public async Task <IActionResult> Login(string UserId, string Password)
{
Password = MD5Helpers.ComputeHash(Password);
Account account = _accountService.GetLogin(UserId, Password);
if (account?.Id > 0 && account?.Status == 0)
{
ClaimsIdentity identity = new ClaimsIdentity(CookieAuthenticationDefaults.AuthenticationScheme);
identity.AddClaim(new Claim(ClaimTypes.Email, account.UserId, ClaimValueTypes.String));
identity.AddClaim(new Claim(ClaimTypes.Name, account.UserName, ClaimValueTypes.String));
await HttpContext.SignInAsync(new ClaimsPrincipal(identity), new AuthenticationProperties { ExpiresUtc = DateTime.UtcNow.AddHours(24) });
return(RedirectToRoute("main"));
}
else
{
return(View());
}
}
public Study ProcessData(XmlDocument d, DateTime?download_datetime)
{
Study s = new Study();
// get date retrieved in object fetch
// transfer to study and data object records
List <StudyIdentifier> study_identifiers = new List <StudyIdentifier>();
List <StudyTitle> study_titles = new List <StudyTitle>();
List <StudyReference> study_references = new List <StudyReference>();
List <StudyContributor> study_contributors = new List <StudyContributor>();
List <StudyTopic> study_topics = new List <StudyTopic>();
List <DataObject> data_objects = new List <DataObject>();
List <ObjectDataset> object_datasets = new List <ObjectDataset>();
List <ObjectTitle> data_object_titles = new List <ObjectTitle>();
List <ObjectInstance> data_object_instances = new List <ObjectInstance>();
StringHelpers sh = new StringHelpers(_logger);
MD5Helpers hh = new MD5Helpers();
// First convert the XML document to a Linq XML Document.
XDocument xDoc = XDocument.Load(new XmlNodeReader(d));
// Obtain the main top level elements of the registry entry.
// In most cases study will have already been registered in CGT.
XElement r = xDoc.Root;
string sid = GetElementAsString(r.Element("sd_sid"));
s.sd_sid = sid;
s.datetime_of_data_fetch = download_datetime;
bool is_yoda_only = GetElementAsBool(r.Element("is_yoda_only"));
string remote_url = GetElementAsString(r.Element("remote_url"));
string therapaeutic_area = GetElementAsString(r.Element("therapaeutic_area"));
string product_class = GetElementAsString(r.Element("product_class"));
string data_partner = GetElementAsString(r.Element("data_partner"));
string conditions_studied = GetElementAsString(r.Element("conditions_studied"));
string last_revised_date = GetElementAsString(r.Element("last_revised_date"));;
string yoda_title = GetElementAsString(r.Element("yoda_title"));
yoda_title = sh.ReplaceApos(yoda_title);
yoda_title = sh.ReplaceTags(yoda_title);
s.display_title = yoda_title;
// display title derived from CTG during download, if possible
string name_base_title = GetElementAsString(r.Element("name_base_title"));
// this required for the moment until nct names improved
name_base_title = sh.ReplaceApos(name_base_title);
// In most cases the name_base will be the NCT title
string name_base = string.IsNullOrEmpty(name_base_title) ? yoda_title : name_base_title;
XElement st_titles = r.Element("study_titles");
if (st_titles != null)
{
var titles = st_titles.Elements("Title");
if (titles?.Any() == true)
{
foreach (XElement t in titles)
{
string title_text = sh.ReplaceApos(GetElementAsString(t.Element("title_text")));
int? title_type_id = GetElementAsInt(t.Element("title_type_id"));
string title_type = GetElementAsString(t.Element("title_type"));
bool is_default = GetElementAsBool(t.Element("is_default"));
string comments = GetElementAsString(t.Element("comments"));
study_titles.Add(new StudyTitle(sid, title_text, title_type_id, title_type, is_default, comments));
}
}
}
// brief description mostly as derived from CTG
s.brief_description = GetElementAsString(r.Element("brief_description"));
// temp for now until ctg descriptions are cleaner
s.brief_description = sh.StringClean(s.brief_description);
s.study_status_id = 21;
s.study_status = "Completed"; // assumption for entry onto web site
// study type only really relevant for non registered studies (others will
// have type identified in registered study entry
// here, usuallypreviously obtained from the ctg or isrctn entry
int?type_id = GetElementAsInt(r.Element("study_type_id"));
s.study_type_id = type_id;
switch (type_id)
{
case 11: s.study_type = "interventional"; break;
case 12: s.study_type = "observational"; break;
case 13: s.study_type = "observational patient registry"; break;
case 14: s.study_type = "expanded access"; break;
case 15: s.study_type = "funded programme"; break;
case 16: s.study_type = "not yet known"; break;
}
string study_enrolment = GetElementAsString(r.Element("enrolment")).Trim();
if (!string.IsNullOrEmpty(study_enrolment))
{
s.study_enrolment = study_enrolment;
}
string percent_female = GetElementAsString(r.Element("percent_female"));
if (!string.IsNullOrEmpty(percent_female) && percent_female != "N/A")
{
if (percent_female.EndsWith("%"))
{
percent_female = percent_female.Substring(0, percent_female.Length - 1);
}
if (Single.TryParse(percent_female, out float female_percentage))
{
if (female_percentage == 0)
{
s.study_gender_elig_id = 910;
s.study_gender_elig = "Male";
}
else if (female_percentage == 100)
{
s.study_gender_elig_id = 905;
s.study_gender_elig = "Female";
}
else
{
s.study_gender_elig_id = 900;
s.study_gender_elig = "All";
}
}
}
else
{
s.study_gender_elig_id = 915;
s.study_gender_elig = "Not provided";
}
// transfer identifier data
// Normally a protocol id will be the only addition (may be a duplicate of one already in the system)
var study_idents = r.Element("study_identifiers")?.Elements("Identifier");
if (study_idents?.Any() == true)
{
foreach (XElement i in study_idents)
{
string identifier_value = GetElementAsString(i.Element("identifier_value"));
int? identifier_type_id = GetElementAsInt(i.Element("identifier_type_id"));
string identifier_type = GetElementAsString(i.Element("identifier_type"));
int? identifier_org_id = GetElementAsInt(i.Element("identifier_org_id"));
string identifier_org = sh.ReplaceApos(GetElementAsString(i.Element("identifier_org")));
study_identifiers.Add(new StudyIdentifier(sid, identifier_value, identifier_type_id, identifier_type,
identifier_org_id, identifier_org));
}
}
// study contributors
// only sponsor knowm, and only relevant for non registered studies (others will
// have the sponsor identified in registered study entry).
int? sponsor_org_id; string sponsor_org;
int? sponsor_id = GetElementAsInt(r.Element("sponsor_id"));
string sponsor = GetElementAsString(r.Element("sponsor"));
if (!string.IsNullOrEmpty(sponsor))
{
sponsor_org_id = sponsor_id;
sponsor_org = sh.TidyOrgName(sponsor, sid);
}
else
{
sponsor_org_id = null;
sponsor_org = "No organisation name provided in source data";
}
// If study registered elsewhere this wil be ignored during the aggregation
study_contributors.Add(new StudyContributor(sid, 54, "Study Sponsor", sponsor_org_id, sponsor_org));
// study topics
string compound_generic_name = GetElementAsString(r.Element("compound_generic_name"));
string compound_product_name = GetElementAsString(r.Element("compound_product_name"));
if (!string.IsNullOrEmpty(compound_generic_name))
{
study_topics.Add(new StudyTopic(sid, 12, "chemical / agent", compound_generic_name));
}
if (!string.IsNullOrEmpty(compound_product_name))
{
string product_name = compound_product_name.Replace(((char)174).ToString(), ""); // drop reg mark
product_name = product_name.Replace(" ", " ").Replace(" ", " ").Trim();
// see if already exists
bool add_product = true;
foreach (StudyTopic t in study_topics)
{
if (product_name.ToLower() == t.original_value.ToLower())
{
add_product = false;
break;
}
}
if (add_product)
{
product_name = CultureInfo.CurrentCulture.TextInfo.ToTitleCase(product_name.ToLower());
study_topics.Add(new StudyTopic(sid, 12, "chemical / agent", product_name));
}
}
if (!string.IsNullOrEmpty(conditions_studied))
{
study_topics.Add(new StudyTopic(sid, 13, "condition", conditions_studied));
}
// create study references (pmids)
XElement refs = r.Element("study_references");
if (refs != null)
{
var study_refs = refs.Elements("Reference");
if (study_refs?.Any() == true)
{
foreach (XElement sr in study_refs)
{
string pmid = GetElementAsString(sr.Element("pmid"));
string primary_citation_link = GetElementAsString(sr.Element("primary_citation_link"));
// normally only 1 if there is one there at all
study_references.Add(new StudyReference(sid, pmid, primary_citation_link, null, null));
}
}
}
// data objects...
// do the yoda web page itself first...
string object_title = "Yoda web page";
string object_display_title = name_base + " :: " + "Yoda web page";
// create hash Id for the data object
string sd_oid = sid + " :: 38 :: " + object_title;
data_objects.Add(new DataObject(sd_oid, sid, object_title, object_display_title, null, 23, "Text", 38, "Study Overview",
101901, "Yoda", 12, download_datetime));
data_object_titles.Add(new ObjectTitle(sd_oid, object_display_title, 22,
"Study short name :: object type", true));
data_object_instances.Add(new ObjectInstance(sd_oid, 101901, "Yoda",
remote_url, true, 35, "Web text"));
// then for each supp doc...
XElement sds = r.Element("supp_docs");
if (sds != null)
{
var supp_docs = sds.Elements("SuppDoc");
if (supp_docs?.Any() == true)
{
foreach (XElement sd in supp_docs)
{
// get object_type
int object_class_id = 0; string object_class = "";
int object_type_id = 0; string object_type = "";
string doc_name = GetElementAsString(sd.Element("doc_name"));
string comment = GetElementAsString(sd.Element("comment"));
string url = GetElementAsString(sd.Element("url"));
object_title = doc_name;
switch (doc_name)
{
case "Collected Datasets":
{
object_type_id = 80;
object_type = "Individual participant data";
object_class_id = 14; object_class = "Datasets";
break;
}
case "Data Definition Specification":
{
object_type_id = 31;
object_type = "Data dictionary";
object_class_id = 23; object_class = "Text";
break;
}
case "Analysis Datasets":
{
object_type_id = 51;
object_type = "IPD final analysis datasets (full study population)";
object_class_id = 14; object_class = "Datasets";
break;
}
case "CSR Summary":
{
object_type_id = 79;
object_type = "CSR summary";
object_class_id = 23; object_class = "Text";
break;
}
case "Annotated Case Report Form":
{
object_type_id = 30;
object_type = "Annotated data collection forms";
object_class_id = 23; object_class = "Text";
break;
}
case "Statistical Analysis Plan":
{
object_type_id = 22;
object_type = "Statistical analysis plan";
object_class_id = 23; object_class = "Text";
break;
}
case "Protocol with Amendments":
{
object_type_id = 11;
object_type = "Study protocol";
object_class_id = 23; object_class = "Text";
break;
}
case "Clinical Study Report":
{
object_type_id = 26;
object_type = "Clinical study report";
object_class_id = 23; object_class = "Text";
break;
}
}
object_display_title = name_base + " :: " + object_type;
sd_oid = sid + " :: " + object_type_id.ToString() + " :: " + object_title;
if (comment == "Available now")
{
data_objects.Add(new DataObject(sd_oid, sid, object_title, object_display_title, null, object_class_id, object_class, object_type_id, object_type,
101901, "Yoda", 11, download_datetime));
data_object_titles.Add(new ObjectTitle(sd_oid, object_display_title, 22, "Study short name :: object type", true));
// create instance as resource exists
// get file type from link if possible
int resource_type_id = 0; string resource_type = "";
if (url.ToLower().EndsWith(".pdf"))
{
resource_type_id = 11;
resource_type = "PDF";
}
else if (url.ToLower().EndsWith(".xls"))
{
resource_type_id = 18;
resource_type = "Excel Spreadsheet(s)";
}
else
{
resource_type_id = 0;
resource_type = "Not yet known";
}
data_object_instances.Add(new ObjectInstance(sd_oid, 101901, "Yoda", url, true, resource_type_id, resource_type));
}
else
{
DateTime date_access_url_checked = new DateTime(2021, 7, 23);
string access_details = "The YODA Project will require that requestors provide basic information about the Principal Investigator, Key Personnel, and the ";
access_details += "project Research Proposal, including a scientific abstract and research methods.The YODA Project will review proposals to ensure that: ";
access_details += "1) the scientific purpose is clearly described; 2) the data requested will be used to enhance scientific and/or medical knowledge; and ";
access_details += "3) the proposed research can be reasonably addressed using the requested data.";
data_objects.Add(new DataObject(sd_oid, sid, object_title, object_display_title, null, object_class_id, object_class, object_type_id, object_type,
101901, "Yoda", 17, "Case by case download", access_details,
"https://yoda.yale.edu/how-request-data", date_access_url_checked, download_datetime));
data_object_titles.Add(new ObjectTitle(sd_oid, object_display_title, 22, "Study short name :: object type", true));
}
// for datasets also add dataset properties - even if they are largely unknown
if (object_type_id == 80)
{
object_datasets.Add(new ObjectDataset(sd_oid, 0, "Not known", null,
2, "De-identification applied",
"Yoda states that “...researchers will be granted access to participant-level study data that are devoid of personally identifiable information; current best guidelines for de-identification of data will be used.”",
0, "Not known", null));
}
}
}
}
// add in the study properties
s.identifiers = study_identifiers;
s.titles = study_titles;
s.references = study_references;
s.contributors = study_contributors;
s.topics = study_topics;
s.data_objects = data_objects;
s.object_datasets = object_datasets;
s.object_titles = data_object_titles;
s.object_instances = data_object_instances;
return(s);
}
public Study ProcessData(XmlDocument d, DateTime?download_datetime)
{
Study s = new Study();
// get date retrieved in object fetch
// transfer to study and data object records
//List<StudyIdentifier> study_identifiers = new List<StudyIdentifier>();
List <StudyTitle> study_titles = new List <StudyTitle>();
List <StudyIdentifier> study_identifiers = new List <StudyIdentifier>();
List <StudyReference> study_references = new List <StudyReference>();
List <StudyContributor> study_contributors = new List <StudyContributor>();
List <DataObject> data_objects = new List <DataObject>();
List <ObjectDataset> object_datasets = new List <ObjectDataset>();
List <ObjectTitle> data_object_titles = new List <ObjectTitle>();
List <ObjectDate> data_object_dates = new List <ObjectDate>();
List <ObjectInstance> data_object_instances = new List <ObjectInstance>();
MD5Helpers hh = new MD5Helpers();
DateHelpers dh = new DateHelpers();
StringHelpers sh = new StringHelpers(_logger);
char[] splitter = { '(' };
// transfer features of main study object
// In most cases study will have already been registered in CGT
// First convert the XML document to a Linq XML Document.
XDocument xDoc = XDocument.Load(new XmlNodeReader(d));
// Obtain the main top level elements of the registry entry.
XElement r = xDoc.Root;
string sid = GetElementAsString(r.Element("sd_sid"));
s.sd_sid = sid;
s.datetime_of_data_fetch = download_datetime;
// For the study, set up two titles, acronym and display title
// NHLBI title not always exactly the same as the trial registry entry.
string title = GetElementAsString(r.Element("title"));
title = sh.ReplaceTags(title);
title = sh.ReplaceApos(title);
// study display title (= default title) always the biolincc one
s.display_title = title;
study_titles.Add(new StudyTitle(sid, title, 18, "Other scientific title", true, "From BioLINCC web page"));
// but set up a 'name base' for data object names
// which will be the CGT name if one exists as this is usually shorter
// Only possible if the study is not one of those that are in a group,
// collectively corresponding to a single NCT entry and public title,
// and only for those where an nct entry exists (Some BioLincc studiues are not registered)
string nct_name = GetElementAsString(r.Element("nct_base_name"));
// this statement temporarily required until nct names improved
nct_name = sh.ReplaceApos(nct_name);
string name_base = "";
bool in_multiple_biolincc_group = GetElementAsBool(r.Element("in_multiple_biolincc_group"));
if (!in_multiple_biolincc_group && !string.IsNullOrEmpty(nct_name))
{
name_base = nct_name;
}
else
{
name_base = title;
}
string acronym = GetElementAsString(r.Element("acronym"));
if (!string.IsNullOrEmpty(acronym))
{
study_titles.Add(new StudyTitle(sid, acronym, 14, "Acronym or Abbreviation", false, "From BioLINCC web page"));
}
string brief_description = GetElementAsString(r.Element("brief_description"));
s.brief_description = sh.StringClean(brief_description);
s.study_type_id = GetElementAsInt(r.Element("study_type_id"));
s.study_type = GetElementAsString(r.Element("study_type"));
s.study_status_id = 21;
s.study_status = "Completed"; // assumption for entry onto web site
// Gender eligibility is never provided for biolincc entries
s.study_gender_elig_id = 915;
s.study_gender_elig = "Not provided";
string study_period = GetElementAsString(r.Element("study_period"));
study_period = study_period.Trim();
if (study_period.Length > 3)
{
string first_four = study_period.Substring(0, 4);
if (first_four == first_four.Trim())
{
if (Int32.TryParse(first_four, out int start_year))
{
s.study_start_year = start_year;
}
else
{
// perhaps full month year - e.g. "December 2008..."
// Get first word
// Is it a month name? - if so, store the number
if (study_period.IndexOf(" ") != -1)
{
int spacepos = study_period.IndexOf(" ");
string month_name = study_period.Substring(0, spacepos);
if (Enum.TryParse <MonthsFull>(month_name, out MonthsFull month_enum))
{
// get value...
int start_month = (int)month_enum;
// ...and get next 4 characters - are they a year?
// if they are it is the start year
string next_four = study_period.Substring(spacepos + 1, 4);
if (Int32.TryParse(next_four, out start_year))
{
s.study_start_month = start_month;
s.study_start_year = start_year;
}
}
}
}
}
}
// Add study attribute records.
string hbli_identifier = GetElementAsString(r.Element("accession_number"));
// identifier type = NHBLI ID, id = 42, org = National Heart, Lung, and Blood Institute, id = 100167.
study_identifiers.Add(new StudyIdentifier(sid, hbli_identifier, 42, "NHLBI ID", 100167, "National Heart, Lung, and Blood Institute (US)"));
// If there is a NCT ID (there usually is...).
var registry_ids = r.Element("registry_ids");
if (registry_ids != null)
{
var ids = registry_ids.Elements("RegistryId");
if (ids != null && ids.Count() > 0)
{
foreach (XElement id in ids)
{
string nct_id = GetElementAsString(id.Element("nct_id"));
study_identifiers.Add(new StudyIdentifier(sid, nct_id, 11, "Trial Registry ID", 100120, "ClinicalTrials.gov"));
}
}
}
int? sponsor_id = GetElementAsInt(r.Element("sponsor_id"));
string sponsor_name = GetElementAsString(r.Element("sponsor_name"));
if (sponsor_id != null)
{
study_contributors.Add(new StudyContributor(sid, 54, "Trial sponsor", sponsor_id, sponsor_name));
}
// Create data object records.
// For the BioLincc web page, set up new data object, object title, object_instance and object dates
// Get publication year if one exists
int?pub_year = null;
int?pyear = GetElementAsInt(r.Element("publication_year"));
if (pyear != null && pyear > 0)
{
pub_year = pyear;
}
string remote_url = GetElementAsString(r.Element("remote_url"));
string object_title = "NHLBI web page";
string object_display_title = name_base + " :: " + "NHLBI web page";
// create hash Id for the data object
string sd_oid = sid + " :: 38 :: " + object_title;
data_objects.Add(new DataObject(sd_oid, sid, object_title, object_display_title, pub_year, 23, "Text", 38, "Study Overview",
100167, "National Heart, Lung, and Blood Institute (US)", 12, download_datetime));
data_object_titles.Add(new ObjectTitle(sd_oid, object_display_title, 22,
"Study short name :: object type", true));
data_object_instances.Add(new ObjectInstance(sd_oid, 101900, "BioLINCC",
remote_url, true, 35, "Web text"));
// Add dates if available
//SplitDate page_prepared = null;
SplitDate last_revised = null;
/*
* // This date no longer available... (explicitly - last revised date may be available in header)
* //string page_prepared_date = GetElementAsString(r.Element("page_prepared_date"));
*
*
* if (!string.IsNullOrEmpty(page_prepared_date))
* {
* page_prepared = dh.GetDatePartsFromISOString(page_prepared_date.Substring(0, 10));
* data_object_dates.Add(new ObjectDate(sd_oid, 12, "Available", page_prepared.year,
* page_prepared.month, page_prepared.day, page_prepared.date_string));
* }
*/
string last_revised_date = GetElementAsString(r.Element("last_revised_date"));
if (!string.IsNullOrEmpty(last_revised_date))
{
// date datasets revised
last_revised = dh.GetDatePartsFromISOString(last_revised_date.Substring(0, 10));
// only add last revised date if it is later than date prepared date
// For early trials run before BioLINCC waas set up this is not the case
/*
* if ((last_revised.year * 400) + (last_revised.month * 32) + last_revised.day
* >= (page_prepared.year * 400) + (page_prepared.month * 32) + page_prepared.day)
*
* {
* data_object_dates.Add(new ObjectDate(sd_oid, 18, "Updated", last_revised.year,
* last_revised.month, last_revised.day, last_revised.date_string));
* }
*/
}
// If there is a study web site...
string study_website = GetElementAsString(r.Element("study_website"));
if (!string.IsNullOrEmpty(study_website))
{
object_title = "Study web site";
object_display_title = name_base + " :: " + "Study web site";
sd_oid = sid + " :: 134 :: " + object_title;
data_objects.Add(new DataObject(sd_oid, sid, object_title, object_display_title, null, 23, "Text", 134, "Website",
sponsor_id, sponsor_name, 12, download_datetime));
data_object_titles.Add(new ObjectTitle(sd_oid, object_display_title, 22,
"Study short name :: object type", true));
data_object_instances.Add(new ObjectInstance(sd_oid, sponsor_id, sponsor_name,
study_website, true, 35, "Web text"));
}
// create the data object relating to the dataset, instance not available, title possible...
// may be a description of the data in 'Data Available...'
// if so add a data object description....with a data object title
string access_details = "Investigators wishing to request materials from studies ... must register (free) on the BioLINCC website. ";
access_details += "Registered investigators may then request detailed searches and submit an application for data sets ";
access_details += "and/or biospecimens. (from the BioLINCC website)";
string de_identification = "All BioLINCC data and biospecimens are de-identified. Obvious subject identifiers ";
de_identification += "and data collected solely for administrative purposes are redacted from datasets, ";
de_identification += "and dates are recoded relative to a specific reference point. ";
de_identification += "In addition recodes of selected low-frequency data values may be ";
de_identification += "carried out to protect subject privacy and minimize re-identification risks (from the BioLINCC documentation).";
string resources_available = GetElementAsString(r.Element("resources_available"));
if (resources_available.ToLower().Contains("datasets"))
{
DateTime date_access_url_checked = new DateTime(2021, 7, 23);
object_title = "Individual participant data";
object_display_title = name_base + " :: " + "Individual participant data";
sd_oid = sid + " :: 80 :: " + object_title;
data_objects.Add(new DataObject(sd_oid, sid, object_title, object_display_title, last_revised.year, 14, "Datasets",
80, "Individual participant data", 100167, "National Heart, Lung, and Blood Institute (US)",
17, "Case by case download", access_details,
"https://biolincc.nhlbi.nih.gov/media/guidelines/handbook.pdf?link_time=2019-12-13_11:33:44.807479#page=15",
date_access_url_checked, download_datetime));
data_object_titles.Add(new ObjectTitle(sd_oid, object_display_title, 22, "Study short name :: object type", true));
data_object_dates.Add(new ObjectDate(sd_oid, 18, "Updated", last_revised.year, last_revised.month, last_revised.day, last_revised.date_string));
// Datasets and consent restrictions
string dataset_consent_restrictions = GetElementAsString(r.Element("dataset_consent_restrictions"));
int consent_type_id = 0;
string consent_type = null;
string restrictions = null;
if (string.IsNullOrEmpty(dataset_consent_restrictions))
{
consent_type_id = 0;
consent_type = "Not known";
}
else if (dataset_consent_restrictions.ToLower() == "none" ||
dataset_consent_restrictions.ToLower() == "none.")
{
consent_type_id = 2;
consent_type = "No restriction";
restrictions = "Explicitly states that there are no restrictions on use";
}
else
{
consent_type_id = 6;
consent_type = "Consent specified, not elsewhere categorised";
restrictions = dataset_consent_restrictions;
}
// do dataset object separately
object_datasets.Add(new ObjectDataset(sd_oid,
0, "Not known", null,
2, "De-identification applied", de_identification,
consent_type_id, consent_type, restrictions));
}
var primary_docs = r.Element("primary_docs");
if (primary_docs != null)
{
var docs = primary_docs.Elements("PrimaryDoc");
if (docs != null && docs.Count() > 0)
{
foreach (XElement doc in docs)
{
string pubmed_id = GetElementAsString(doc.Element("pubmed_id"));
string url = GetElementAsString(doc.Element("url"));
study_references.Add(new StudyReference(sid, pubmed_id, null, url, "primary"));;
}
}
}
var resources = r.Element("resources");
if (resources != null)
{
var docs = resources.Elements("Resource");
if (docs != null && docs.Count() > 0)
{
foreach (XElement doc in docs)
{
string doc_name = GetElementAsString(doc.Element("doc_name"));
int? object_type_id = GetElementAsInt(doc.Element("object_type_id"));
string object_type = GetElementAsString(doc.Element("object_type"));
int? access_type_id = GetElementAsInt(doc.Element("access_type_id"));
string url = GetElementAsString(doc.Element("url"));
int? doc_type_id = GetElementAsInt(doc.Element("doc_type_id"));
string doc_type = GetElementAsString(doc.Element("doc_type"));
string size = GetElementAsString(doc.Element("size"));
string size_units = GetElementAsString(doc.Element("size_units"));
// for parity and test expectations
if (size == "")
{
size = null;
}
if (size_units == "")
{
size_units = null;
}
object_title = doc_name;
object_display_title = name_base + " :: " + doc_name;
sd_oid = sid + " :: " + object_type_id.ToString() + " :: " + object_title;
// N.B. 'pub_year' no longer known
data_objects.Add(new DataObject(sd_oid, sid, object_title, object_display_title, null, 23, "Text", object_type_id, object_type,
100167, "National Heart, Lung, and Blood Institute (US)", access_type_id, download_datetime));
data_object_titles.Add(new ObjectTitle(sd_oid, object_display_title, 21, "Study short name :: object name", true));
data_object_instances.Add(new ObjectInstance(sd_oid, 101900, "BioLINCC", url, true, doc_type_id, doc_type, size, size_units));
}
}
}
var assoc_docs = r.Element("assoc_docs");
if (assoc_docs != null)
{
var docs = assoc_docs.Elements("AssocDoc");
if (docs != null && docs.Count() > 0)
{
foreach (XElement doc in docs)
{
string pubmed_id = GetElementAsString(doc.Element("pubmed_id"));
string display_title = sh.ReplaceApos(GetElementAsString(doc.Element("display_title")));
string link_id = GetElementAsString(doc.Element("link_id"));
study_references.Add(new StudyReference(s.sd_sid, pubmed_id, display_title, link_id, "associated"));
}
}
}
// check that the primary doc is not duplicated in the associated docs (it sometimes is)
if (study_references.Count > 0)
{
foreach (StudyReference p in study_references)
{
if (p.comments == "primary")
{
foreach (StudyReference a in study_references)
{
if (a.comments == "associated" && p.pmid == a.pmid)
{
// update the primary link
p.citation = a.citation;
p.doi = a.doi;
// drop the redundant associated link
a.comments = "to go";
break;
}
}
}
}
}
List <StudyReference> study_references2 = new List <StudyReference>();
foreach (StudyReference a in study_references)
{
if (a.comments != "to go")
{
study_references2.Add(a);
}
}
// add in the study properties
s.titles = study_titles;
s.identifiers = study_identifiers;
s.references = study_references2;
s.contributors = study_contributors;
s.data_objects = data_objects;
s.object_datasets = object_datasets;
s.object_titles = data_object_titles;
s.object_dates = data_object_dates;
s.object_instances = data_object_instances;
return(s);
}
