public List <Beneficiary> GetBeneficiariesList(int genomeID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var gdataList = db.genomedatas.Where(_ => _.genomeid == genomeID).ToList();
var allben = db.coding_ns_stem_bendef.ToList();
var benList = (from b in allben
join g in gdataList on b.gdataid equals g.id
select b).ToList();
var distinctBen = benList.GroupBy(x => x.name).Select(x => x.FirstOrDefault());
var beneficiaryList = new List <Beneficiary>();
var count = 0;
foreach (var ben in distinctBen)
{
var beneficiary = new Beneficiary();
beneficiary.BeneficiaryID = count;
beneficiary.Name = ben.name;
beneficiaryList.Add(beneficiary);
count++;
}
return(beneficiaryList);
}
}
private void ProcessCodingGroupItems(Effects effects)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var codingItems = db.coding_groups_items.Where(_ => _.groupid == effects.CodingGroupID);
foreach (var item in codingItems)
{
switch (item.objkey)
{
case "program_bendef":
break;
case "program_outcome":
break;
case "program_characteristics":
break;
case "program_activities":
break;
}
}
}
}
public List <Characteristic> GetCharacteristicsList(int genomeID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var gdataList = db.genomedatas.Where(_ => _.genomeid == genomeID).ToList();
var allChar = db.coding_program_characteristics.ToList();
var charList = (from c in allChar
join g in gdataList on c.gdataid equals g.id
select c).ToList();
var distinctChar = charList.GroupBy(x => x.name).Select(x => x.FirstOrDefault());
var charateristicsList = new List <Characteristic>();
var count = 0;
foreach (var c in distinctChar)
{
var characteristic = new Characteristic();
characteristic.CharacteristicID = count;
characteristic.Name = c.name;
charateristicsList.Add(characteristic);
}
return(charateristicsList);
}
}
public static void ProcessOutcomes(Effects effects)
{
var max = 0;
using (GenomeManagerData db = new GenomeManagerData())
{
//var codingItems = db.coding_groups_items.Where(_ => _.groupid == effects.CodingGroupID && _.objkey == "program_outcome").FirstOrDefault();
var codingItems = db.coding_groups_items.Where(_ => _.groupid == effects.CodingGroupID && _.objkey == "program_outcome").ToList();
if (codingItems.Count() != 0)
{
for (int i = 0; i < codingItems.Count(); ++i)
{
var objID = codingItems[i].objkeyid;
var outcome = db.coding_ns_stem_outcomes.Where(_ => _.id == objID).FirstOrDefault();
foreach (var o in effects.Outcomes)
{
if (outcome.standardized_outcome == o.Name)
{
o.IsPresent = true;
}
}
}
}
}
}
private genomedata GetDocumentInfo(long gDataID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var doc = db.genomedatas.Where(_ => _.id == gDataID).FirstOrDefault();
return(doc);
}
}
public List <master_universalgene_types> GetGeneList(int genomeID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var uGenes = db.master_universalgene_types.Where(_ => _.genomeid == genomeID).ToList();
return(uGenes);
}
}
private static void GetActivities(long objKeyID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var activities = db.coding_program_activities.Where(_ => _.id == objKeyID).FirstOrDefault();
var gene = db.coding_activities_ugs.Where(_ => _.pactid == activities.id).FirstOrDefault();
}
}
private static void ProcessCodingGroups(long gDataID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var groups = db.coding_groups.Where(_ => _.gdataid == gDataID).Select(x => x.id);
foreach (var groupID in groups)
{
//ProcessCodingGroupItems(groupID);
}
}
}
public static void GetAllGenes(int genomeID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var genes = db.master_universalgene_types.Where(_ => _.genomeid == genomeID);
foreach (var g in genes)
{
Console.WriteLine(g.ugtname);
}
}
}
public List <long> GetCodingGroupIDs(int genomeID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var codingGroups = from g in db.genomedatas
join cg in db.coding_groups on g.id equals cg.gdataid
where g.genomeid == genomeID
select cg.id;
return(codingGroups.ToList());
}
}
private List <Gene> BuildGeneList(int genomeID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var uGenelist = GetGeneList(genomeID);
var genes = new List <Gene>();
foreach (var g in uGenelist)
{
var gene = new Gene();
gene.GeneID = g.id;
gene.Name = g.ugtname;
gene.GenomeID = g.genomeid;
genes.Add(gene);
}
return(genes);
}
}
public static void GetGeneList(int genomeID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var distinctActivities = from cpa in db.coding_program_activities
join cgi in db.coding_groups_items on cpa.id equals cgi.objkeyid
join cg in db.coding_groups on cgi.groupid equals cg.id
join g in db.genomedatas on cg.gdataid equals g.id
where g.genomeid == genomeID
select cpa;
foreach (var a in distinctActivities)
{
Console.WriteLine(a.name);
}
}
}
public List <Effects> GetEffects(long cgID, int genomeID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var groupEffects = db.coding_groups_items.Where(_ => _.groupid == cgID && _.objkey == "program_effects").ToList();
List <Effects> effects = new List <Effects>();
foreach (var ge in groupEffects)
{
var coding_Program_Effects = db.coding_program_effects.Where(_ => _.id == ge.objkeyid).FirstOrDefault();
if (coding_Program_Effects != null)
{
effects.Add(new Effects(coding_Program_Effects, cgID, genomeID));
}
}
return(effects);
}
}
public List <Gene> GetGeneList(int genomeID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var uGenelist = db.master_universalgene_types.Where(_ => _.genomeid == genomeID).ToList();
var genes = new List <Gene>();
foreach (var g in uGenelist)
{
var gene = new Gene();
gene.GeneID = g.id;
gene.Name = g.ugtname;
gene.GenomeID = g.genomeid;
genes.Add(gene);
}
return(genes);
}
}
//Processing blocks
public static void ProcessActivityGenes(Effects effects)
{
using (GenomeManagerData db = new GenomeManagerData())
{
//var activities = db.coding_groups_items.Where(_ => _.gdataid == document.GDataID && _.objkey == "program_activities");
var docGenes = db.coding_activities_ugs.Where(_ => _.gdataid == effects.GDataID);
foreach (var g in docGenes)
{
var gene = effects.Genes.Where(_ => _.GeneID == g.ugtid).FirstOrDefault();
if (gene != null)
{
gene.IsPresent = true;
//Console.WriteLine(gene.GeneID + " | " + gene.IsPresent);
}
}
}
}
public List <DocumentInfo> GetDocuments(int genomeID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var docs = from g in db.genomedatas
join cg in db.coding_groups on g.id equals cg.gdataid
where g.genomeid == genomeID
select new DocumentCodingGroup
{
GDataID = g.id,
CodingGroupID = cg.id,
CreatedBy = cg.createdby
};
var documents = new List <DocumentInfo>();
foreach (var doc in docs)
{
documents.Add(new DocumentInfo(doc));
}
return(documents);
}
}
public List <Outcome> GetOutcomesList(int genomeID)
{
using (GenomeManagerData db = new GenomeManagerData())
{
var uOutcomesList = db.master_outcome_list.Where(_ => _.genomeid == genomeID).ToList();
var outcomes = new List <Outcome>();
foreach (var item in uOutcomesList)
{
//ignore dead outcomes
if (item.outcomeid != 51 && item.outcomeid != 52)
{
var outcome = new Outcome();
outcome.OutcomeID = item.outcomeid;
outcome.Name = item.std_outcome_name;
outcomes.Add(outcome);
}
}
return(outcomes);
}
}
