<commit_before>create table ABSTRACT_CLINICAL_SOURCE_CONFIGURATION (
    ID bigint not null auto_increment, 
    STUDY_CONFIGURATION_ID bigint, 
    LIST_INDEX integer, 
    primary key (ID)
) ENGINE=InnoDB;

create table ANNOTATION_FIELD_DESCRIPTOR (
    ID bigint not null auto_increment, 
    NAME varchar(255), 
    TYPE varchar(255), 
    ANNOTATION_DEFINITION_ID bigint, 
    primary key (ID)
) ENGINE=InnoDB;

create table ANNOTATION_FIELD_DESCRIPTOR_KEYWORDS (
    descriptor_id bigint not null, 
    keyword varchar(255)
) ENGINE=InnoDB;

create table ANNOTATION_FILE (
    ID bigint not null auto_increment, 
    PATH varchar(255), 
    IDENTIFIER_COLUMN_ID bigint, 
    TIMEPOINT_COLUMN_ID bigint, 
    primary key (ID)
) ENGINE=InnoDB;

create table DELIMITED_TEXT_CLINICAL_SOURCE_CONFIGURATION (
    ID bigint not null, <commit_msg>Added proper file management functionality; revised persistence to use DataSource; added database-based configuration.<commit_after>create table ABSTRACT_CLINICAL_SOURCE_CONFIGURATION (
    ID bigint not null auto_increment, 
    STUDY_CONFIGURATION_ID bigint, 
    LIST_INDEX integer, 
    primary key (ID)
) ENGINE=InnoDB;

create table ANNOTATION_FIELD_DESCRIPTOR (
    ID bigint not null auto_increment, 
    NAME varchar(255), 
    TYPE varchar(255), 
    ANNOTATION_DEFINITION_ID bigint, 
    primary key (ID)
) ENGINE=InnoDB;

create table ANNOTATION_FIELD_DESCRIPTOR_KEYWORDS (
    descriptor_id bigint not null, 
    keyword varchar(255)
) ENGINE=InnoDB;

create table ANNOTATION_FILE (
    ID bigint not null auto_increment, 
    PATH varchar(255), 
    IDENTIFIER_COLUMN_ID bigint, 
    TIMEPOINT_COLUMN_ID bigint, 
    primary key (ID)
) ENGINE=InnoDB;

create table CONFIGURATION_PARAMETER (
    PARAMETER varchar(255), 
    RAW_VALUE varchar(255), 
    primary key (PARAMETER)
) ENGINE=InnoDB;

create table DELIMITED_TEXT_CLINICAL_SOURCE_CONFIGURATION (
    ID bigint not null, 
{'fraction_non_alphanumeric': 0.05675954592363261, 'fraction_numerical': 0.015479876160990712, 'mean_word_length': 4.283378746594005, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3136476', 'n_tokens_mistral': 710, 'n_tokens_neox': 638, 'n_words': 161}