diff --git a/specimen/src/org/labkey/specimen/importer/ImportableColumn.java b/specimen/src/org/labkey/specimen/importer/ImportableColumn.java index c556a687278..ee71e0fb59a 100644 --- a/specimen/src/org/labkey/specimen/importer/ImportableColumn.java +++ b/specimen/src/org/labkey/specimen/importer/ImportableColumn.java @@ -24,7 +24,7 @@ public class ImportableColumn private final boolean _maskOnExport; private final boolean _unique; private final int _size; - private final Class _javaClass; + private final Class _javaClass; private final JdbcType _jdbcType; private Object _defaultValue = null; @@ -88,7 +88,7 @@ public ImportableColumn(String tsvColumnName, Collection tsvColumnAliase } // Can't use standard JdbcType.valueOf() method since this uses contains() - private static Class determineJavaType(String dbType) + private static Class determineJavaType(String dbType) { if (dbType.contains(ImportTypes.DATETIME_TYPE)) throw new IllegalStateException("Java types for DateTime/Timestamp columns should be previously initialized."); @@ -148,7 +148,7 @@ public boolean isUnique() return _unique; } - public Class getJavaClass() + public Class getJavaClass() { return _javaClass; } diff --git a/specimen/src/org/labkey/specimen/importer/RequestabilityManager.java b/specimen/src/org/labkey/specimen/importer/RequestabilityManager.java index cc6ccdc0045..3b718aca949 100644 --- a/specimen/src/org/labkey/specimen/importer/RequestabilityManager.java +++ b/specimen/src/org/labkey/specimen/importer/RequestabilityManager.java @@ -395,8 +395,6 @@ public RequestableRule(Container container) public int updateRequestability(User user, List vials) throws InvalidRuleException { TableInfo tableInfoVial = SpecimenSchema.get().getTableInfoVial(_container); - if (null == tableInfoVial) - throw new IllegalStateException("Expected Vial table to exist."); SQLFragment reason = getAvailabilityReason(); SQLFragment updateSQL = new SQLFragment("UPDATE "); @@ -573,7 +571,7 @@ public SQLFragment getFilterSQL(Container container, User user, List vials @Override public SQLFragment getAvailabilityReason() { - return new SQLFragment("'This vial is " + getMarkType().getLabel().toLowerCase() + " because it was found in the set called \"" + _queryName + "\".'"); + return new SQLFragment("?", "This vial is " + getMarkType().getLabel().toLowerCase() + " because it was found in the set called \"" + _queryName + "\"."); } @Override @@ -695,8 +693,6 @@ public LockedWhileProcessingRule(Container container) public SQLFragment getFilterSQL(Container container, User user, List vials) { TableInfo tableInfoVial = SpecimenSchema.get().getTableInfoVial(_container); - if (null == tableInfoVial) - throw new IllegalStateException("Expected Vial table to exist."); SQLFragment sql = new SQLFragment(); if (vials != null && !vials.isEmpty()) @@ -792,8 +788,6 @@ private void updateRequestability(Container container, User user, boolean resetT if (resetToAvailable) { TableInfo tableInfoVial = SpecimenSchema.get().getTableInfoVial(container); - if (null == tableInfoVial) - throw new IllegalStateException("Expected Vial table to exist."); if (logger != null) logger.info("\tResetting vials to default available state."); @@ -847,10 +841,9 @@ public void updateRequestability(Container container, User user, boolean resetTo public static String makeSpecimenUnavailableMessage(Vial vial, @Nullable String additionalText) { - String message = String.format("Specimen %s%s%s", + return String.format("Specimen %s%s%s", vial.getGlobalUniqueId(), null != vial.getAvailabilityReason() ? vial.getAvailabilityReason().replaceFirst("This vial", "") : " is not available.", null != additionalText ? " " + additionalText : ""); - return message; } } diff --git a/specimen/src/org/labkey/specimen/importer/SimpleSpecimenImporter.java b/specimen/src/org/labkey/specimen/importer/SimpleSpecimenImporter.java index 09d4f5f5b1d..13a5cfd54bc 100644 --- a/specimen/src/org/labkey/specimen/importer/SimpleSpecimenImporter.java +++ b/specimen/src/org/labkey/specimen/importer/SimpleSpecimenImporter.java @@ -84,11 +84,6 @@ public class SimpleSpecimenImporter extends SpecimenImporter private final Map _columnLabels; private final TimepointType _timepointType; - public SimpleSpecimenImporter(Container container, User user) - { - this(container, user, TimepointType.DATE, "Subject"); - } - public SimpleSpecimenImporter(Container container, User user, TimepointType timepointType, String participantIdLabel) { super(container, user); @@ -130,15 +125,6 @@ public void fixupSpecimenColumns(TabLoader tl) throws IOException tl.setColumns(mappedCols); } - // UNDONE: Converting values belongs in _process - public List> fixupSpecimenRows(List> rows) - { - List> result = new ArrayList<>(); - for (Map row : rows) - result.add(fixupSpecimenRow(row)); - return result; - } - private Map fixupSpecimenRow(Map row) { Map result = new HashMap<>(); diff --git a/specimen/src/org/labkey/specimen/importer/SpecimenSchemaImporter.java b/specimen/src/org/labkey/specimen/importer/SpecimenSchemaImporter.java index 7ace1092f9b..d4a479bdef7 100644 --- a/specimen/src/org/labkey/specimen/importer/SpecimenSchemaImporter.java +++ b/specimen/src/org/labkey/specimen/importer/SpecimenSchemaImporter.java @@ -185,7 +185,7 @@ public void process(SimpleStudyImportContext ctx, VirtualFile studyDir, BindExce current.put(pd.getName(), pd); } - DomainURIFactory factory = name -> new Pair<>(domain.getTypeURI(), container); + DomainURIFactory factory = _ -> new Pair<>(domain.getTypeURI(), container); ImportPropertyDescriptorsList pds = importHelper.getImportPropertyDescriptors(factory, propErrors, container); if (!propErrors.isEmpty())