Code Cleanliness: Address reported Errors in taglist report. #187
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We went from 926 to 499. |
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SubstanceReferenceInformation and SubstancePolymer 127 of the issues. |
prb112
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Jan 25, 2020
Signed-off-by: Paul Bastide <[email protected]> #187
<?xml version="1.0" encoding="UTF-8"?>
<report xmlns="org.codehaus.mojo.taglist-maven-plugin">
<tags>
<tag name="DOCUMENT_ME" count="0" />
<tag name="NOT_YET_DOCUMENTED" count="0" />
<tag name="FIXME" count="0" />
<tag name="XXX" count="1">
<files>
<file name="com.ibm.fhir.persistence.jdbc.dao.impl.ParameterVisitorBatchDAO" count="1">
<comments>
<comment>
<lineNumber>432</lineNumber>
<comment>why no check for isBase on this one?</comment>
</comment>
</comments>
</file>
</files>
</tag>
<tag name="TODO" count="198">
<files>
<file name="com.ibm.fhir.operation.bulkdata.client.BulkDataClient" count="2">
<comments>
<comment>
<lineNumber>264</lineNumber>
<comment>Here is where we NEED to check the tenantId = the tenant id on the job before responding.</comment>
</comment>
<comment>
<lineNumber>314</lineNumber>
<comment>Convert to yyyy-MM-dd'T'HH:mm:ss</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.schema.control.FhirSchemaGenerator" count="3">
<comments>
<comment>
<lineNumber>379</lineNumber>
<comment>should not need to add as a table and an object. Get the table to add itself?</comment>
</comment>
<comment>
<lineNumber>414</lineNumber>
<comment>should not need to add as a table and an object. Get the table to add itself?</comment>
</comment>
<comment>
<lineNumber>521</lineNumber>
<comment>Table should be immutable, so add support to the Builder for this</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.jdbc.test.spec.Main" count="2">
<comments>
<comment>
<lineNumber>48</lineNumber>
<comment>refactor to reduce duplication with the fhir-server-test Main app.</comment>
</comment>
<comment>
<lineNumber>257</lineNumber>
<comment>add as part of a regression test</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.schema.control.TransactionProviderTest" count="2">
<comments>
<comment>
<lineNumber>25</lineNumber>
<comment>Auto-generated method stub</comment>
</comment>
<comment>
<lineNumber>31</lineNumber>
<comment>Auto-generated method stub</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.database.utils.model.DatabaseObject" count="1">
<comments>
<comment>
<lineNumber>192</lineNumber>
<comment>find a better way to track database-level type stuff (not schema-specific)</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.registry.spec.test.VitalSignsProfileTest" count="3">
<comments>
<comment>
<lineNumber>117</lineNumber>
<comment>pattern</comment>
</comment>
<comment>
<lineNumber>119</lineNumber>
<comment>value set binding</comment>
</comment>
<comment>
<lineNumber>121</lineNumber>
<comment>reference types</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.openapi.generator.FHIROpenApiGenerator" count="8">
<comments>
<comment>
<lineNumber>127</lineNumber>
<comment>make this configurable</comment>
</comment>
<comment>
<lineNumber>593</lineNumber>
<comment>add patch</comment>
</comment>
<comment>
<lineNumber>1032</lineNumber>
<comment>when a filter was passed, limit this to just the resource types included in the filter</comment>
</comment>
<comment>
<lineNumber>1039</lineNumber>
<comment>how to "overwrite" the Resource definition and say that the value is fixed? https://github.com/OAI/OpenAPI-Specification/issues/1313 property.add("enum", modelClass.getSimpleName());</comment>
</comment>
<comment>
<lineNumber>1376</lineNumber>
<comment>add patch</comment>
</comment>
<comment>
<lineNumber>1484</lineNumber>
<comment>introspect the resourceModelClass to tell if its truly applicable or not</comment>
</comment>
<comment>
<lineNumber>1509</lineNumber>
<comment>introspect the resourceModelClass to tell if its truly applicable or not</comment>
</comment>
<comment>
<lineNumber>1532</lineNumber>
<comment>introspect the resourceModelClass to tell if its truly applicable or not</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.model.resource.SubstancePolymer" count="67">
<comments>
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<lineNumber>34</lineNumber>
<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<lineNumber>1279</lineNumber>
<comment>.</comment>
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<comment>.</comment>
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<lineNumber>1488</lineNumber>
<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<lineNumber>1880</lineNumber>
<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<lineNumber>1970</lineNumber>
<comment>.</comment>
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<lineNumber>1988</lineNumber>
<comment>.</comment>
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<lineNumber>1998</lineNumber>
<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
</comment>
<comment>
<lineNumber>2476</lineNumber>
<comment>.</comment>
</comment>
<comment>
<lineNumber>2490</lineNumber>
<comment>.</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.jdbc.impl.FHIRPersistenceJDBCImpl" count="8">
<comments>
<comment>
<lineNumber>1087</lineNumber>
<comment>support component expressions that result in multiple nodes On the current schema, this means creating a different CompositeParmValue for each ordered set of component values. For example, if a composite has two components and each one's expression results in two nodes ([Code1,Code2] and [Quantity1,Quantity2]) and each node results in a single ExtractedParameterValue, then we need to generate CompositeParmVal objects for [Code1,Quantity1], [Code1,Quantity2], [Code2,Quantity1], and [Code2,Quantity2]. Assumption: this should be rare.</comment>
</comment>
<comment>
<lineNumber>1111</lineNumber>
<comment>support component searchParms that lead to multiple ExtractedParameterValues On the current schema, this means creating a different CompositeParmValue for each ordered set of component values. For example: If a composite has two components and each results in two extracted parameters ([A,B] and [1,2] respectively) then we need to generate CompositeParmVal objects for [A,1], [A,2], [B,1], and [B,2] Assumption: this should only be common for Quantity search parameters with both a coded unit and a display unit, and in these cases, the coded unit is almost always the preferred value for search.</comment>
</comment>
<comment>
<lineNumber>1142</lineNumber>
<comment>return this as a OperationOutcomeIssue with severity of WARNING</comment>
</comment>
<comment>
<lineNumber>1155</lineNumber>
<comment>add an issue to the OperationOutcome in the return object</comment>
</comment>
<comment>
<lineNumber>1186</lineNumber>
<comment>return this as a OperationOutcomeIssue with severity of WARNING</comment>
</comment>
<comment>
<lineNumber>1199</lineNumber>
<comment>add an issue to the OperationOutcome in the return object</comment>
</comment>
<comment>
<lineNumber>1438</lineNumber>
<comment>this method needs to either get merged or better differentiated with the old one used for search</comment>
</comment>
<comment>
<lineNumber>1465</lineNumber>
<comment>this method needs to either get merged or better differentiated with the new one that supports history operation via generics. Start by better understanding what happens for `_include` and `_revinclude` search results that contain multiple different types</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDataAccessException" count="1">
<comments>
<comment>
<lineNumber>16</lineNumber>
<comment>replace with Builder fluent pattern to align with the new R4 model style</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.search.util.SearchUtil" count="3">
<comments>
<comment>
<lineNumber>613</lineNumber>
<comment>do we really need to forbid this?</comment>
</comment>
<comment>
<lineNumber>669</lineNumber>
<comment>this will fire on each search result parameter; maybe move this above to where we handle _sort + _include/_revinclude?</comment>
</comment>
<comment>
<lineNumber>908</lineNumber>
<comment>start enforcing this: "For token parameters on elements of type ContactPoint, uri, or boolean, the presence of the pipe symbol SHALL NOT be used - only the [parameter]=[code] form is allowed</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDBCleanupException" count="1">
<comments>
<comment>
<lineNumber>16</lineNumber>
<comment>use Builder fluent pattern to align with R4 model style</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.database.utils.db2.Db2TableInfo" count="1">
<comments>
<comment>
<lineNumber>14</lineNumber>
<comment>...add useful info</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.model.test.TestUtil" count="1">
<comments>
<comment>
<lineNumber>116</lineNumber>
<comment>review Reference id</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.path.test.FHIRPathSpecTest" count="1">
<comments>
<comment>
<lineNumber>237</lineNumber>
<comment>use the groupName to define a TestNG group (or suite)</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.jdbc.dao.impl.ResourceDAOImpl" count="2">
<comments>
<comment>
<lineNumber>523</lineNumber>
<comment>avoid the round-trip and use the configured data schema name</comment>
</comment>
<comment>
<lineNumber>545</lineNumber>
<comment>FHIR_ADMIN schema name needs to come from the configuration/context</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.util.FHIRPersistenceUtil" count="1">
<comments>
<comment>
<lineNumber>85</lineNumber>
<comment>this will clone the entire resource, but we only want the minimal parameters</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.jdbc.util.JDBCQueryBuilder" count="1">
<comments>
<comment>
<lineNumber>1271</lineNumber>
<comment>What does returning null do here? We should handle this better.</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.path.test.FHIRPathNodeVisitorTest" count="1">
<comments>
<comment>
<lineNumber>77</lineNumber>
<comment>make sure Resource.id paths work in FHIRPath</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.test.common.AbstractPersistenceTest" count="1">
<comments>
<comment>
<lineNumber>87</lineNumber>
<comment>it would be better for our unit tests if we could load config files from the classpath</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.server.test.FHIRUrlParserTest" count="1">
<comments>
<comment>
<lineNumber>75</lineNumber>
<comment>should be parsed into two parameters</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.jdbc.util.SortedQuerySegmentAggregator" count="1">
<comments>
<comment>
<lineNumber>262</lineNumber>
<comment>This is probably wrong</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.model.resource.MedicinalProductPharmaceutical" count="2">
<comments>
<comment>
<lineNumber>92</lineNumber>
<comment>.</comment>
</comment>
<comment>
<lineNumber>502</lineNumber>
<comment>.</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.search.test.AbstractSearchStringTest" count="2">
<comments>
<comment>
<lineNumber>51</lineNumber>
<comment>add test for diacritics and other unusual characters</comment>
</comment>
<comment>
<lineNumber>69</lineNumber>
<comment>add test for diacritics and other unusual characters</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.jdbc.dao.impl.ParameterNameDAOImpl" count="1">
<comments>
<comment>
<lineNumber>114</lineNumber>
<comment>schema should be known by application. Fix to avoid an extra round-trip.</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.swagger.generator.FHIRSwaggerGenerator" count="4">
<comments>
<comment>
<lineNumber>428</lineNumber>
<comment>add patch</comment>
</comment>
<comment>
<lineNumber>810</lineNumber>
<comment>when a filter was passed, limit this to just the resource types included in the filter</comment>
</comment>
<comment>
<lineNumber>817</lineNumber>
<comment>how to "overwrite" the Resource definition and say that the value is fixed? https://github.com/OAI/OpenAPI-Specification/issues/1313 property.add("enum", modelClass.getSimpleName());</comment>
</comment>
<comment>
<lineNumber>1145</lineNumber>
<comment>add patch</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.model.util.JsonSupport" count="1">
<comments>
<comment>
<lineNumber>164</lineNumber>
<comment>replace this method with a class that converts Resource to JsonObject directly</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.test.ProcessorTest" count="2">
<comments>
<comment>
<lineNumber>81</lineNumber>
<comment>update tests</comment>
</comment>
<comment>
<lineNumber>82</lineNumber>
<comment>add processor support for R4 types Rewritten for R4 to drive tests by introspecting model</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.search.test.AbstractSearchURITest" count="1">
<comments>
<comment>
<lineNumber>65</lineNumber>
<comment>add test for diacritics and other unusual characters</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.jdbc.util.JDBCParameterBuildingVisitor" count="3">
<comments>
<comment>
<lineNumber>163</lineNumber>
<comment>get the implicit code system</comment>
</comment>
<comment>
<lineNumber>251</lineNumber>
<comment>consider moving integer values to separate column so they can be searched different from decimals</comment>
</comment>
<comment>
<lineNumber>605</lineNumber>
<comment>how to properly calculate the outer limits if there are no "bounds"?</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.database.utils.common.DateMath" count="1">
<comments>
<comment>
<lineNumber>21</lineNumber>
<comment>use java.time instead</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.jdbc.dao.impl.ParameterVisitorBatchDAO" count="1">
<comments>
<comment>
<lineNumber>518</lineNumber>
<comment>figure out how to use the visitor here and still get back the generated id THE ORDER OF THESE IF STATEMENTS MUST MATCH THE ORDER OF THE INSERT FIELDS</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.model.resource.SubstanceReferenceInformation" count="60">
<comments>
<comment>
<lineNumber>36</lineNumber>
<comment>.</comment>
</comment>
<comment>
<lineNumber>64</lineNumber>
<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<lineNumber>627</lineNumber>
<comment>.</comment>
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<lineNumber>817</lineNumber>
<comment>.</comment>
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<lineNumber>831</lineNumber>
<comment>.</comment>
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<lineNumber>845</lineNumber>
<comment>.</comment>
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<lineNumber>863</lineNumber>
<comment>.</comment>
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<lineNumber>900</lineNumber>
<comment>.</comment>
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<lineNumber>921</lineNumber>
<comment>.</comment>
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<lineNumber>931</lineNumber>
<comment>.</comment>
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<comment>.</comment>
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<lineNumber>1131</lineNumber>
<comment>.</comment>
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<lineNumber>1145</lineNumber>
<comment>.</comment>
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<comment>.</comment>
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<lineNumber>1177</lineNumber>
<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
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<comment>.</comment>
</comment>
<comment>
<lineNumber>1688</lineNumber>
<comment>.</comment>
</comment>
<comment>
<lineNumber>1903</lineNumber>
<comment>.</comment>
</comment>
<comment>
<lineNumber>1917</lineNumber>
<comment>.</comment>
</comment>
<comment>
<lineNumber>1931</lineNumber>
<comment>.</comment>
</comment>
<comment>
<lineNumber>1945</lineNumber>
<comment>.</comment>
</comment>
<comment>
<lineNumber>1959</lineNumber>
<comment>.</comment>
</comment>
<comment>
<lineNumber>1973</lineNumber>
<comment>.</comment>
</comment>
<comment>
<lineNumber>1994</lineNumber>
<comment>.</comment>
</comment>
<comment>
<lineNumber>2008</lineNumber>
<comment>.</comment>
</comment>
<comment>
<lineNumber>2026</lineNumber>
<comment>.</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.path.evaluator.FHIRPathEvaluator" count="3">
<comments>
<comment>
<lineNumber>343</lineNumber>
<comment>add to log</comment>
</comment>
<comment>
<lineNumber>545</lineNumber>
<comment>log this</comment>
</comment>
<comment>
<lineNumber>766</lineNumber>
<comment>"equals" and "equivalent" have different semantics</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.model.visitor.CopyingVisitor" count="2">
<comments>
<comment>
<lineNumber>234</lineNumber>
<comment>can we wrap all the setters so that subclasses don't need to explicitly call markDirty()?</comment>
</comment>
<comment>
<lineNumber>248</lineNumber>
<comment>can we wrap all the setters so that subclasses don't need to explicitly call markDirty()?</comment>
</comment>
</comments>
</file>
<file name="com.ibm.fhir.persistence.search.test.AbstractSearchReferenceTest" count="3">
<comments>
<comment>
<lineNumber>39</lineNumber>
<comment>does this work if you define the extension in a StructureDefinition and declare the allowed types? assertSearchReturnsSavedResource("Reference-relative", "123");</comment>
</comment>
<comment>
<lineNumber>45</lineNumber>
<comment>if this matched the hostname that the test was running on, would it work? assertSearchReturnsSavedResource("Reference-relative", "https://example.com/Patient/123");</comment>
</comment>
<comment>
<lineNumber>76</lineNumber>
<comment>if the resource contained an absolute URI which matches the hostname where the current test was running, would these work? assertSearchReturnsSavedResource("Reference-absolute", "123"); assertSearchReturnsSavedResource("Reference-absolute", "Patient/123"); assertSearchReturnsSavedResource("Reference-absolute:Patient", "123");</comment>
</comment>
</comments>
</file>
</files>
</tag>
</tags>
</report> |
prb112
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Jan 25, 2020
Code Cleanliness: Address reported Errors in taglist report. #187
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The purpose of this issue/epic is to improve the code cleanliness: Address reported Errors in taglist report.
Report
fhir-parent
FHIR-TOOLS
To Generate the Report:
1 - Add the plugin to the pom.xml in each project
2 - Run the command
mvn taglist:taglist -f fhir-parent/pom.xml -Daggregate=true3 - Retrieve the taglist.xml from the target/taglist directory.
REPORTS
The following XML files identify the use of TODO in a module (rename from txt to xml):
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