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TASK-4248 - improve usage documentation of REST search endpoint by adding regexp comment #2327

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merged 4 commits into from
Sep 4, 2023
Merged

TASK-4248 - improve usage documentation of REST search endpoint by adding regexp comment #2327

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aed710f
core: add REGEX comment to /search and /distinct, #TASK-4248
pfurio Aug 28, 2023
88ed0ea
core: improve regex description, #TASK-4906
pfurio Aug 30, 2023
48babe1
Merge branch 'develop' into TASK-4248
pfurio Sep 1, 2023
48889d0
app: generate cli automatically, #TASK-4248
pfurio Sep 1, 2023
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66 changes: 34 additions & 32 deletions opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,8 @@ public class ParamConstants {
public static final String RELEASE_DESCRIPTION = "Release when it was created";
public static final String INTERNAL_STATUS_PARAM = "internalStatus";
public static final String INTERNAL_STATUS_DESCRIPTION = "Filter by internal status";
private static final String REGEX_SUPPORT = ". Also admits basic regular expressions using the operator '~', "
+ "i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.";
@Deprecated // Use INTERNAL_VARIANT_INDEX_STATUS_PARAM
public static final String INTERNAL_INDEX_STATUS_PARAM = "internalIndexStatus";
public static final String INTERNAL_VARIANT_INDEX_STATUS_PARAM = "internalVariantIndexStatus";
Expand Down Expand Up @@ -169,20 +171,20 @@ public class ParamConstants {
+ "exception whenever one of the entries looked for cannot be shown for whichever reason";
public static final String FILE_ID_DESCRIPTION = "File ID";
public static final String FILE_NAME_DESCRIPTION = "File name";
public static final String FILE_NAMES_DESCRIPTION = "Comma separated list of file names";
public static final String FILE_NAMES_DESCRIPTION = "Comma separated list of file names" + REGEX_SUPPORT;
// ---------------------------------------------
public static final String FILE_PATH_PARAM = "path";
public static final String FILE_PATH_DESCRIPTION = "File path";
public static final String FILE_PATHS_DESCRIPTION = "Comma separated list of paths";
public static final String FILE_URIS_DESCRIPTION = "Comma separated list of uris";
public static final String FILE_PATHS_DESCRIPTION = "Comma separated list of paths" + REGEX_SUPPORT;
public static final String FILE_URIS_DESCRIPTION = "Comma separated list of uris" + REGEX_SUPPORT;
public static final String FILE_TYPE_DESCRIPTION = "File type, either FILE or DIRECTORY";
public static final String FILE_FORMAT_DESCRIPTION = "Comma separated Format values. For existing Formats see files/formats";
public static final String FILE_EXTERNAL_DESCRIPTION = "Boolean field indicating whether to filter by external or non external files";
public static final String FILE_BIOFORMAT_DESCRIPTION = "Comma separated Bioformat values. For existing Bioformats see " +
"files/bioformats";
public static final String FILE_STATUS_DESCRIPTION = "File status";
public static final String FILE_DESCRIPTION_DESCRIPTION = "Description";
public static final String FILE_TAGS_DESCRIPTION = "Tags";
public static final String FILE_TAGS_DESCRIPTION = "Tags" + REGEX_SUPPORT;
public static final String FILE_SOFTWARE_NAME_PARAM = "softwareName";
public static final String FILE_SOFTWARE_NAME_DESCRIPTION = "Software name";
public static final String FILE_JOB_ID_DESCRIPTION = "Job ID that created the file(s) or folder(s)";
Expand Down Expand Up @@ -316,12 +318,12 @@ public class ParamConstants {
public static final String INDIVIDUAL_MOTHER_DESCRIPTION = "Mother ID, name or UUID";
public static final String INDIVIDUAL_SAMPLES_DESCRIPTION = "Sample ID, name or UUID";
public static final String INDIVIDUAL_SEX_DESCRIPTION = "Individual sex";
public static final String INDIVIDUAL_ETHNICITY_DESCRIPTION = "Individual ethnicity";
public static final String INDIVIDUAL_ETHNICITY_DESCRIPTION = "Individual ethnicity" + REGEX_SUPPORT;
public static final String INDIVIDUAL_DATE_OF_BIRTH_DESCRIPTION = "Individual date of birth";
public static final String INDIVIDUAL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION;
public static final String INDIVIDUAL_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION;
public static final String INDIVIDUAL_POPULATION_NAME_DESCRIPTION = "Population name";
public static final String INDIVIDUAL_POPULATION_SUBPOPULATION_DESCRIPTION = "Subpopulation name";
public static final String INDIVIDUAL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT;
public static final String INDIVIDUAL_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION + REGEX_SUPPORT;
public static final String INDIVIDUAL_POPULATION_NAME_DESCRIPTION = "Population name" + REGEX_SUPPORT;
public static final String INDIVIDUAL_POPULATION_SUBPOPULATION_DESCRIPTION = "Subpopulation name" + REGEX_SUPPORT;
public static final String INDIVIDUAL_KARYOTYPIC_SEX_DESCRIPTION = "Individual karyotypic sex";
public static final String INDIVIDUAL_LIFE_STATUS_DESCRIPTION = "Individual life status";
public static final String INDIVIDUAL_DELETED_DESCRIPTION = DELETED_DESCRIPTION;
Expand Down Expand Up @@ -358,8 +360,8 @@ public class ParamConstants {
public static final String FAMILY_MEMBERS_DESCRIPTION = "Comma separated list of family members";
public static final String FAMILY_SAMPLES_DESCRIPTION = "Comma separated list of member's samples";
public static final String FAMILY_EXPECTED_SIZE_DESCRIPTION = "Expected size of the family (number of members)";
public static final String FAMILY_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION;
public static final String FAMILY_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION;
public static final String FAMILY_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION + REGEX_SUPPORT;
public static final String FAMILY_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT;
public static final String FAMILY_CREATION_DATE_DESCRIPTION = CREATION_DATE_DESCRIPTION;
public static final String FAMILY_MODIFICATION_DATE_DESCRIPTION = MODIFICATION_DATE_DESCRIPTION;
public static final String FAMILY_DELETED_DESCRIPTION = DELETED_DESCRIPTION;
Expand Down Expand Up @@ -422,7 +424,7 @@ public class ParamConstants {
public static final String CLINICAL_STATUS_PARAM = STATUS_PARAM;
public static final String CLINICAL_INTERNAL_STATUS_PARAM = INTERNAL_STATUS_PARAM;
public static final String CLINICAL_TYPE_DESCRIPTION = "Clinical Analysis type";
public static final String CLINICAL_DISORDER_DESCRIPTION = "Clinical Analysis disorder";
public static final String CLINICAL_DISORDER_DESCRIPTION = "Clinical Analysis disorder" + REGEX_SUPPORT;
public static final String CLINICAL_FILES_DESCRIPTION = "Clinical Analysis files";
public static final String CLINICAL_SAMPLE_DESCRIPTION = "Sample associated to the proband or any member of a family";
public static final String CLINICAL_INDIVIDUAL_DESCRIPTION = "Proband or any member of a family";
Expand Down Expand Up @@ -466,7 +468,7 @@ public class ParamConstants {
public static final String INTERPRETATION_LOCKED_PARAM = "locked";
public static final String INTERPRETATION_CLINICAL_ANALYSIS_ID_DESCRIPTION = "Clinical Analysis id";
public static final String INTERPRETATION_ANALYST_ID_DESCRIPTION = "Analyst ID";
public static final String INTERPRETATION_METHOD_NAME_DESCRIPTION = "Interpretation method name";
public static final String INTERPRETATION_METHOD_NAME_DESCRIPTION = "Interpretation method name" + REGEX_SUPPORT;
public static final String INTERPRETATION_PANELS_DESCRIPTION = "Interpretation panels";
public static final String INTERPRETATION_PRIMARY_FINDINGS_IDS_DESCRIPTION = "Interpretation primary findings";
public static final String INTERPRETATION_SECONDARY_FINDINGS_IDS_DESCRIPTION = "Interpretation secondary findings";
Expand Down Expand Up @@ -498,12 +500,12 @@ public class ParamConstants {
public static final String PANEL_ACL_PARAM = ACL_PARAM;
public static final String PANEL_RELEASE_PARAM = RELEASE_PARAM;
public static final String PANEL_SNAPSHOT_PARAM = SNAPSHOT_PARAM;
public static final String PANEL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION;
public static final String PANEL_VARIANTS_DESCRIPTION = "Comma separated list of variant ids";
public static final String PANEL_GENES_DESCRIPTION = "Comma separated list of gene ids";
public static final String PANEL_REGIONS_DESCRIPTION = "Comma separated list of regions";
public static final String PANEL_CATEGORIES_DESCRIPTION = "Comma separated list of category names";
public static final String PANEL_TAGS_DESCRIPTION = "Panel tags";
public static final String PANEL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT;
public static final String PANEL_VARIANTS_DESCRIPTION = "Comma separated list of variant ids" + REGEX_SUPPORT;
public static final String PANEL_GENES_DESCRIPTION = "Comma separated list of gene ids" + REGEX_SUPPORT;
public static final String PANEL_REGIONS_DESCRIPTION = "Comma separated list of regions" + REGEX_SUPPORT;
public static final String PANEL_CATEGORIES_DESCRIPTION = "Comma separated list of category names" + REGEX_SUPPORT;
public static final String PANEL_TAGS_DESCRIPTION = "Panel tags" + REGEX_SUPPORT;
public static final String PANEL_DELETED_DESCRIPTION = DELETED_DESCRIPTION;
public static final String PANEL_STATUS_DESCRIPTION = STATUS_DESCRIPTION;

Expand Down Expand Up @@ -539,7 +541,7 @@ public class ParamConstants {
public static final String JOB_DEPENDS_ON_DESCRIPTION = "Comma separated list of existing job IDs the job will depend on.";
public static final String JOB_TOOL_ID_PARAM = "toolId";
public static final String JOB_TOOL_TYPE_PARAM = "toolType";
public static final String JOB_TOOL_ID_DESCRIPTION = "Tool ID executed by the job";
public static final String JOB_TOOL_ID_DESCRIPTION = "Tool ID executed by the job" + REGEX_SUPPORT;
public static final String JOB_TOOL_TYPE_DESCRIPTION = "Tool type executed by the job [OPERATION, ANALYSIS]";
public static final String JOB_USER_PARAM = "userId";
public static final String JOB_USER_DESCRIPTION = "User that created the job";
Expand Down Expand Up @@ -1475,34 +1477,34 @@ public class ParamConstants {
public static final String ADMIN_CATALOG_JWT_SECRETKEY = "The body web service secretKey parameter";
private static final String UP_TO_100 = " up to a maximum of 100";
public static final String FILES_DESCRIPTION = "Comma separated list of file IDs or names" + UP_TO_100;
public static final String FILES_ID_DESCRIPTION = "Comma separated list of file IDs" + UP_TO_100;
public static final String FILES_ID_DESCRIPTION = "Comma separated list of file IDs" + UP_TO_100 + REGEX_SUPPORT;
public static final String FILES_UUID_DESCRIPTION = "Comma separated list file UUIDs" + UP_TO_100;
public static final String SAMPLES_DESCRIPTION = "Comma separated list sample IDs or UUIDs" + UP_TO_100;
public static final String SAMPLES_ID_DESCRIPTION = "Comma separated list sample IDs" + UP_TO_100;
public static final String SAMPLES_UUID_DESCRIPTION = "Comma separated list sample UUIDs" + UP_TO_100;
public static final String INDIVIDUALS_DESCRIPTION = "Comma separated list of individual IDs, names or UUIDs" + UP_TO_100;
public static final String INDIVIDUALS_ID_DESCRIPTION = "Comma separated list individual IDs" + UP_TO_100;
public static final String INDIVIDUAL_NAME_DESCRIPTION = "Comma separated list individual names" + UP_TO_100;
public static final String INDIVIDUALS_ID_DESCRIPTION = "Comma separated list individual IDs" + UP_TO_100 + REGEX_SUPPORT;
public static final String INDIVIDUAL_NAME_DESCRIPTION = "Comma separated list individual names" + UP_TO_100 + REGEX_SUPPORT;
public static final String INDIVIDUAL_UUID_DESCRIPTION = "Comma separated list individual UUIDs" + UP_TO_100;
public static final String FAMILIES_DESCRIPTION = "Comma separated list of family IDs or names" + UP_TO_100;
public static final String FAMILY_ID_DESCRIPTION = "Comma separated list family IDs" + UP_TO_100;
public static final String FAMILY_NAME_DESCRIPTION = "Comma separated list family names" + UP_TO_100;
public static final String FAMILY_ID_DESCRIPTION = "Comma separated list family IDs" + UP_TO_100 + REGEX_SUPPORT;
public static final String FAMILY_NAME_DESCRIPTION = "Comma separated list family names" + UP_TO_100 + REGEX_SUPPORT;
public static final String FAMILY_UUID_DESCRIPTION = "Comma separated list family UUIDs" + UP_TO_100;
public static final String COHORTS_DESCRIPTION = "Comma separated list of cohort IDs or UUIDs" + UP_TO_100;
public static final String COHORT_IDS_DESCRIPTION = "Comma separated list of cohort IDs" + UP_TO_100;
public static final String COHORT_NAMES_DESCRIPTION = "Comma separated list of cohort names" + UP_TO_100;
public static final String COHORT_IDS_DESCRIPTION = "Comma separated list of cohort IDs" + UP_TO_100 + REGEX_SUPPORT;
public static final String COHORT_NAMES_DESCRIPTION = "Comma separated list of cohort names" + UP_TO_100 + REGEX_SUPPORT;
public static final String COHORT_UUIDS_DESCRIPTION = "Comma separated list of cohort IDs" + UP_TO_100;
public static final String CLINICAL_ID_DESCRIPTION = "Comma separated list of Clinical Analysis IDs" + UP_TO_100;
public static final String CLINICAL_ID_DESCRIPTION = "Comma separated list of Clinical Analysis IDs" + UP_TO_100 + REGEX_SUPPORT;
public static final String CLINICAL_UUID_DESCRIPTION = "Comma separated list of Clinical Analysis UUIDs" + UP_TO_100;
public static final String CLINICAL_ANALYSES_DESCRIPTION = "Comma separated list of clinical analysis IDs or names" + UP_TO_100;
public static final String INTERPRETATION_ID_DESCRIPTION = "Comma separated list of Interpretation IDs" + UP_TO_100;
public static final String INTERPRETATION_ID_DESCRIPTION = "Comma separated list of Interpretation IDs" + UP_TO_100 + REGEX_SUPPORT;
public static final String INTERPRETATION_UUID_DESCRIPTION = "Comma separated list of Interpretation UUIDs" + UP_TO_100;
public static final String INTERPRETATION_DESCRIPTION = "Comma separated list of clinical interpretation IDs " + UP_TO_100;
public static final String PANEL_ID_DESCRIPTION = "Comma separated list of panel IDs " + UP_TO_100;
public static final String PANEL_ID_DESCRIPTION = "Comma separated list of panel IDs " + UP_TO_100 + REGEX_SUPPORT;
public static final String PANEL_UUID_DESCRIPTION = "Comma separated list of panel UUIDs " + UP_TO_100;
public static final String PANEL_NAME_DESCRIPTION = "Comma separated list of panel names " + UP_TO_100;
public static final String PANEL_NAME_DESCRIPTION = "Comma separated list of panel names " + UP_TO_100 + REGEX_SUPPORT;
public static final String JOBS_DESCRIPTION = "Comma separated list of job IDs or UUIDs" + UP_TO_100;
public static final String JOB_IDS_DESCRIPTION = "Comma separated list of job IDs" + UP_TO_100;
public static final String JOB_IDS_DESCRIPTION = "Comma separated list of job IDs" + UP_TO_100 + REGEX_SUPPORT;
public static final String JOB_UUIDS_DESCRIPTION = "Comma separated list of job UUIDs" + UP_TO_100;
// ---------------------------------------------
public static final String PROJECTS_DESCRIPTION = "Comma separated list of projects [user@]project" + UP_TO_100;
Expand Down
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