public study_relationship(int _id, lookup _relationship_type,
int _target_study_id)
{
id = _id;
relationship_type = _relationship_type;
target_study_id = _target_study_id;
}
public object_relationship(int _id, lookup _relationship_type,
int _target_object_id)
{
id = _id;
relationship_type = _relationship_type;
target_object_id = _target_object_id;
}
public study_feature(int _id, lookup _feature_type,
lookup _feature_value)
{
id = _id;
feature_type = _feature_type;
feature_value = _feature_value;
}
public object_instance(int _id, lookup _repository_org,
access_details _access_details, resource_details _resource_details)
{
id = _id;
repository_org = _repository_org;
access_details = _access_details;
resource_details = _resource_details;
}
public object_contributor(int _id, lookup _contribution_type, bool?_is_individual,
individual _person, lookup _organisation)
{
id = _id;
contribution_type = _contribution_type;
is_individual = _is_individual;
person = _person;
organisation = _organisation;
}
public object_title(int _id, lookup _title_type, string _title_text,
string _lang_code, string _comments)
{
id = _id;
title_type = _title_type;
title_text = _title_text;
lang_code = _lang_code;
comments = _comments;
}
public object_identifier(int _id, string _identifier_value,
lookup _identifier_type, lookup _identifier_org,
string _identifier_date)
{
id = _id;
identifier_type = _identifier_type;
identifier_org = _identifier_org;
identifier_value = _identifier_value;
identifier_date = _identifier_date;
}
public study_identifier(int _id, string _identifier_value,
lookup _identifier_type, lookup _identifier_org,
string _identifier_date, string _identifier_link)
{
id = _id;
identifier_value = _identifier_value;
identifier_type = _identifier_type;
identifier_org = _identifier_org;
identifier_date = _identifier_date;
identifier_link = _identifier_link;
}
public object_description(int _id, lookup _description_type,
string _description_label, string _description_text,
string _lang_code, bool?_contains_html)
{
id = _id;
description_type = _description_type;
description_label = _description_label;
description_text = _description_text;
lang_code = _lang_code;
contains_html = _contains_html;
}
public object_date(int _id, lookup _date_type, bool?_is_date_range, string _date_as_string,
sdate_as_ints _start_date, edate_as_ints _end_date, string _comments)
{
id = _id;
date_type = _date_type;
is_date_range = _is_date_range;
date_as_string = _date_as_string;
start_date = _start_date;
end_date = _end_date;
comments = _comments;
}
public study_topic(int _id, lookup _topic_type,
bool _mesh_coded, string _topic_code,
string _topic_value, string _topic_qualcode,
string _topic_qualvalue, string _original_value)
{
id = _id;
topic_type = _topic_type;
mesh_coded = _mesh_coded;
topic_code = _topic_code;
topic_value = _topic_value;
topic_qualcode = _topic_qualcode;
topic_qualvalue = _topic_qualvalue;
original_value = _original_value;
}
public JSONStudy(int _id, string _display_title,
text_block _brief_description, text_block _data_sharing_statement,
lookup _study_type, lookup _study_status, int?_study_enrolment,
lookup _study_gender_elig, age_param _min_age, age_param _max_age,
string _provenance_string)
{
file_type = "study";
id = _id;
display_title = _display_title;
brief_description = _brief_description;
data_sharing_statement = _data_sharing_statement;
study_type = _study_type;
study_status = _study_status;
study_enrolment = _study_enrolment;
study_gender_elig = _study_gender_elig;
min_age = _min_age;
max_age = _max_age;
provenance_string = _provenance_string;
}
public JSONDataObject(int _id, string _doi, string _display_title, string _version,
lookup _object_class, lookup _object_type, int?_publication_year,
lookup _managing_organisation, string _lang_code,
lookup _access_type, object_access _access_details,
int?_eosc_category, string _provenance_string)
{
file_type = "data_object";
id = _id;
doi = _doi;
display_title = _display_title;
version = _version;
object_class = _object_class;
object_type = _object_type;
publication_year = _publication_year;
managing_organisation = _managing_organisation;
lang_code = _lang_code;
access_type = _access_type;
access_details = _access_details;
eosc_category = _eosc_category;
provenance_string = _provenance_string;
}
public JSONStudy CreateStudyObject(int id)
{
// Re-initialise these compound properties.
brief_description = null;
data_sharing_statement = null;
study_type = null;
study_status = null;
study_gender_elig = null;
min_age = null;
max_age = null;
study_identifiers = null;
study_titles = null;
study_topics = null;
study_features = null;
study_relationships = null;
linked_data_objects = null;
// Get the singleton study properties from DB
var s = repo.FetchDbStudy(id);
// Instantiate the top level lookup types
if (s.brief_description != null)
{
brief_description = new text_block(s.brief_description, s.bd_contains_html);
}
if (s.data_sharing_statement != null)
{
data_sharing_statement = new text_block(s.data_sharing_statement, s.dss_contains_html);
}
if (s.study_type_id != null)
{
study_type = new lookup(s.study_type_id, s.study_type);
}
if (s.study_status_id != null)
{
study_status = new lookup(s.study_status_id, s.study_status);
}
if (s.study_gender_elig_id != null)
{
study_gender_elig = new lookup(s.study_gender_elig_id, s.study_gender_elig);
}
if (s.min_age != null)
{
min_age = new age_param(s.min_age, s.min_age_units_id, s.min_age_units);
}
if (s.max_age != null)
{
max_age = new age_param(s.max_age, s.max_age_units_id, s.max_age_units);
}
// instantiate a (json) study object and
// fill it with study level details
JSONStudy jst = new JSONStudy(s.id, s.display_title, brief_description,
data_sharing_statement, study_type, study_status, s.study_enrolment,
study_gender_elig, min_age, max_age, s.provenance_string);
// add the study identifier details
var db_study_identifiers = new List <DBStudyIdentifier>(repo.FetchDbStudyIdentifiers(id));
if (db_study_identifiers.Count > 0)
{
study_identifiers = new List <study_identifier>();
foreach (DBStudyIdentifier t in db_study_identifiers)
{
study_identifiers.Add(new study_identifier(t.id, t.identifier_value,
new lookup(t.identifier_type_id, t.identifier_type),
new lookup(t.identifier_org_id, t.identifier_org),
t.identifier_date, t.identifier_link));
}
}
// add the study title details
var db_study_titles = new List <DBStudyTitle>(repo.FetchDbStudyTitles(id));
if (db_study_titles.Count > 0)
{
study_titles = new List <study_title>();
foreach (DBStudyTitle t in db_study_titles)
{
study_titles.Add(new study_title(t.id, new lookup(t.title_type_id, t.title_type), t.title_text,
t.lang_code, t.comments));
}
}
// add the study feature details
var db_study_features = new List <DBStudyFeature>(repo.FetchDbStudyFeatures(id));
if (db_study_features.Count > 0)
{
study_features = new List <study_feature>();
foreach (DBStudyFeature t in db_study_features)
{
study_features.Add(new study_feature(t.id, new lookup(t.feature_type_id, t.feature_type),
new lookup(t.feature_value_id, t.feature_value)));
}
}
// add the study topic details
var db_study_topics = new List <DBStudyTopic>(repo.FetchDbStudyTopics(id));
if (db_study_topics.Count > 0)
{
study_topics = new List <study_topic>();
foreach (DBStudyTopic t in db_study_topics)
{
study_topics.Add(new study_topic(t.id, new lookup(t.topic_type_id, t.topic_type),
t.mesh_coded, t.topic_code, t.topic_value, t.topic_qualcode,
t.topic_qualvalue, t.original_value));
}
}
// add the study relationships, if any
var db_study_relationships = new List <DBStudyRelationship>(repo.FetchDbStudyRelationships(id));
if (db_study_relationships.Count > 0)
{
study_relationships = new List <study_relationship>();
foreach (DBStudyRelationship t in db_study_relationships)
{
study_relationships.Add(new study_relationship(t.id,
new lookup(t.relationship_type_id, t.relationship_type),
t.target_study_id));
}
}
// add the related objects data
var db_study_object_links = new List <DBStudyObjectLink>(repo.FetchDbStudyObjectLinks(id));
if (db_study_object_links.Count > 0)
{
linked_data_objects = new List <int>();
foreach (DBStudyObjectLink t in db_study_object_links)
{
linked_data_objects.Add(t.object_id);
}
}
// return the resulting 'json ready' study
jst.study_identifiers = study_identifiers;
jst.study_titles = study_titles;
jst.study_features = study_features;
jst.study_topics = study_topics;
jst.study_relationships = study_relationships;
jst.linked_data_objects = linked_data_objects;
return(jst);
}
public JSONDataObject CreateObject(int id)
{
// Re-initialise these compound properties.
object_class = null;
object_type = null;
access_type = null;
managing_organisation = null;
access_details = null;
ds_record_keys = null;
ds_deident_level = null;
ds_consent = null;
object_titles = null;
object_contributors = null;
object_dates = null;
object_instances = null;
object_topics = null;
object_identifiers = null;
object_descriptions = null;
object_rights = null;
object_relationships = null;
linked_studies = null;
// Get the singleton data object properties from DB
ob = repo.FetchDbDataObject(id);
// First check there is at least one linked study
// (several hundred of the journal articles are not linked).
linked_studies = new List <int>(repo.FetchLinkedStudies(id));
if (linked_studies.Count == 0)
{
// May occur in a few hundred cases, therefore
// if it does need to investigate further !!!!!!!
// Possible (minor) error in data object linkage with journal articles.
logging_repo.LogError("object " + ob.id + " does not appear to be linked to studies");
return(null);
}
// Instantiate the top level lookup types
object_class = new lookup(ob.object_class_id, ob.object_class);
object_type = new lookup(ob.object_type_id, ob.object_type);
if (ob.managing_org != null)
{
managing_organisation = new lookup(ob.managing_org_id, ob.managing_org);
}
if (ob.access_type_id != null)
{
access_type = new lookup(ob.access_type_id, ob.access_type);
}
if (ob.access_details != null || ob.access_details_url != null)
{
access_details = new object_access(ob.access_details, ob.access_details_url, ob.url_last_checked);
}
// Instantiate data object with those details
JSONDataObject dobj = new JSONDataObject(ob.id, ob.doi, ob.display_title, ob.version, object_class,
object_type, ob.publication_year, managing_organisation, ob.lang_code,
access_type, access_details, ob.eosc_category, ob.provenance_string);
// Get dataset properties, if there are any...
var db_ds = repo.FetchDbDatasetProperties(id);
if (db_ds != null)
{
ds_record_keys = new record_keys(db_ds.record_keys_type_id, db_ds.record_keys_type, db_ds.record_keys_details);
ds_deident_level = new deidentification(db_ds.deident_type_id, db_ds.deident_type, db_ds.deident_direct,
db_ds.deident_hipaa, db_ds.deident_dates, db_ds.deident_nonarr,
db_ds.deident_kanon, db_ds.deident_details);
ds_consent = new consent(db_ds.consent_type_id, db_ds.consent_type, db_ds.consent_noncommercial,
db_ds.consent_geog_restrict, db_ds.consent_research_type, db_ds.consent_genetic_only,
db_ds.consent_no_methods, db_ds.consent_details);
dobj.dataset_record_keys = ds_record_keys;
dobj.dataset_deident_level = ds_deident_level;
dobj.dataset_consent = ds_consent;
}
// Get object instances.
var db_object_instances = new List <DBObjectInstance>(repo.FetchObjectInstances(id));
if (db_object_instances.Count > 0)
{
object_instances = new List <object_instance>();
foreach (DBObjectInstance i in db_object_instances)
{
lookup repo_org = null;
access_details access = null;
resource_details resource = null;
if (i.repository_org != null)
{
repo_org = new lookup(i.repository_org_id, i.repository_org);
}
if (i.url != null || i.url_accessible != null)
{
access = new access_details(i.url, i.url_accessible, i.url_last_checked);
}
if (i.resource_type_id != null || i.comments != null)
{
resource = new resource_details(i.resource_type_id, i.resource_type,
i.resource_size, i.resource_size_units, i.comments);
}
object_instances.Add(new object_instance(i.id, repo_org, access, resource));
}
}
// Get object titles.
var db_object_titles = new List <DBObjectTitle>(repo.FetchObjectTitles(id));
if (db_object_titles.Count > 0)
{
object_titles = new List <object_title>();
foreach (DBObjectTitle t in db_object_titles)
{
object_titles.Add(new object_title(t.id, new lookup(t.title_type_id, t.title_type), t.title_text,
t.lang_code, t.comments));
}
}
// Get object dates.
var db_object_dates = new List <DBObjectDate>(repo.FetchObjectDates(id));
if (db_object_dates.Count > 0)
{
object_dates = new List <object_date>();
sdate_as_ints start_date = null;
edate_as_ints end_date = null;
foreach (DBObjectDate d in db_object_dates)
{
if (d.start_year != null || d.start_month != null || d.start_day != null)
{
start_date = new sdate_as_ints(d.start_year, d.start_month, d.start_day);
}
if (d.end_year != null || d.end_month != null || d.end_day != null)
{
end_date = new edate_as_ints(d.end_year, d.end_month, d.end_day);
}
object_dates.Add(new object_date(d.id, new lookup(d.date_type_id, d.date_type), d.is_date_range,
d.date_as_string, start_date, end_date, d.comments));
}
}
// Get object contributors -
var db_object_contributors = new List <DBObjectContributor>(repo.FetchObjectContributors(id, ob.add_study_contribs));
if (db_object_contributors.Count > 0)
{
individual person; lookup org;
object_contributors = new List <object_contributor>();
foreach (DBObjectContributor c in db_object_contributors)
{
person = null; org = null;
if (c.is_individual)
{
person = new individual(c.person_family_name, c.person_given_name, c.person_full_name,
c.person_identifier, c.affiliation);
}
else
{
org = new lookup(c.organisation_id, c.organisation_name);
}
object_contributors.Add(new object_contributor(c.id, new lookup(c.contrib_type_id, c.contrib_type),
c.is_individual, person, org));
}
}
// Get object topics -
// source will depend on boolean flag, itself dependent on the type of object.
var db_object_topics = new List <DBObjectTopic>(repo.FetchObjectTopics(id, ob.add_study_topics));
if (db_object_topics.Count > 0)
{
object_topics = new List <object_topic>();
foreach (DBObjectTopic t in db_object_topics)
{
object_topics.Add(new object_topic(t.id, new lookup(t.topic_type_id, t.topic_type),
t.mesh_coded, t.topic_code, t.topic_value, t.topic_qualcode,
t.topic_qualvalue, t.original_value));
}
}
// Get object identifiers.
var db_object_identifiers = new List <DBObjectIdentifier>(repo.FetchObjectIdentifiers(id));
if (db_object_identifiers.Count > 0)
{
object_identifiers = new List <object_identifier>();
foreach (DBObjectIdentifier i in db_object_identifiers)
{
object_identifiers.Add(new object_identifier(i.id, i.identifier_value,
new lookup(i.identifier_type_id, i.identifier_type),
new lookup(i.identifier_org_id, i.identifier_org), i.identifier_date));
}
}
// Get object descriptions.
var db_object_descriptions = new List <DBObjectDescription>(repo.FetchObjectDescriptions(id));
if (db_object_descriptions.Count > 0)
{
object_descriptions = new List <object_description>();
foreach (DBObjectDescription i in db_object_descriptions)
{
object_descriptions.Add(new object_description(i.id, new lookup(i.description_type_id, i.description_type),
i.label, i.description_text, i.lang_code, i.contains_html));
}
}
// Get object rights.
var db_object_rights = new List <DBObjectRight>(repo.FetchObjectRights(id));
if (db_object_rights.Count > 0)
{
object_rights = new List <object_right>();
foreach (DBObjectRight i in db_object_rights)
{
object_rights.Add(new object_right(i.id, i.rights_name, i.rights_uri, i.comments));
}
}
// Get object relationships.
var db_object_relationships = new List <DBObjectRelationship>(repo.FetchObjectRelationships(id));
if (db_object_relationships.Count > 0)
{
object_relationships = new List <object_relationship>();
foreach (DBObjectRelationship i in db_object_relationships)
{
object_relationships.Add(new object_relationship(i.id, new lookup(i.relationship_type_id, i.relationship_type),
i.target_object_id));
}
}
// Construct the final data object by setting the composite
// and repreated properties to the classess and List<>s created above.
dobj.dataset_consent = ds_consent;
dobj.dataset_record_keys = ds_record_keys;
dobj.dataset_deident_level = ds_deident_level;
dobj.object_identifiers = object_identifiers;
dobj.object_titles = object_titles;
dobj.object_contributors = object_contributors;
dobj.object_dates = object_dates;
dobj.object_instances = object_instances;
dobj.object_descriptions = object_descriptions;
dobj.object_rights = object_rights;
dobj.object_topics = object_topics;
dobj.object_relationships = object_relationships;
dobj.linked_studies = linked_studies;
return(dobj);
}
