public static void Stats(string[] args)
{
// Load the file
var parms = new ParameterParser <InstallParameters>().Parse(args);
ApplicationContext.Current.Start();
var ds = DatasetInstall.Load(parms.DatasetFile);
Console.WriteLine("Statistics for {0} ({1} objects)...", ds.Action.Count, ds.Id);
foreach (var gc in ds.Action?.GroupBy(o => o.Element?.GetType()))
{
Console.WriteLine("{0} - {1} items", gc.Key, gc.Count());
}
}
/// <summary>
/// Will layout the object in a referentially proper way
/// </summary>
private static void LayoutObject(IdentifiedData obj, DatasetInstall dsOutput, bool insert = false)
{
// Add myself
if (!insert)
{
dsOutput.Action.Add(new DataUpdate()
{
Element = obj,
InsertIfNotExists = true
});
}
else
{
dsOutput.Action.Insert(0, new DataUpdate()
{
Element = obj,
InsertIfNotExists = true
});
}
// Iterate properties
foreach (var prop in obj.GetType().GetRuntimeProperties())
{
var sra = prop.GetCustomAttribute <SerializationReferenceAttribute>();
var value = prop.GetValue(obj);
// Value is list
if (value is IList && prop.GetCustomAttribute <XmlElementAttribute>() != null)
{
foreach (var v in (value as IList))
{
LayoutObject(v as IdentifiedData, dsOutput, true);
}
}
else if (value == null && sra != null) // No XmlElement .. hmm we might have to insert this stuff
{
value = OpenIZ.Core.Model.ExtensionMethods.LoadProperty(obj, prop.Name);
}
if (value is IdentifiedData)
{
dsOutput.Action.Insert(0, new DataUpdate()
{
Element = value as IdentifiedData,
InsertIfNotExists = true
});
}
}
}
public static void Install(string[] args)
{
// Load the file
var parms = new ParameterParser <InstallParameters>().Parse(args);
ApplicationContext.Current.Start();
var dsi = new DataInitializationService();
var ds = DatasetInstall.Load(parms.DatasetFile);
Console.WriteLine("Will install dataset {0} ({1} objects)...", ds.Action.Count, ds.Id);
dsi.ProgressChanged += (o, e) =>
{
Console.CursorLeft = 4;
Console.Write("{0} ({1:0%})", e.State, e.Progress);
};
dsi.InstallDataset(ds);
}
public static void TsvToDataset(String[] args)
{
var options = new ParameterParser <CvxOptions>().Parse(args);
DatasetInstall conceptDataset = new DatasetInstall()
{
Id = "TSV File"
};
using (var codeReader = File.OpenText(options.Input))
{
var sourceLine = codeReader.ReadLine();
var components = sourceLine.Split('\t').Select(o => o.Trim()).ToArray();
// Create vaccine code concept set
var conceptSet = new DataUpdate()
{
InsertIfNotExists = true,
Element = new ConceptSet()
{
Key = Guid.NewGuid(),
Mnemonic = options.ConceptSetName ?? "TsvConceptSet",
Name = components[5],
Oid = components[6],
Url = "http://openiz.org/conceptset/imported/" + (options.ConceptSetName ?? "TsvConceptSet")
},
Association = new List <DataAssociation>()
};
var codeSystem = new DataUpdate()
{
InsertIfNotExists = true,
Element = new CodeSystem(components[5], components[6], (options.ConceptSetName ?? "TsvConceptSet"))
{
Key = Guid.NewGuid(),
Url = "http://openiz.org/conceptset/imported/" + (options.ConceptSetName ?? "TsvConceptSet"),
}
};
conceptDataset.Action.Add(codeSystem);
// Now import the concepts from CVX to their OpenIZ Concepts
while (!codeReader.EndOfStream)
{
ReferenceTerm refTerm = new ReferenceTerm()
{
CodeSystemKey = codeSystem.Element.Key,
Mnemonic = components[1],
DisplayNames = new List <ReferenceTermName>()
{
new ReferenceTermName()
{
Language = "en", Name = components[2]
}
},
Key = Guid.NewGuid()
};
var mnemonic = String.Format("{0}-{1}", options.ConceptSetName ?? "Tsv", components[1].Replace(" ", "").Replace(".", "").Replace("(", "").Replace(")", ""));
if (mnemonic.Length > 64)
{
mnemonic = mnemonic.Substring(0, 64);
}
Concept concept = new Concept()
{
Key = Guid.Parse(components[0]),
Mnemonic = mnemonic,
ClassKey = ConceptClassKeys.Material,
ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Language = "en", Name = components[2]
}
},
ReferenceTerms = new List <ConceptReferenceTerm>()
{
new ConceptReferenceTerm()
{
ReferenceTermKey = refTerm.Key,
RelationshipTypeKey = ConceptRelationshipTypeKeys.SameAs
}
},
StatusConceptKey = StatusKeys.Active
};
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = refTerm
});
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = concept
});
(conceptSet.Element as ConceptSet).ConceptsXml.Add(concept.Key.Value);
sourceLine = codeReader.ReadLine();
components = sourceLine.Split('\t').Select(o => o.Trim()).ToArray();
}
conceptDataset.Action.Add(conceptSet);
}
XmlSerializer xsz = new XmlSerializer(typeof(DatasetInstall));
using (FileStream fs = File.Create(options.Output))
xsz.Serialize(fs, conceptDataset);
}
public static void CvxToDataset(String[] args)
{
var options = new ParameterParser <CvxOptions>().Parse(args);
DatasetInstall conceptDataset = new DatasetInstall()
{
Id = "CDC CVX Codes"
};
// Create vaccine code concept set
var conceptSet = new DataUpdate()
{
InsertIfNotExists = true,
Element = new ConceptSet()
{
Key = Guid.NewGuid(),
Mnemonic = "VaccineTypeCodes",
Name = "Vaccines",
Oid = "1.3.6.1.4.1.33349.3.1.5.9.1.25",
Url = "http://openiz.org/conceptset/VaccineTypeCodes"
},
Association = new List <DataAssociation>()
};
var codeSystem = new DataUpdate()
{
InsertIfNotExists = true,
Element = new CodeSystem("HL7 CVX Codes", "2.16.840.1.113883.3.88.12.80.22", "CVX")
{
Url = "http://hl7.org/fhir/sid/cvx",
Key = Guid.Parse("EBA4F94A-2CAD-4BB3-ACA7-F4E54EAAC4BD")
}
};
conceptDataset.Action.Add(codeSystem);
using (var codeReader = File.OpenText(options.Input))
{
// Now import the concepts from CVX to their OpenIZ Concepts
while (!codeReader.EndOfStream)
{
var sourceLine = codeReader.ReadLine();
var components = sourceLine.Split('|').Select(o => o.Trim()).ToArray();
ReferenceTerm refTerm = new ReferenceTerm()
{
CodeSystemKey = codeSystem.Element.Key,
Mnemonic = components[0],
DisplayNames = new List <ReferenceTermName>()
{
new ReferenceTermName()
{
Language = "en", Name = components[1]
}
},
Key = Guid.NewGuid()
};
var mnemonic = String.Format("VaccineType-{0}", components[1].Replace(" ", "").Replace(".", "").Replace("(", "").Replace(")", ""));
if (mnemonic.Length > 64)
{
mnemonic = mnemonic.Substring(0, 64);
}
Concept concept = new Concept()
{
Key = Guid.NewGuid(),
Mnemonic = mnemonic,
ClassKey = ConceptClassKeys.Material,
ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Language = "en", Name = components[2]
},
new ConceptName()
{
Language = "en", Name = components[1]
}
},
ReferenceTerms = new List <ConceptReferenceTerm>()
{
new ConceptReferenceTerm()
{
ReferenceTermKey = refTerm.Key,
RelationshipTypeKey = ConceptRelationshipTypeKeys.SameAs
}
},
StatusConceptKey = components[3] == "Inactive" ? StatusKeys.Obsolete : StatusKeys.Active,
CreationTime = DateTime.Parse(components[6])
};
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = refTerm
});
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = concept
});
(conceptSet.Element as ConceptSet).ConceptsXml.Add(concept.Key.Value);
}
}
conceptDataset.Action.Add(conceptSet);
XmlSerializer xsz = new XmlSerializer(typeof(DatasetInstall));
using (FileStream fs = File.Create(options.Output))
xsz.Serialize(fs, conceptDataset);
}
public static void PhinVadsToDataset(String[] args)
{
var options = new ParameterParser <CvxOptions>().Parse(args);
DatasetInstall conceptDataset = new DatasetInstall();
using (var sr = File.OpenText(options.Input))
{
// Consume the first line
sr.ReadLine();
var components = sr.ReadLine().Split('\t');
// Next line is the value set information
// Create code concept set
var conceptSet = new ConceptSet()
{
Key = Guid.NewGuid(),
Mnemonic = options.ConceptSetName ?? components[1],
Name = options.ConceptSetDescription ?? components[0],
Oid = options.ConceptSetOid ?? components[2],
CreationTime = DateTime.Parse(String.IsNullOrEmpty(components[6]) ? DateTime.Now.ToString() : components[6]),
Url = !String.IsNullOrEmpty(options.ConceptSetName) ? "http://openiz.org/conceptset/" + options.ConceptSetName :
"http://openiz.org/conceptsets/contrib/" + components[1]
};
Dictionary <String, CodeSystem> codeSystems = new Dictionary <string, CodeSystem>();
// Consume the next set of lines
while (!sr.ReadLine().StartsWith("Concept Code"))
{
;
}
while (!sr.EndOfStream)
{
components = sr.ReadLine().Split('\t');
// Try to get the code system
CodeSystem codeSys = null;
if (!codeSystems.TryGetValue(components[4], out codeSys))
{
codeSys = new CodeSystem()
{
Key = Guid.NewGuid(),
Authority = components[8],
Name = components[6],
Oid = components[4],
Description = components[5],
CreationTime = conceptSet.CreationTime
};
codeSystems.Add(codeSys.Oid, codeSys);
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = codeSys
});
}
// Insert the code
var refTerm = new ReferenceTerm()
{
Key = Guid.NewGuid(),
CodeSystemKey = codeSys.Key,
CreationTime = conceptSet.CreationTime,
DisplayNames = new List <ReferenceTermName>()
{
new ReferenceTermName()
{
Name = components[1],
Language = "en"
}
},
Mnemonic = components[0]
};
var concept = new Concept()
{
Key = Guid.NewGuid(),
Mnemonic = components[6] + "-" + components[1].Replace("[", "").Replace("]", "").Replace("-", "").Replace(" ", ""),
CreationTime = conceptSet.CreationTime,
StatusConceptKey = StatusKeys.Active,
ClassKey = ConceptClassKeys.Other,
ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Name = components[1],
Language = "en"
}
},
ReferenceTerms = new List <ConceptReferenceTerm>()
{
new ConceptReferenceTerm()
{
ReferenceTermKey = refTerm.Key,
RelationshipTypeKey = ConceptRelationshipTypeKeys.SameAs
}
}
};
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true, Element = refTerm
});
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true, Element = concept
});
conceptSet.ConceptsXml.Add(concept.Key.Value);
}
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true, Element = conceptSet
});
}
XmlSerializer xsz = new XmlSerializer(typeof(DatasetInstall));
using (FileStream fs = File.Create(options.Output))
xsz.Serialize(fs, conceptDataset);
}
public static void Extract(string[] args)
{
var parms = new ParameterParser <ExtractionParameters>().Parse(args);
// Is there any type specified, or no
List <Type> targetTypes = new List <Type>();
if (parms.Type.Count == 0) // All types
{
targetTypes = typeof(DataInstallAction).GetRuntimeProperty("Element").GetCustomAttributes <XmlElementAttribute>().Select(o => o.Type).ToList();
}
else
{
targetTypes = typeof(DataInstallAction).GetRuntimeProperty("Element").GetCustomAttributes <XmlElementAttribute>().Where(o => parms.Type.Contains(o.ElementName)).Select(o => o.Type).ToList();
}
// Now time to get the DPE and extract
IEnumerable <IdentifiedData> objects = new List <IdentifiedData>();
foreach (var itm in targetTypes)
{
Console.Write("Extracting {0}.", itm.Name);
try
{
// Load persister
var idt = typeof(IDataPersistenceService <>).MakeGenericType(itm);
var idp = ApplicationContext.Current.GetService(idt) as IDataPersistenceService;
if (idp == null)
{
throw new InvalidOperationException("Cannot find data persistence service");
}
// Convert query
var mi = typeof(QueryExpressionParser).GetGenericMethod("BuildLinqExpression", new Type[] { itm }, new Type[] { typeof(OpenIZ.Core.Model.Query.NameValueCollection) });
var qd = mi.Invoke(null, new object[] { OpenIZ.Core.Model.Query.NameValueCollection.ParseQueryString(parms.Filter) }) as Expression;
// Exec query
int tr = 1, ofs = 0;
while (ofs < tr)
{
ofs += 100;
(objects as List <IdentifiedData>).AddRange(idp.Query(qd, ofs, 100, out tr).OfType <IdentifiedData>());
Console.Write(".");
}
Console.WriteLine("ok");
}
catch (Exception ex)
{
Trace.TraceError(ex.ToString());
Console.WriteLine("fail");
}
}
// Now we want to organize the file properly
Console.WriteLine("Preliminary remove duplicates...");
objects = objects.Distinct(new IdentifiedEntityComparer());
// Now we flatten the objects and re-organize them
DatasetInstall dsOutput = new DatasetInstall();
Console.Write("Flattening objects: ( 0 / {0} )", objects.Count());
int i = 0;
foreach (var obj in objects)
{
Console.CursorLeft = 0;
Console.Write("Flattening objects: ( {0} / {1} )", i++, objects.Count());
if (!parms.IncludeRelated)
{
dsOutput.Action.Add(new DataUpdate()
{
Element = obj,
InsertIfNotExists = true
});
}
else
{
LayoutObject(obj, dsOutput);
}
}
// Now we want to organize the file properly
Console.WriteLine("Secondary remove duplicates...");
objects = objects.Distinct(new IdentifiedEntityComparer());
}
public static void EnumToDataset(String[] args)
{
var parms = new ParameterParser <ConsoleParameters>().Parse(args);
var asm = Assembly.LoadFile(parms.AssemblyFile);
foreach (var en in asm.ExportedTypes.Where(o => o.IsEnum && o.GetCustomAttribute <StructureAttribute>() != null))
{
StructureAttribute sta = en.GetCustomAttribute <StructureAttribute>();
DatasetInstall conceptDataset = new DatasetInstall()
{
Id = String.Format("HL7v3 {0} Concept Set", sta.Name)
};
// Create vaccine code concept set
var conceptSet = new DataUpdate()
{
InsertIfNotExists = true,
Element = new ConceptSet()
{
Key = Guid.NewGuid(),
Mnemonic = en.Name,
Name = sta.Name,
Oid = sta.CodeSystem,
Url = String.Format("http://openiz.org/valuset/v3-{0}", en.Name)
},
Association = new List <DataAssociation>()
};
var codeSystem = new DataUpdate()
{
InsertIfNotExists = true,
Element = new CodeSystem(sta.Name, sta.CodeSystem, en.Name)
{
Url = String.Format("http://hl7.org/fhir/v3-{0}", en.Name),
Key = Guid.NewGuid(),
}
};
conceptDataset.Action.Add(codeSystem);
foreach (var enm in en.GetFields())
{
var ena = enm.GetCustomAttribute <EnumerationAttribute>();
if (ena == null)
{
continue;
}
var dsa = enm.GetCustomAttribute <DescriptionAttribute>();
ReferenceTerm refTerm = new ReferenceTerm()
{
CodeSystemKey = codeSystem.Element.Key,
Mnemonic = ena.Value,
DisplayNames = new List <ReferenceTermName>()
{
new ReferenceTermName()
{
Language = "en", Name = dsa?.Description ?? enm.Name
}
},
Key = Guid.NewGuid()
};
var mnemonic = String.Format("{0}-{1}", en.Name, enm.Name);
if (mnemonic.Length > 64)
{
mnemonic = mnemonic.Substring(0, 64);
}
Concept concept = new Concept()
{
Key = Guid.NewGuid(),
Mnemonic = mnemonic,
ClassKey = ConceptClassKeys.Other,
ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Language = "en", Name = dsa?.Description
}
},
ReferenceTerms = new List <ConceptReferenceTerm>()
{
new ConceptReferenceTerm()
{
ReferenceTermKey = refTerm.Key,
RelationshipTypeKey = ConceptRelationshipTypeKeys.SameAs
}
},
StatusConceptKey = StatusKeys.Active,
CreationTime = DateTime.Now
};
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = refTerm
});
conceptDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = concept
});
(conceptSet.Element as ConceptSet).ConceptsXml.Add(concept.Key.Value);
}
conceptDataset.Action.Add(conceptSet);
XmlSerializer xsz = new XmlSerializer(typeof(DatasetInstall));
using (FileStream fs = File.Create(en.Name + ".dataset"))
xsz.Serialize(fs, conceptDataset);
}
}
public static void ImportSvs(string[] args)
{
var parameters = new ParameterParser <SvsOptions>().Parse(args);
var svsDatasetInstall = new DatasetInstall
{
Action = new List <DataInstallAction>()
};
var fileInfo = new FileInfo(parameters.File);
var serializer = new XmlSerializer(typeof(RetrieveValueSetResponseType));
var svs = (RetrieveValueSetResponseType)serializer.Deserialize(new StreamReader(parameters.File));
svsDatasetInstall.Id = svs.ValueSet.displayName;
foreach (var conceptListType in svs.ValueSet.ConceptList)
{
var codeSystem = new CodeSystem
{
Key = Guid.NewGuid(),
Name = svs.ValueSet.displayName,
Oid = svs.ValueSet.id,
VersionText = svs.ValueSet.version
};
svsDatasetInstall.Action.Add(new DataUpdate
{
Element = codeSystem,
InsertIfNotExists = true
});
foreach (var cpt in conceptListType.Concept)
{
var referenceTerm = new ReferenceTerm
{
CodeSystemKey = codeSystem.Key,
DisplayNames = new List <ReferenceTermName>
{
new ReferenceTermName(conceptListType.lang?.Length > 2 ? conceptListType.lang?.Substring(0, 2) : "en", cpt.displayName)
},
Key = Guid.NewGuid(),
Mnemonic = cpt.code
};
svsDatasetInstall.Action.Add(new DataUpdate
{
Element = referenceTerm,
InsertIfNotExists = true
});
var concept = new Concept
{
ClassKey = ConceptClassKeys.Other,
ConceptNames = new List <ConceptName>
{
new ConceptName(conceptListType.lang?.Length > 2 ? conceptListType.lang?.Substring(0, 2) : "en", cpt.displayName)
},
CreationTime = DateTimeOffset.Now,
Key = Guid.NewGuid(),
Mnemonic = cpt.code,
ReferenceTerms = new List <ConceptReferenceTerm>
{
new ConceptReferenceTerm(referenceTerm.Key, ConceptRelationshipTypeKeys.SameAs)
},
StatusConceptKey = StatusKeys.Active
};
svsDatasetInstall.Action.Add(new DataUpdate
{
Element = concept,
InsertIfNotExists = true
});
}
}
serializer = new XmlSerializer(typeof(DatasetInstall));
using (var fileStream = File.Create($"999-SVS-import-{fileInfo.Name}.dataset"))
{
serializer.Serialize(fileStream, svsDatasetInstall);
}
}
public static void ImportCsd(string[] args)
{
ApplicationContext.Current.Start();
ShowInfoMessage("Adding service providers...");
ApplicationContext.Current.AddServiceProvider(typeof(LocalEntityRepositoryService));
ApplicationContext.Current.AddServiceProvider(typeof(LocalMetadataRepositoryService));
ApplicationContext.Current.AddServiceProvider(typeof(LocalConceptRepositoryService));
AuthenticationContext.Current = new AuthenticationContext(AuthenticationContext.SystemPrincipal);
ApplicationContext.Current.Started += (o, e) =>
{
emergencyMessage = ApplicationContext.Current.GetLocaleString("01189998819991197253");
};
var parameters = new ParameterParser <CsdOptions>().Parse(args);
var csdDatasetInstall = new DatasetInstall("HFR via CSD, Organizations, Places, Providers, Services");
var actions = new List <DataInstallAction>();
var serializer = new XmlSerializer(typeof(CSD));
var fileInfo = new FileInfo(parameters.File);
ShowInfoMessage($"Loading file: {fileInfo.Name}...");
var csd = (CSD)serializer.Deserialize(new StreamReader(parameters.File));
ShowInfoMessage($"File: {fileInfo.Name} loaded successfully, starting mapping process...");
int limit = Int32.MaxValue;
if (!String.IsNullOrEmpty(parameters.Limit))
{
limit = Int32.Parse(parameters.Limit);
}
if (parameters.RelationshipsOnly)
{
int idx = 0;
foreach (var fac in csd.facilityDirectory.Take(limit))
{
var place = GetOrCreateEntity <Place>(fac.entityID, parameters.EntityUidAuthority, parameters);
var rels = CreateEntityRelationships(place, fac, csd.organizationDirectory, parameters);
actions.AddRange(rels.Select(o => new DataUpdate()
{
Element = o,
InsertIfNotExists = true,
IgnoreErrors = true
}));
Console.ForegroundColor = ConsoleColor.Magenta;
Console.WriteLine($"Mapped place: ({idx++}/{csd.facilityDirectory.Take(limit).Count()}) {place.Key.Value} {string.Join(" ", place.Names.SelectMany(n => n.Component).Select(c => c.Value))}");
Console.ResetColor();
}
}
else
{
var stopwatch = new Stopwatch();
stopwatch.Start();
// map organizations
var organizations = !parameters.SkipOrganizations ? MapOrganizations(csd.organizationDirectory.Take(limit), parameters).Select(o => new DataUpdate
{
InsertIfNotExists = true,
Element = o
}) : new List <DataUpdate>();
actions.AddRange(organizations);
// map places
var places = !parameters.SkipFacilties ? MapPlaces(csd.facilityDirectory.Take(limit), csd.organizationDirectory, parameters).Select(p => new DataUpdate
{
InsertIfNotExists = true,
Element = p
}) : new List <DataUpdate>();
actions.AddRange(places);
// map providers
var providers = MapProviders(csd.providerDirectory.Take(limit), parameters).Select(p => new DataUpdate
{
InsertIfNotExists = true,
Element = p
});
actions.AddRange(providers);
// map services
var services = MapServices(csd.serviceDirectory.Take(limit)).Select(s => new DataUpdate
{
InsertIfNotExists = true,
Element = s
});
actions.AddRange(services);
stopwatch.Stop();
ShowPerformanceMessage($"Mapped {places.Count()} Places, {providers.Count()} Providers, {organizations.Count()} Organizations, and {services.Count()} Services in {stopwatch.Elapsed.Minutes} minutes and {stopwatch.Elapsed.Seconds} seconds");
}
if (parameters.RelationshipsOnly)
{
csdDatasetInstall.Action = actions;
}
else
{
var entities = new List <Entity>();
var relationships = new List <EntityRelationship>();
foreach (var entity in actions.Where(a => a.Element is Entity).Select(c => c.Element as Entity))
{
entity.Relationships.ForEach(o => o.SourceEntityKey = entity.Key);
relationships.AddRange(entity.Relationships);
// HACK: clear the entity relationships because we are going to import them separately
entity.Relationships.Clear();
entities.Add(entity);
}
// add entities to the list of items to import
csdDatasetInstall.Action.AddRange(entities.Select(e => new DataUpdate
{
InsertIfNotExists = true,
Element = e
}).ToList());
// add relationships to the list of items to import
csdDatasetInstall.Action.AddRange(relationships.Select(e => new DataUpdate
{
InsertIfNotExists = true,
Element = e
}).ToList());
}
csdDatasetInstall.Action = csdDatasetInstall.Action.Distinct(new EntityComparison()).ToList();
if (parameters.RelationshipsOnly)
{
csdDatasetInstall.Action.RemoveAll(o => !(o.Element is EntityRelationship) || (o.Element as EntityRelationship).RelationshipTypeKey == EntityRelationshipTypeKeys.Parent);
}
serializer = new XmlSerializer(typeof(DatasetInstall));
var filename = $"999-CSD-import-{fileInfo.Name}.dataset";
using (var fileStream = File.Create(filename))
{
serializer.Serialize(fileStream, csdDatasetInstall);
}
ShowInfoMessage($"Dataset file created: {filename}");
if (parameters.Live)
{
ShowWarningMessage("Warning, the live flag is set to true, data will be imported directly into the database");
ShowInfoMessage("Starting live import");
var stopwatch = new Stopwatch();
stopwatch.Start();
var bundle = new Bundle
{
Item = actions.Select(a => a.Element).ToList()
};
var bundlePersistenceService = ApplicationContext.Current.GetService <IDataPersistenceService <Bundle> >();
ShowInfoMessage("Importing data directly into the database...");
bundlePersistenceService.Insert(bundle, AuthenticationContext.SystemPrincipal, TransactionMode.Commit);
ShowInfoMessage("The CSD live import is now complete");
stopwatch.Stop();
ShowPerformanceMessage($"Imported {bundle.Item.OfType<Place>().Count()} Places, {bundle.Item.OfType<Provider>().Count()} Providers, {bundle.Item.OfType<Organization>().Count()} Organizations, and {bundle.Item.OfType<PlaceService>().Count()} Services in {stopwatch.Elapsed.Minutes} minutes and {stopwatch.Elapsed.Seconds} seconds");
}
}
static void Main(string[] args)
{
// Concepts
Console.WriteLine("Generating OpenIZ Concepts to support GIIS data");
DatasetInstall conceptDataset = new DatasetInstall()
{
Id = "Concepts to support TIIS data", Action = new List <DataInstallAction>()
};
DataInsert healthFacilityTypes = new DataInsert()
{
Element = new ConceptSet()
{
Key = Guid.NewGuid(),
Mnemonic = "HealthFacilityTypes",
Oid = "1.3.6.1.4.1.45219.1.3.5.99.1",
Name = "Health Facility Types",
Url = "http://ivd.moh.go.tz/valueset/timr/HealthFacilityTypes"
},
Association = new List <DataAssociation>()
},
placeTypes = new DataInsert()
{
Element = new ConceptSet()
{
Key = Guid.NewGuid(),
Mnemonic = "PlaceTypes",
Oid = "1.3.6.1.4.1.45219.1.3.5.99.2",
Name = "Place Sub-Classifications",
Url = "http://openiz.org/valueset/timr/PlaceTypes"
},
Association = new List <DataAssociation>()
{
new DataAssociation()
{
PropertyName = "Concepts",
Element = new Concept()
{
Key = PT_DISTRICT,
StatusConceptKey = StatusKeys.Active,
IsSystemConcept = false,
ClassKey = ConceptClassKeys.Other,
Mnemonic = "PlaceType-District",
ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Language = "en",
Name = "District"
}
}
}
},
new DataAssociation()
{
PropertyName = "Concepts",
Element = new Concept()
{
Key = PT_DISTRICT_COUNCIL,
StatusConceptKey = StatusKeys.Active,
IsSystemConcept = false,
ClassKey = ConceptClassKeys.Other,
Mnemonic = "PlaceType-DistrictCouncil",
ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Language = "en",
Name = "District Council"
}
}
}
},
new DataAssociation()
{
PropertyName = "Concepts",
Element = new Concept()
{
Key = PT_REGION,
StatusConceptKey = StatusKeys.Active,
IsSystemConcept = false,
ClassKey = ConceptClassKeys.Other,
Mnemonic = "PlaceType-Region",
ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Language = "en",
Name = "Region"
}
}
}
},
new DataAssociation()
{
PropertyName = "Concepts",
Element = new Concept()
{
Key = PT_TERRITORY,
StatusConceptKey = StatusKeys.Active,
IsSystemConcept = false,
ClassKey = ConceptClassKeys.Other,
Mnemonic = "PlaceType-Territory",
ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Language = "en",
Name = "Territory"
}
}
}
},
new DataAssociation()
{
PropertyName = "Concepts",
Element = new Concept()
{
Key = PT_VILLAGE,
StatusConceptKey = StatusKeys.Active,
IsSystemConcept = false,
ClassKey = ConceptClassKeys.Other,
Mnemonic = "PlaceType-Village",
ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Language = "en",
Name = "Village"
}
}
}
}
}
};
foreach (var itm in HealthFacilityType.GetHealthFacilityTypeList().OrderBy(o => o.Id))
{
facilityTypeId.Add(itm.Id, Guid.NewGuid());
healthFacilityTypes.Association.Add(
new DataAssociation()
{
PropertyName = "Concepts",
Element = new Concept()
{
Key = facilityTypeId[itm.Id],
StatusConceptKey = StatusKeys.Active,
IsSystemConcept = false,
ClassKey = ConceptClassKeys.Other,
Mnemonic = "Facility-" + itm.Name.Replace(" ", ""),
ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Language = "en",
Name = itm.Name
}
}
}
}
);
}
(healthFacilityTypes.Element as ConceptSet).ConceptsXml = healthFacilityTypes.Association.Select(o => o.Element.Key.Value).ToList();
(placeTypes.Element as ConceptSet).ConceptsXml = placeTypes.Association.Select(o => o.Element.Key.Value).ToList();
conceptDataset.Action.AddRange(healthFacilityTypes.Association.Select(o => new DataInsert()
{
Element = o.Element
}));
conceptDataset.Action.AddRange(placeTypes.Association.Select(o => new DataInsert()
{
Element = o.Element
}));
conceptDataset.Action.AddRange(new DataInstallAction[]
{
new DataInsert()
{
Element = new Concept()
{
Key = industryManufacturer, Mnemonic = "Industry-Manufacturing", ClassKey = ConceptClassKeys.Other, IsSystemConcept = false, StatusConceptKey = StatusKeys.Active, ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Language = "en", Name = "Manufacturing"
}
}, ConceptSetsXml = new List <Guid>()
{
Guid.Parse("d1597e50-845a-46e1-b9ae-6f99ff93d9db")
}
}
},
new DataInsert()
{
Element = new Concept()
{
Key = industryOther, Mnemonic = "Industry-OtherUnknown", ClassKey = ConceptClassKeys.Other, IsSystemConcept = false, StatusConceptKey = StatusKeys.Active, ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Language = "en", Name = "Other/Unknown"
}
}, ConceptSetsXml = new List <Guid>()
{
Guid.Parse("d1597e50-845a-46e1-b9ae-6f99ff93d9db")
}
}
},
new DataInsert()
{
Element = new Concept()
{
Key = industryHealthDelivery, Mnemonic = "Industry-HealthDelivery", ClassKey = ConceptClassKeys.Other, IsSystemConcept = false, StatusConceptKey = StatusKeys.Active, ConceptNames = new List <ConceptName>()
{
new ConceptName()
{
Language = "en", Name = "Healthcare"
}
}, ConceptSetsXml = new List <Guid>()
{
Guid.Parse("d1597e50-845a-46e1-b9ae-6f99ff93d9db")
}
}
}
});
healthFacilityTypes.Association.Clear();
placeTypes.Association.Clear();
conceptDataset.Action.Add(healthFacilityTypes);
conceptDataset.Action.Add(placeTypes);
// Facilities
Console.WriteLine("Exporting GIIS Facilities to OpenIZ IMS Format");
DatasetInstall facilityDataset = new DatasetInstall()
{
Action = new List <DataInstallAction>()
};
facilityDataset.Id = "Facilities from GIIS";
foreach (var itm in HealthFacility.GetHealthFacilityList().OrderBy(o => o.Id))
{
facilityDataset.Action.Add(new DataInsert()
{
Element = MapFacility(itm)
});
}
// Places
Console.WriteLine("Exporting GIIS Places to OpenIZ IMS Format");
DatasetInstall placeDataset = new DatasetInstall()
{
Action = new List <DataInstallAction>()
};
placeDataset.Id = "Places from GIIS";
foreach (var itm in GIIS.DataLayer.Place.GetPlaceList().OrderBy(o => o.ParentId))
{
placeDataset.Action.Add(new DataInsert()
{
Element = MapPlace(itm)
});
}
// Users
Console.WriteLine("Exporting GIIS Users to OpenIZ IMS Format");
DatasetInstall userDataset = new DatasetInstall()
{
Action = new List <DataInstallAction>()
};
userDataset.Id = "Users from TIIS";
foreach (var itm in User.GetUserList())
{
if (userDataset.Action.Any(o => (o.Element as SecurityUser)?.UserName.Trim().ToLower() == itm.Username.Trim().ToLower()) ||
itm.Username.ToLower() == "administrator")
{
continue; /// Apparently user names are distinct based on case?
}
Guid userId = Guid.NewGuid(), entityId = Guid.NewGuid();
userMap.Add(itm.Id, userId);
if (!userEntityMap.TryGetValue(itm.Id, out entityId))
{
entityId = Guid.NewGuid();
userEntityMap.Add(itm.Id, entityId);
}
var securityUser = new SecurityUser()
{
Key = userId,
UserName = itm.Username,
Email = itm.Email,
EmailConfirmed = !String.IsNullOrEmpty(itm.Email),
LastLoginTime = itm.Lastlogin,
SecurityHash = Guid.Empty.ToString(),
Lockout = itm.IsActive ? null : (DateTime?)DateTime.MaxValue,
PasswordHash = BitConverter.ToString(Convert.FromBase64String(itm.Password)).Replace("-", ""),
UserClass = UserClassKeys.HumanUser,
TwoFactorEnabled = false,
ObsoletionTime = itm.Deleted ? (DateTime?)DateTime.Now : null,
ObsoletedByKey = itm.Deleted ? (Guid?)Guid.Parse(AuthenticationContext.SystemUserSid) : null,
};
var userEntity = new UserEntity()
{
Key = entityId,
Names = new List <EntityName>()
{
new EntityName(NameUseKeys.OfficialRecord, itm.Lastname, itm.Firstname)
},
SecurityUserKey = userId,
Identifiers = new List <EntityIdentifier>()
{
new EntityIdentifier(new AssigningAuthority("TIIS_USER_ID", "TIIS User Identifiers", "1.3.6.1.4.1.45219.1.3.5.2"), itm.Id.ToString())
},
Tags = new List <EntityTag>()
{
new EntityTag("http://openiz.org/tags/contrib/importedData", "true")
},
StatusConceptKey = itm.IsActive ? StatusKeys.Active : StatusKeys.Obsolete
};
if (!String.IsNullOrEmpty(itm.Email))
{
userEntity.Telecoms = new List <EntityTelecomAddress>()
{
new EntityTelecomAddress(TelecomAddressUseKeys.WorkPlace, itm.Email)
}
}
;
Guid facilityId = Guid.Empty;
if (facilityMap.TryGetValue(itm.HealthFacilityId, out facilityId))
{
userEntity.Relationships.Add(new EntityRelationship(EntityRelationshipTypeKeys.Employee, new Entity()
{
Key = facilityId
}));
}
// data element
var securityUserData = new DataInsert()
{
Element = securityUser,
Association = new List <DataAssociation>()
};
// Role
foreach (var r in Role.GetRolesOfUser(itm.Id))
{
Guid roleId = Guid.Empty;
if (!roleMap.TryGetValue(r.Id, out roleId))
{
roleId = Guid.NewGuid();
roleMap.Add(r.Id, roleId);
}
var role = new SecurityRole()
{
Key = roleId,
Name = r.Name,
ObsoletionTime = r.IsActive ? null : (DateTime?)DateTime.Now,
ObsoletedByKey = r.IsActive ? null : (Guid?)Guid.Parse(AuthenticationContext.SystemUserSid)
};
// Add roles to the user
securityUserData.Association.Add(new DataAssociation()
{
PropertyName = "Roles",
Element = new SecurityRole()
{
Key = role.Key
}
});
// Add role
userDataset.Action.Add(new DataInsert()
{
Element = role
});
// Vaccinator?
if (r.Name == "Vaccinator")
{
// Provider entity
var providerEntity = new Provider()
{
Key = Guid.NewGuid(),
Names = userEntity.Names,
Telecoms = userEntity.Telecoms,
Identifiers = userEntity.Identifiers.Select(o => new EntityIdentifier(new AssigningAuthority("PROVIDER_ID", "TImR Assigned Provider ID", "1.3.6.1.4.1.45219.1.3.5.80"), o.Value)).ToList(),
Tags = new List <EntityTag>()
{
new EntityTag("http://openiz.org/tags/contrib/importedData", "true")
},
StatusConceptKey = itm.IsActive ? StatusKeys.Active : StatusKeys.Obsolete
};
userDataset.Action.Add(new DataInsert()
{
Element = providerEntity
});
// Create a heath care provider
userEntity.Relationships.Add(new EntityRelationship()
{
RelationshipTypeKey = EntityRelationshipTypeKeys.AssignedEntity,
TargetEntityKey = providerEntity.Key
});
}
}
userDataset.Action.Add(securityUserData);
userDataset.Action.Add(new DataInsert()
{
Element = userEntity
});
}
var materialDataset = new DatasetInstall()
{
Id = "Manufactured Materials from GIIS"
};
foreach (var il in ItemLot.GetItemLotList())
{
var itm = MapMaterial(il, materialDataset);
materialDataset.Action.Add(new DataUpdate()
{
InsertIfNotExists = true, Element = itm
});
}
// Write datasets
XmlSerializer xsz = new XmlSerializer(typeof(DatasetInstall));
using (var fs = File.Create("990-tiis.concepts.dataset"))
xsz.Serialize(fs, conceptDataset);
using (var fs = File.Create("991-tiis.facilities.dataset"))
xsz.Serialize(fs, facilityDataset);
using (var fs = File.Create("992-tiis.places.dataset"))
xsz.Serialize(fs, placeDataset);
using (var fs = File.Create("993-tiis.users.dataset"))
xsz.Serialize(fs, userDataset);
using (var fs = File.Create("994-tiis.materials.dataset"))
xsz.Serialize(fs, materialDataset);
}
}
/// <summary>
/// Map a facility
/// </summary>
static OpenIZ.Core.Model.Entities.ManufacturedMaterial MapMaterial(ItemLot item, DatasetInstall context)
{
Guid id = Guid.NewGuid();
manufacturedMaterialMap.Add(item.Id, id);
EntitySource.Current = new EntitySource(new DummyEntitySource());
Guid materialId = Guid.Empty;
if (!materialMap.TryGetValue(item.ItemId, out materialId))
{
materialId = Guid.NewGuid();
Material material = new Material()
{
Key = materialId,
ExpiryDate = item.ItemObject.ExitDate,
FormConceptKey = Guid.Parse(item.ItemObject.Name == "OPV" ? "66CBCE3A-2E77-401D-95D8-EE0361F4F076" : "9902267C-8F77-4233-BFD3-E6B068AB326A"),
DeterminerConceptKey = DeterminerKeys.Described,
Identifiers = new List <EntityIdentifier>()
{
new EntityIdentifier(new AssigningAuthority("TIIS_ITEM", "TIIS Item Identifiers", "1.3.6.1.4.1.33349.3.1.5.102.3.5.12"), item.ItemId.ToString())
},
Names = new List <EntityName>()
{
new EntityName(NameUseKeys.OfficialRecord, item.ItemObject.Name)
},
StatusConceptKey = item.ItemObject.IsActive ? StatusKeys.Active : StatusKeys.Obsolete
};
context.Action.Add(new DataUpdate()
{
InsertIfNotExists = true, Element = material
});
materialMap.Add(item.ItemId, materialId);
}
// Organization map?
Guid organizationId = Guid.Empty;
var gtinObject = ItemManufacturer.GetItemManufacturerByGtin(item.Gtin);
if (gtinObject != null && !manufacturerMap.TryGetValue(gtinObject.ManufacturerId, out organizationId))
{
organizationId = Guid.NewGuid();
Organization organization = new Organization()
{
Key = organizationId,
Identifiers = new List <EntityIdentifier>()
{
new EntityIdentifier(new AssigningAuthority("MANUFACTURER_CODE", "Manufacturer Codes", "1.3.6.1.4.1.33349.3.1.5.102.3.5.14"), gtinObject.ManufacturerObject.Code),
new EntityIdentifier(new AssigningAuthority("TIIS_MANUFACTURER", "TIIS Manufacturer Identifiers", "1.3.6.1.4.1.33349.3.1.5.102.3.5.13"), gtinObject.ManufacturerId.ToString())
},
Names = new List <EntityName>()
{
new EntityName(NameUseKeys.OfficialRecord, gtinObject.ManufacturerObject.Name)
},
StatusConceptKey = gtinObject.ManufacturerObject.IsActive ? StatusKeys.Active : StatusKeys.Obsolete,
IndustryConceptKey = industryManufacturer
};
context.Action.Add(new DataUpdate()
{
InsertIfNotExists = true, Element = organization
});
manufacturerMap.Add(gtinObject.ManufacturerId, organizationId);
}
Guid typeConceptKey = Guid.Empty;
materialTypeMap.TryGetValue(item.ItemId, out typeConceptKey);
// TODO: Migrate over kit items
// TODO: Link boxes/vials/doses
// Core construction of place
ManufacturedMaterial retVal = new ManufacturedMaterial()
{
Key = id,
TypeConceptKey = typeConceptKey == Guid.Empty ? (Guid?)null : typeConceptKey,
Relationships = new List <EntityRelationship>()
{
new EntityRelationship(EntityRelationshipTypeKeys.ManufacturedProduct, id)
{
SourceEntityKey = materialId
},
},
Names = new List <EntityName>()
{
new EntityName(NameUseKeys.Assigned, String.Format("{0} ({1})", item.ItemObject.Name, gtinObject?.ManufacturerObject.Name))
},
ExpiryDate = item.ExpireDate,
LotNumber = item.LotNumber,
Identifiers = new List <EntityIdentifier>()
{
new EntityIdentifier(new AssigningAuthority("GTIN", "GS1 Global Trade Identification Number (GTIN)", "1.3.160"), item.Gtin),
new EntityIdentifier(new AssigningAuthority("GIIS_ITEM_ID", "GIIS Item Identifiers", "1.3.6.1.4.1.33349.3.1.5.102.3.5.15"), item.Id.ToString())
},
IsAdministrative = false,
StatusConceptKey = StatusKeys.Active
};
if (organizationId != Guid.Empty)
{
retVal.Relationships.Add(new EntityRelationship(EntityRelationshipTypeKeys.WarrantedProduct, id)
{
SourceEntityKey = organizationId
});
}
return(retVal);
}
