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Temp fix until data is repaired by Sharra
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@Gcolon021
Gcolon021 committed Nov 13, 2024
1 parent 4ca002b commit 64aedc6
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Showing 2 changed files with 244 additions and 8 deletions.
232 changes: 232 additions & 0 deletions fucked_data.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,232 @@
{
'columnmeta_is_stigmatized': 'false',
'columnmeta_name': 'cih_care',
'description': 'cih_care from form weekly_covid_infection_history and visit Acute week 2 from pediatric cohort answerdata.tsv.',
'columnmeta_min': '',
'HPDS_PATH': '\\phs003461\\recover_pediatric\\acute_week_2\\weekly_covid_infection_history\\cih_care\\',
'derived_group_id': None,
'columnmeta_hpds_path': '\\phs003461\\recover_pediatric\\acute_week_2\\weekly_covid_infection_history\\cih_care\\',
'columnmeta_var_id': 'weekly_covid_infection_history',
'columnmeta_var_group_description': None,
'derived_var_description': 'cih_care from form weekly_covid_infection_history and visit Acute week 2 from pediatric cohort answerdata.tsv.',
'derived_variable_level_data': '{}',
'data_hierarchy': '',
'derived_group_description': None,
'columnmeta_max': '',
'columnmeta_description': 'cih_care from form weekly_covid_infection_history and visit Acute week 2 from pediatric cohort answerdata.tsv.',
'derived_study_id': 'phs003461',
'hashed_var_id': '9ca7dd0ad806dbad3bf00ce358abc174184f005ab40b06b8b3770a5cc8d15f85',
'columnmeta_data_type': 'categorical',
'derived_var_id': 'weekly_covid_infection_history',
'columnmeta_study_id': 'phs003461',
'is_stigmatized': 'false',
'derived_var_name': 'cih_care',
'derived_study_abv_name': 'RECOVER_Pediatric',
'derived_study_description': 'Researching COVID to Enhance Recovery (RECOVER): Post Acute Sequelae of SARS-CoV-2 (PASC) Pediatric Cohort Study',
'columnmeta_var_group_id': None,
'derived_group_name': None,
'columnmeta_HPDS_PATH': '\\phs003461\\recover_pediatric\\acute_week_2\\weekly_covid_infection_history\\cih_care\\'
}
{
'columnmeta_is_stigmatized': 'false',
'columnmeta_name': 'hcn_adhdcause',
'description': 'hcn_adhdcause from form special_health_care_needs_screener and visit 24_month_arm_5 from pediatric cohort answerdata.tsv.',
'columnmeta_min': '',
'HPDS_PATH': '\\phs003461\\recover_pediatric\\24_month_arm_5\\special_health_care_needs_screener\\hcn_adhdcause\\',
'derived_group_id': None,
'columnmeta_hpds_path': '\\phs003461\\recover_pediatric\\24_month_arm_5\\special_health_care_needs_screener\\hcn_adhdcause\\',
'columnmeta_var_id': 'special_health_care_needs_screener',
'columnmeta_var_group_description': None,
'derived_var_description': 'hcn_adhdcause from form special_health_care_needs_screener and visit 24_month_arm_5 from pediatric cohort answerdata.tsv.',
'derived_variable_level_data': '{}',
'data_hierarchy': '',
'derived_group_description': None,
'columnmeta_max': '',
'columnmeta_description': 'hcn_adhdcause from form special_health_care_needs_screener and visit 24_month_arm_5 from pediatric cohort answerdata.tsv.',
'derived_study_id': 'phs003461',
'hashed_var_id': 'e2319b340b23c63240d82572e93d71820dad9cfdcb0f6faadc990e915568fb48',
'columnmeta_data_type': 'categorical',
'derived_var_id': 'special_health_care_needs_screener',
'columnmeta_study_id': 'phs003461',
'is_stigmatized': 'false',
'derived_var_name': 'hcn_adhdcause',
'derived_study_abv_name': 'RECOVER_Pediatric',
'derived_study_description': 'Researching COVID to Enhance Recovery (RECOVER): Post Acute Sequelae of SARS-CoV-2 (PASC) Pediatric Cohort Study',
'columnmeta_var_group_id': None,
'derived_group_name': None,
'columnmeta_HPDS_PATH': '\\phs003461\\recover_pediatric\\24_month_arm_5\\special_health_care_needs_screener\\hcn_adhdcause\\'
}
{
'columnmeta_is_stigmatized': 'false',
'columnmeta_name': 'miscpots_colldt',
'description': 'miscpots_colldt from form related_conditions and visit 12month from pediatric congenital cohort answerdata.tsv.',
'columnmeta_min': '',
'HPDS_PATH': '\\phs003461\\recover_pediatric_congenital\\12month\\related_conditions\\miscpots_colldt\\',
'derived_group_id': None,
'columnmeta_hpds_path': '\\phs003461\\recover_pediatric_congenital\\12month\\related_conditions\\miscpots_colldt\\',
'columnmeta_var_id': 'related_conditions',
'columnmeta_var_group_description': None,
'derived_var_description': 'miscpots_colldt from form related_conditions and visit 12month from pediatric congenital cohort answerdata.tsv.',
'derived_variable_level_data': '{}',
'data_hierarchy': '',
'derived_group_description': None,
'columnmeta_max': '',
'columnmeta_description': 'miscpots_colldt from form related_conditions and visit 12month from pediatric congenital cohort answerdata.tsv.',
'derived_study_id': 'phs003461',
'hashed_var_id': '646316e761435c1cde7c3678c3e188c20594df8eba7679200cfa8d6dd90fc5f9',
'columnmeta_data_type': 'categorical',
'derived_var_id': 'related_conditions',
'columnmeta_study_id': 'phs003461',
'is_stigmatized': 'false',
'derived_var_name': 'miscpots_colldt',
'derived_study_abv_name': 'RECOVER_Pediatric',
'derived_study_description': 'Researching COVID to Enhance Recovery (RECOVER): Post Acute Sequelae of SARS-CoV-2 (PASC) Pediatric Cohort Study',
'columnmeta_var_group_id': None,
'derived_group_name': None,
'columnmeta_HPDS_PATH': '\\phs003461\\recover_pediatric_congenital\\12month\\related_conditions\\miscpots_colldt\\'
}
{
'columnmeta_is_stigmatized': 'false',
'columnmeta_name': 'participant_id',
'description': '',
'columnmeta_min': '',
'HPDS_PATH': '\\phs003461\\recover_pediatric\\24_month_arm_5\\spirometry\\participant_id\\',
'derived_group_id': None,
'columnmeta_hpds_path': '\\phs003461\\recover_pediatric\\24_month_arm_5\\spirometry\\participant_id\\',
'columnmeta_var_id': 'spirometry',
'columnmeta_var_group_description': None,
'derived_var_description': '',
'derived_variable_level_data': '{}',
'data_hierarchy': '',
'derived_group_description': None,
'columnmeta_max': '',
'columnmeta_description': '',
'derived_study_id': 'phs003461',
'hashed_var_id': 'b3e1ad429e14a615446a9841ca4a00b287403b3952c2e2841bdc7f76403b76f4',
'columnmeta_data_type': 'categorical',
'derived_var_id': 'spirometry',
'columnmeta_study_id': 'phs003461',
'is_stigmatized': 'false',
'derived_var_name': 'participant_id',
'derived_study_abv_name': 'RECOVER_Pediatric',
'derived_study_description': 'Researching COVID to Enhance Recovery (RECOVER): Post Acute Sequelae of SARS-CoV-2 (PASC) Pediatric Cohort Study',
'columnmeta_var_group_id': None,
'derived_group_name': None,
'columnmeta_HPDS_PATH': '\\phs003461\\recover_pediatric\\24_month_arm_5\\spirometry\\participant_id\\'
}
{
'columnmeta_is_stigmatized': 'false',
'columnmeta_name': 'participant_id',
'description': '',
'columnmeta_min': '',
'HPDS_PATH': '\\phs003461\\recover_pediatric\\24_month_arm_5\\visit_form\\participant_id\\',
'derived_group_id': None,
'columnmeta_hpds_path': '\\phs003461\\recover_pediatric\\24_month_arm_5\\visit_form\\participant_id\\',
'columnmeta_var_id': 'visit_form',
'columnmeta_var_group_description': None,
'derived_var_description': '',
'derived_variable_level_data': '{}',
'data_hierarchy': '',
'derived_group_description': None,
'columnmeta_max': '',
'columnmeta_description': '',
'derived_study_id': 'phs003461',
'hashed_var_id': '8e6edfdf3985f65e5740348642823b047341c26d67841cb8f41f697c3ef69433',
'columnmeta_data_type': 'categorical',
'derived_var_id': 'visit_form',
'columnmeta_study_id': 'phs003461',
'is_stigmatized': 'false',
'derived_var_name': 'participant_id',
'derived_study_abv_name': 'RECOVER_Pediatric',
'derived_study_description': 'Researching COVID to Enhance Recovery (RECOVER): Post Acute Sequelae of SARS-CoV-2 (PASC) Pediatric Cohort Study',
'columnmeta_var_group_id': None,
'derived_group_name': None,
'columnmeta_HPDS_PATH': '\\phs003461\\recover_pediatric\\24_month_arm_5\\visit_form\\participant_id\\'
}
{
'columnmeta_is_stigmatized': 'false',
'columnmeta_name': 'participant_id',
'description': '',
'columnmeta_min': '',
'HPDS_PATH': '\\phs003461\\recover_pediatric\\24_month_arm_5\\visits_data\\participant_id\\',
'derived_group_id': None,
'columnmeta_hpds_path': '\\phs003461\\recover_pediatric\\24_month_arm_5\\visits_data\\participant_id\\',
'columnmeta_var_id': 'visits_data',
'columnmeta_var_group_description': None,
'derived_var_description': '',
'derived_variable_level_data': '{}',
'data_hierarchy': '',
'derived_group_description': None,
'columnmeta_max': '',
'columnmeta_description': '',
'derived_study_id': 'phs003461',
'hashed_var_id': '3a8cae20696355deaa3016ff8e05270f9cb3b4856fe7b9a04fc5dcba9ed8f0fa',
'columnmeta_data_type': 'categorical',
'derived_var_id': 'visits_data',
'columnmeta_study_id': 'phs003461',
'is_stigmatized': 'false',
'derived_var_name': 'participant_id',
'derived_study_abv_name': 'RECOVER_Pediatric',
'derived_study_description': 'Researching COVID to Enhance Recovery (RECOVER): Post Acute Sequelae of SARS-CoV-2 (PASC) Pediatric Cohort Study',
'columnmeta_var_group_id': None,
'derived_group_name': None,
'columnmeta_HPDS_PATH': '\\phs003461\\recover_pediatric\\24_month_arm_5\\visits_data\\participant_id\\'
}
{
'columnmeta_is_stigmatized': 'false',
'columnmeta_name': 'participant_id',
'description': '',
'columnmeta_min': '',
'HPDS_PATH': '\\phs003461\\recover_pediatric\\follow-up_month_6\\research_labs\\participant_id\\',
'derived_group_id': None,
'columnmeta_hpds_path': '\\phs003461\\recover_pediatric\\follow-up_month_6\\research_labs\\participant_id\\',
'columnmeta_var_id': 'research_labs',
'columnmeta_var_group_description': None,
'derived_var_description': '',
'derived_variable_level_data': '{}',
'data_hierarchy': '',
'derived_group_description': None,
'columnmeta_max': '',
'columnmeta_description': '',
'derived_study_id': 'phs003461',
'hashed_var_id': 'f167930b4fb4de087e688b7d4e6ac107859c5d976f64124e9be8d4259900784d',
'columnmeta_data_type': 'categorical',
'derived_var_id': 'research_labs',
'columnmeta_study_id': 'phs003461',
'is_stigmatized': 'false',
'derived_var_name': 'participant_id',
'derived_study_abv_name': 'RECOVER_Pediatric',
'derived_study_description': 'Researching COVID to Enhance Recovery (RECOVER): Post Acute Sequelae of SARS-CoV-2 (PASC) Pediatric Cohort Study',
'columnmeta_var_group_id': None,
'derived_group_name': None,
'columnmeta_HPDS_PATH': '\\phs003461\\recover_pediatric\\follow-up_month_6\\research_labs\\participant_id\\'
}
{
'columnmeta_is_stigmatized': 'true',
'columnmeta_name': 'participant_id (mhp_fitbit)',
'description': 'participant_id for visit type mhp_fitbit in pediatric cohort visits.tsv.',
'columnmeta_min': '',
'HPDS_PATH': '\\phs003461\\recover_pediatric_caregiver\\mhp_fitbit\\participant_id',
'derived_group_id': None,
'columnmeta_hpds_path': '\\phs003461\\recover_pediatric_caregiver\\mhp_fitbit\\participant_id',
'columnmeta_var_id': 'participant_id',
'columnmeta_var_group_description': None,
'derived_var_description': 'participant_id for visit type mhp_fitbit in pediatric cohort visits.tsv.',
'derived_variable_level_data': '{}',
'data_hierarchy': '',
'derived_group_description': None,
'columnmeta_max': '',
'columnmeta_description': 'participant_id for visit type mhp_fitbit in pediatric cohort visits.tsv.',
'derived_study_id': 'phs003461',
'hashed_var_id': '5132338ece374ab34264f0c08a5a7f49b85fbbc13fef35352e5572e6e4a5a59e',
'columnmeta_data_type': 'categorical',
'derived_var_id': 'participant_id',
'columnmeta_study_id': 'phs003461',
'is_stigmatized': 'true',
'derived_var_name': 'participant_id (mhp_fitbit)',
'derived_study_abv_name': 'RECOVER_Pediatric',
'derived_study_description': 'Researching COVID to Enhance Recovery (RECOVER): Post Acute Sequelae of SARS-CoV-2 (PASC) Pediatric Cohort Study',
'columnmeta_var_group_id': None,
'derived_group_name': None,
'columnmeta_HPDS_PATH': '\\phs003461\\recover_pediatric_caregiver\\mhp_fitbit\\participant_id'
}
20 changes: 12 additions & 8 deletions src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/SearchResultRowMapper.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -44,20 +44,24 @@ private SearchResult mapSearchResults(ResultSet rs) throws SQLException {
String description =
rs.getString("description") == null || rs.getString("description").isBlank() ? "" : rs.getString("description");

String parentName = rs.getString("parentName") == null || rs.getString("parentName").isBlank() ? "" : rs.getString("parentName");
String parentDisplay =
rs.getString("parentDisplay") == null || rs.getString("parentDisplay").isBlank() ? "" : rs.getString("parentDisplay");

Metadata metadata = new Metadata(
rs.getString("stigmatized"), rs.getString("display"), description,
isContinuous ? String.valueOf(jsonBlobParser.parseMin(rs.getString("values"))) : "", rs.getString("conceptPath"),
rs.getString("parentName"), rs.getString("conceptPath"), rs.getString("name"), rs.getString("parentDisplay"), description, // changed
"{}", "", rs.getString("parentName"), isContinuous ? String.valueOf(jsonBlobParser.parseMax(rs.getString("values"))) : "",
description, rs.getString("dataset"), hashedVarId, rs.getString("conceptType"), rs.getString("name"), rs.getString("dataset"),
rs.getString("stigmatized"), rs.getString("display"), rs.getString("studyAcronym"), rs.getString("dsFullName"),
rs.getString("parentName"), rs.getString("parentDisplay"), rs.getString("conceptPath")
isContinuous ? String.valueOf(jsonBlobParser.parseMin(rs.getString("values"))) : "", rs.getString("conceptPath"), parentName,
rs.getString("conceptPath"), rs.getString("name"), parentDisplay, description, // changed
"{}", "", parentName, isContinuous ? String.valueOf(jsonBlobParser.parseMax(rs.getString("values"))) : "", description,
rs.getString("dataset"), hashedVarId, rs.getString("conceptType"), rs.getString("name"), rs.getString("dataset"),
rs.getString("stigmatized"), rs.getString("display"), rs.getString("studyAcronym"), rs.getString("dsFullName"), parentName,
parentDisplay, rs.getString("conceptPath")
);

Result result = new Result(
metadata, jsonBlobParser.parseValues(rs.getString("values")), rs.getString("dataset"),
rs.getString("parentName") == null || rs.getString("parentName").isBlank() ? "All Variables" : rs.getString("parentName"),
rs.getString("name"), "categorical".equalsIgnoreCase(rs.getString("conceptType")), isContinuous
parentName == null || parentName.isBlank() ? "All Variables" : parentName, rs.getString("name"),
"categorical".equalsIgnoreCase(rs.getString("conceptType")), isContinuous
);

return new SearchResult(result);
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