in the sample catalog:
+
+    >>> catmap = archetype_tool.catalog_map.get("AnalysisRequest")
+
+    >>> len(catmap)
+    2
+
+    >>> SAMPLE_CATALOG in catmap
+    True
+
+    >>> AUDITLOG_CATALOG in catmap
+    True
+
+
+Analysis Catalog
+................
+
+Analyses should be registered in the analysis catalog:
+
+    >>> catmap = archetype_tool.catalog_map.get("Analysis")
+
+    >>> len(catmap)
+    2
+
+    >>> ANALYSIS_CATALOG in catmap
+    True
+
+    >>> AUDITLOG_CATALOG in catmap
+    True

src/senaite/core/upgrade/v02_03_000.py

@@ -27,8 +27,11 @@
 from senaite.core.catalog import SETUP_CATALOG
 from senaite.core.catalog.report_catalog import ReportCatalog
 from senaite.core.config import PROJECTNAME as product
+from senaite.core.setuphandlers import CATALOG_MAPPINGS
 from senaite.core.setuphandlers import _run_import_step
 from senaite.core.setuphandlers import add_senaite_setup
+from senaite.core.setuphandlers import setup_auditlog_catalog_mappings
+from senaite.core.setuphandlers import setup_catalog_mappings
 from senaite.core.setuphandlers import setup_core_catalogs
 from senaite.core.upgrade import upgradestep
 from senaite.core.upgrade.utils import UpgradeUtils
@@ -70,6 +73,12 @@ def upgrade(tool):
     setup.runImportStepFromProfile(profile, "plone.app.registry")
     setup.runImportStepFromProfile(profile, "controlpanel")
 
+    # Ensure the catalog mappings for Analyses and Samples is correct
+    # https://github.com/senaite/senaite.core/pull/2130
+    setup_catalog_mappings(portal, catalog_mappings=CATALOG_MAPPINGS)
+    # remap auditlog catalog
+    setup_auditlog_catalog_mappings(portal)
+
     # Add new setup folder to portal
     add_senaite_setup(portal)