Merge remote-tracking branch 'refs/remotes/origin/main' into dexamund…

…sen/5718

cli/src/main/java/bio/terra/tanagra/cli/utils/Context.java

@@ -9,12 +9,10 @@ public final class Context {
   private static final String LOG_FILENAME = "tanagra.log";
   public static final String IS_TEST = "IS_TEST";
   private static final String IS_TEST_TRUE_VALUE = "true";
-
   // Env var name to optionally override where the context is persisted on disk.
   private static final String CONTEXT_DIR_OVERRIDE_NAME = "TANAGRA_CONTEXT_PARENT_DIR";
   // File paths related to persisting the context on disk.
   private static final String CONTEXT_DIRNAME = ".tanagra";
-
   // Singleton object that defines the current context or state.
   private static Config currentConfig;
 

indexer/src/main/java/bio/terra/tanagra/indexing/job/dataflow/beam/PathUtils.java

@@ -22,12 +22,12 @@
     value = {"NP_NULL_PARAM_DEREF", "RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE"},
     justification = "PCollection is using a Nullable coder")
 public final class PathUtils {
-  private PathUtils() {}
-
   // the path of nodes is currently encoded as a string. use this as the delimiter between nodes.
   private static final String PATH_DELIMITER = ".";
   private static final String PATH_DELIMITER_REGEX = "\\.";
 
+  private PathUtils() {}
+
   /**
    * Compute one path from each node in a hierarchy to a root node. If there are multiple paths from
    * a given node to a root node, then select one at random.

service/src/main/java/bio/terra/tanagra/db/ActivityLogDao.java

@@ -141,7 +141,6 @@ public List<ActivityLog> getAllActivityLogs(
         ACTIVITY_LOG_SELECT_SQL
             + (filterSql.isEmpty() ? "" : " WHERE " + filterSql)
             + " ORDER BY logged DESC LIMIT :limit OFFSET :offset";
-    LOGGER.debug("GET all activity logs: {}", sql);
     return getActivityLogsHelper(sql, params);
   }
 
@@ -186,7 +185,6 @@ private String renderSqlForActivityLogFilter(
   @ReadTransaction
   public ActivityLog getActivityLog(String activityLogId) {
     String sql = ACTIVITY_LOG_SELECT_SQL + " WHERE id = :id";
-    LOGGER.debug("GET activity log: {}", sql);
     MapSqlParameterSource params = new MapSqlParameterSource().addValue("id", activityLogId);
     List<ActivityLog> activityLogs = getActivityLogsHelper(sql, params);
 

service/src/main/java/bio/terra/tanagra/db/AnnotationDao.java

@@ -117,7 +117,6 @@ public List<AnnotationKey> getAllAnnotationKeys(String cohortId, int offset, int
     String sql =
         ANNOTATION_KEY_SELECT_SQL
             + " WHERE cohort_id = :cohort_id ORDER BY display_name LIMIT :limit OFFSET :offset";
-    LOGGER.debug("GET all annotation keys: {}", sql);
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("cohort_id", cohortId)
@@ -137,7 +136,6 @@ public List<AnnotationKey> getAnnotationKeysMatchingList(
     String sql =
         ANNOTATION_KEY_SELECT_SQL
             + " WHERE cohort_id = :cohort_id AND id IN (:ids) ORDER BY display_name LIMIT :limit OFFSET :offset";
-    LOGGER.debug("GET matching annotation keys: {}", sql);
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("cohort_id", cohortId)
@@ -150,7 +148,6 @@ public List<AnnotationKey> getAnnotationKeysMatchingList(
   @ReadTransaction
   public AnnotationKey getAnnotationKey(String cohortId, String annotationKeyId) {
     String sql = ANNOTATION_KEY_SELECT_SQL + " WHERE cohort_id = :cohort_id AND id = :id";
-    LOGGER.debug("GET annotation key: {}", sql);
     MapSqlParameterSource params =
         new MapSqlParameterSource().addValue("cohort_id", cohortId).addValue("id", annotationKeyId);
     List<AnnotationKey> annotationKeys = getAnnotationKeysHelper(sql, params);
@@ -269,7 +266,6 @@ public void updateAnnotationValues(
   @ReadTransaction
   public List<AnnotationValue.Builder> getAllAnnotationValues(String cohortId) {
     String sql = ANNOTATION_VALUE_SELECT_SQL + " WHERE av.cohort_id = :cohort_id";
-    LOGGER.debug("GET annotation values: {}", sql);
     MapSqlParameterSource params = new MapSqlParameterSource().addValue("cohort_id", cohortId);
     return jdbcTemplate.query(sql, params, ANNOTATION_VALUE_ROW_MAPPER);
   }

service/src/main/java/bio/terra/tanagra/db/CohortDao.java

@@ -160,7 +160,6 @@ public List<Cohort> getAllCohorts(String studyId, int offset, int limit) {
     String sql =
         COHORT_SELECT_SQL
             + " WHERE study_id = :study_id AND NOT is_deleted ORDER BY display_name LIMIT :limit OFFSET :offset";
-    LOGGER.debug("GET ALL cohorts: {}", sql);
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("study_id", studyId)
@@ -174,7 +173,6 @@ public List<Cohort> getCohortsMatchingList(Set<String> ids, int offset, int limi
     String sql =
         COHORT_SELECT_SQL
             + " WHERE id IN (:ids) AND NOT is_deleted ORDER BY display_name LIMIT :limit OFFSET :offset";
-    LOGGER.debug("GET MATCHING cohorts: {}", sql);
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("ids", ids)
@@ -187,7 +185,6 @@ public List<Cohort> getCohortsMatchingList(Set<String> ids, int offset, int limi
   public Cohort getCohort(String id) {
     // Fetch cohort.
     String sql = COHORT_SELECT_SQL + " WHERE id = :id";
-    LOGGER.debug("GET cohort: {}", sql);
     MapSqlParameterSource params = new MapSqlParameterSource().addValue("id", id);
     List<Cohort> cohorts = getCohortsHelper(sql, params);
 

service/src/main/java/bio/terra/tanagra/db/FeatureSetDao.java

@@ -91,7 +91,6 @@ public List<FeatureSet> getAllFeatureSets(String studyId, int offset, int limit)
     String sql =
         FEATURE_SET_SELECT_SQL
             + " WHERE study_id = :study_id AND NOT is_deleted ORDER BY display_name LIMIT :limit OFFSET :offset";
-    LOGGER.debug("GET ALL feature sets: {}", sql);
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("study_id", studyId)
@@ -105,7 +104,6 @@ public List<FeatureSet> getFeatureSetsMatchingList(Set<String> ids, int offset,
     String sql =
         FEATURE_SET_SELECT_SQL
             + " WHERE id IN (:ids) AND NOT is_deleted ORDER BY display_name LIMIT :limit OFFSET :offset";
-    LOGGER.debug("GET MATCHING feature sets: {}", sql);
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("ids", ids)
@@ -118,7 +116,6 @@ public List<FeatureSet> getFeatureSetsMatchingList(Set<String> ids, int offset,
   public FeatureSet getFeatureSet(String id) {
     // Fetch feature set.
     String sql = FEATURE_SET_SELECT_SQL + " WHERE id = :id";
-    LOGGER.debug("GET feature set: {}", sql);
     MapSqlParameterSource params = new MapSqlParameterSource().addValue("id", id);
     List<FeatureSet> featureSets = getFeatureSetsHelper(sql, params);
 

service/src/main/java/bio/terra/tanagra/db/ReviewDao.java

@@ -83,7 +83,6 @@ public List<Review> getAllReviews(String cohortId, int offset, int limit) {
     String sql =
         REVIEW_SELECT_SQL
             + " WHERE cohort_id = :cohort_id AND NOT is_deleted ORDER BY created DESC LIMIT :limit OFFSET :offset";
-    LOGGER.debug("GET ALL reviews: {}", sql);
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("cohort_id", cohortId)
@@ -97,7 +96,6 @@ public List<Review> getReviewsMatchingList(Set<String> ids, int offset, int limi
     String sql =
         REVIEW_SELECT_SQL
             + " WHERE id IN (:ids) AND NOT is_deleted ORDER BY created DESC LIMIT :limit OFFSET :offset";
-    LOGGER.debug("GET MATCHING reviews: {}", sql);
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("ids", ids)
@@ -110,7 +108,6 @@ public List<Review> getReviewsMatchingList(Set<String> ids, int offset, int limi
   public Review getReview(String id) {
     // Fetch review.
     String sql = REVIEW_SELECT_SQL + " WHERE id = :id";
-    LOGGER.debug("GET review: {}", sql);
     MapSqlParameterSource params = new MapSqlParameterSource().addValue("id", id);
     List<Review> reviews = getReviewsHelper(sql, params);
 
@@ -196,7 +193,6 @@ public Map<Literal, Integer> getPrimaryEntityIdsToStableIndex(String reviewId) {
     String sql =
         PRIMARY_ENTITY_INSTANCE_SELECT_SQL
             + " WHERE review_id = :review_id ORDER BY stable_index ASC";
-    LOGGER.debug("GET primary entity instance ids: {}", sql);
     MapSqlParameterSource params = new MapSqlParameterSource().addValue("review_id", reviewId);
     List<Pair<Literal, Integer>> idIndexPairs =
         jdbcTemplate.query(sql, params, PRIMARY_ENTITY_INSTANCE_ROW_MAPPER);

service/src/main/java/bio/terra/tanagra/db/StudyDao.java

@@ -130,7 +130,6 @@ public List<Study> getAllStudies(
         STUDY_SELECT_SQL
             + (filterSql.isEmpty() ? "" : " WHERE " + filterSql)
             + " ORDER BY display_name LIMIT :limit OFFSET :offset";
-    LOGGER.debug("GET all studies: {}", sql);
     return getStudiesHelper(sql, params);
   }
 
@@ -160,7 +159,6 @@ public List<Study> getStudiesMatchingList(
             + " WHERE id IN (:ids) "
             + (filterSql.isEmpty() ? "" : "AND " + filterSql + " ")
             + "ORDER BY display_name LIMIT :limit OFFSET :offset";
-    LOGGER.debug("GET matching studies: {}", sql);
     return getStudiesHelper(sql, params);
   }
 
@@ -217,7 +215,6 @@ private String renderSqlForStudyFilter(
   public Optional<Study> getStudyIfExists(String id) {
     // Fetch study.
     String sql = STUDY_SELECT_SQL + " WHERE id = :id";
-    LOGGER.debug("GET study: {}", sql);
     MapSqlParameterSource params = new MapSqlParameterSource().addValue("id", id);
     List<Study> studies = getStudiesHelper(sql, params);
 

service/src/main/java/bio/terra/tanagra/service/authentication/AppDefaultUtils.java

@@ -11,7 +11,6 @@
 
 /** Utilities for working with Google application default credentials. */
 public final class AppDefaultUtils {
-
   private static final String GCP_ADC_JWT_ISSUER_URL = "https://accounts.google.com";
 
   private AppDefaultUtils() {}

service/src/main/java/bio/terra/tanagra/service/authentication/UserId.java

@@ -4,7 +4,6 @@
 
 public final class UserId implements Serializable {
   private static final String DISABLED_AUTHENTICATION_USER_ID = "authentication-disabled";
-
   private final String subject;
   private final String email;
   private final String token;

service/src/test/java/bio/terra/tanagra/service/criteriaconstants/cmssynpuf/Criteria.java

@@ -11,8 +11,6 @@
 import org.apache.commons.lang3.tuple.Pair;
 
 public final class Criteria {
-  private Criteria() {}
-
   public static final Pair<String, bio.terra.tanagra.service.artifact.model.Criteria>
       DEMOGRAPHICS_PREPACKAGED_DATA_FEATURE =
           Pair.of(
@@ -67,6 +65,7 @@ private Criteria() {}
                           .build()))
               .uiConfig("")
               .build());
+
   public static final Pair<String, bio.terra.tanagra.service.artifact.model.Criteria>
       ETHNICITY_EQ_HISPANIC_OR_LATINO =
           Pair.of(
@@ -115,6 +114,7 @@ private Criteria() {}
                   .uiConfig("")
                   .tags(Map.of())
                   .build());
+
   public static final Pair<String, bio.terra.tanagra.service.artifact.model.Criteria>
       PROCEDURE_EQ_AMPUTATION =
           Pair.of(
@@ -163,4 +163,6 @@ private Criteria() {}
                               .build()))
                   .uiConfig("")
                   .build());
+
+  private Criteria() {}
 }

service/src/test/java/bio/terra/tanagra/service/criteriaconstants/cmssynpuf/CriteriaGroup.java

@@ -9,37 +9,42 @@
 import java.util.List;
 
 public final class CriteriaGroup {
-  private CriteriaGroup() {}
-
   public static final CohortRevision.CriteriaGroup CRITERIA_GROUP_GENDER =
       CohortRevision.CriteriaGroup.builder()
           .displayName("group gender")
           .criteria(List.of(GENDER_EQ_WOMAN.getValue()))
           .build();
+
   public static final CohortRevision.CriteriaGroup CRITERIA_GROUP_AGE =
       CohortRevision.CriteriaGroup.builder()
           .displayName("group gender")
           .criteria(List.of(GENDER_EQ_WOMAN.getValue()))
           .build();
+
   public static final CohortRevision.CriteriaGroup CRITERIA_GROUP_DEMOGRAPHICS =
       CohortRevision.CriteriaGroup.builder()
           .displayName("group 1")
           .criteria(List.of(GENDER_EQ_WOMAN.getValue(), ETHNICITY_EQ_HISPANIC_OR_LATINO.getValue()))
           .build();
+
   public static final CohortRevision.CriteriaGroup DISABLED_CRITERIA_GROUP_DEMOGRAPHICS =
       CohortRevision.CriteriaGroup.builder()
           .displayName("disabled group demographics")
           .criteria(List.of(GENDER_EQ_WOMAN.getValue(), ETHNICITY_EQ_HISPANIC_OR_LATINO.getValue()))
           .isDisabled(true)
           .build();
+
   public static final CohortRevision.CriteriaGroup CRITERIA_GROUP_CONDITION =
       CohortRevision.CriteriaGroup.builder()
           .displayName("group condition")
           .criteria(List.of(CONDITION_EQ_TYPE_2_DIABETES.getValue()))
           .build();
+
   public static final CohortRevision.CriteriaGroup CRITERIA_GROUP_PROCEDURE =
       CohortRevision.CriteriaGroup.builder()
           .displayName("group procedure")
           .criteria(List.of(PROCEDURE_EQ_AMPUTATION.getValue()))
           .build();
+
+  private CriteriaGroup() {}
 }

service/src/test/java/bio/terra/tanagra/service/criteriaconstants/cmssynpuf/CriteriaGroupSection.java

@@ -7,23 +7,24 @@
 import java.util.List;
 
 public final class CriteriaGroupSection {
-  private CriteriaGroupSection() {}
-
   public static final CohortRevision.CriteriaGroupSection CRITERIA_GROUP_SECTION_GENDER =
       CohortRevision.CriteriaGroupSection.builder()
           .displayName("section gender")
           .criteriaGroups(List.of(CriteriaGroup.CRITERIA_GROUP_GENDER))
           .build();
+
   public static final CohortRevision.CriteriaGroupSection CRITERIA_GROUP_SECTION_AGE =
       CohortRevision.CriteriaGroupSection.builder()
           .displayName("section age")
           .criteriaGroups(List.of(CriteriaGroup.CRITERIA_GROUP_AGE))
           .build();
+
   public static final CohortRevision.CriteriaGroupSection CRITERIA_GROUP_SECTION_DEMOGRAPHICS =
       CohortRevision.CriteriaGroupSection.builder()
           .displayName("section demographics")
           .criteriaGroups(List.of(CriteriaGroup.CRITERIA_GROUP_DEMOGRAPHICS))
           .build();
+
   public static final CohortRevision.CriteriaGroupSection
       CRITERIA_GROUP_SECTION_DEMOGRAPHICS_AND_CONDITION =
           CohortRevision.CriteriaGroupSection.builder()
@@ -96,4 +97,6 @@ private CriteriaGroupSection() {}
               .joinOperatorValue(null)
               .setIsExcluded(false)
               .build();
+
+  private CriteriaGroupSection() {}
 }

service/src/test/java/bio/terra/tanagra/service/criteriaconstants/cmssynpuf/FeatureSet.java

@@ -8,8 +8,6 @@
 public final class FeatureSet {
   private static final String UNDERLAY_NAME = "cmssynpuf";
 
-  private FeatureSet() {}
-
   public static final bio.terra.tanagra.service.artifact.model.FeatureSet CS_DEMOGRAPHICS =
       bio.terra.tanagra.service.artifact.model.FeatureSet.builder()
           .underlay(UNDERLAY_NAME)
@@ -23,4 +21,6 @@ private FeatureSet() {}
               .criteria(List.of(DEMOGRAPHICS_PREPACKAGED_DATA_FEATURE.getRight()))
               .excludeOutputAttributesPerEntity(Map.of("person", List.of("id", "gender")))
               .build();
+
+  private FeatureSet() {}
 }

service/src/test/java/bio/terra/tanagra/service/criteriaconstants/sd/CohortRevision.java

@@ -9,8 +9,6 @@
 import java.util.List;
 
 public final class CohortRevision {
-  private CohortRevision() {}
-
   private static final String UNDERLAY_NAME = "sd";
 
   public static final bio.terra.tanagra.service.artifact.model.CohortRevision CR_EMPTY =
@@ -34,12 +32,14 @@ private CohortRevision() {}
               .sections(List.of(CGS_CONDITION_EXCLUDED, CGS_GENDER))
               .setIsMostRecent(true)
               .build();
+
   public static final bio.terra.tanagra.service.artifact.model.CohortRevision CR_PROCEDURE =
       bio.terra.tanagra.service.artifact.model.CohortRevision.builder()
           .id("cr4")
           .sections(List.of(CGS_PROCEDURE))
           .setIsMostRecent(true)
           .build();
+
   public static final bio.terra.tanagra.service.artifact.model.CohortRevision
       CR_GENDER_AND_DISABLED_CONDITION =
           bio.terra.tanagra.service.artifact.model.CohortRevision.builder()
@@ -50,18 +50,23 @@ private CohortRevision() {}
 
   public static final Cohort C_EMPTY =
       Cohort.builder().underlay(UNDERLAY_NAME).id("c1").revisions(List.of(CR_EMPTY)).build();
+
   public static final Cohort C_CONDITION_EXCLUDED =
       Cohort.builder()
           .underlay(UNDERLAY_NAME)
           .id("c2")
           .revisions(List.of(CR_CONDITION_EXCLUDED))
           .build();
+
   public static final Cohort C_CONDITION_EXCLUDED_AND_GENDER =
       Cohort.builder()
           .underlay(UNDERLAY_NAME)
           .id("c3")
           .revisions(List.of(CR_CONDITION_EXCLUDED_AND_GENDER))
           .build();
+
   public static final Cohort C_PROCEDURE =
       Cohort.builder().underlay(UNDERLAY_NAME).id("c5").revisions(List.of(CR_PROCEDURE)).build();
+
+  private CohortRevision() {}
 }

service/src/test/java/bio/terra/tanagra/service/criteriaconstants/sd/Criteria.java

@@ -10,8 +10,6 @@
 import java.util.Map;
 
 public final class Criteria {
-  private Criteria() {}
-
   public static final bio.terra.tanagra.service.artifact.model.Criteria GENDER_EQ_WOMAN =
       bio.terra.tanagra.service.artifact.model.Criteria.builder()
           .selectorOrModifierName("tanagra-gender")
@@ -99,6 +97,7 @@ private Criteria() {}
                               .build())
                       .build()))
           .build();
+
   public static final bio.terra.tanagra.service.artifact.model.Criteria
       PROCEDURE_AGE_AT_OCCURRENCE_EQ_45 =
           bio.terra.tanagra.service.artifact.model.Criteria.builder()
@@ -126,4 +125,6 @@ private Criteria() {}
               .selectionData("")
               .uiConfig("")
               .build();
+
+  private Criteria() {}
 }