public async Task TestITISPlantInfoProcessor()
{
var transformer = new ITISPlantInfoTransformer();
var itisData = ITISPlantInfoData();
var plantInfos = new List <PlantInfo>();
itisData.ForEach(i => plantInfos.AddRange(transformer.Transform(new List <TaxonomicUnit> {
i
})));
var originRepository = RepositoryMocks.GetStandardMockOriginRepository(new List <Stores.Origin>());
var locationRepository = RepositoryMocks.GetStandardMockLocationRepository(new List <Stores.Location>());
var lifeformRepository = RepositoryMocks.GetStandardMockLifeformRepository(new List <Stores.Lifeform>());
var plantInfoRepository = RepositoryMocks.GetStandardMockPlantInfoRepository(new List <Stores.PlantInfo>());
var plantLocationRepository = RepositoryMocks.GetStandardMockPlantLocationRepository(new List <Stores.PlantLocation>());
var synonymRepository = RepositoryMocks.GetStandardMockSynonymRepository();
var taxonRepository = RepositoryMocks.GetStandardMockTaxonRepository(new List <Stores.Taxon>());
var plantSynonymRepository = new Mock <IRepository <Stores.PlantSynonym> >();
var plantInfoIndex = SearchMocks.GetStandardMockPlantInfoIndex();
var lifeformIndex = SearchMocks.GetStandardMockLifeformIndex();
var locationService = new LocationService(locationRepository.Object);
var originService = new OriginService(originRepository.Object, locationService);
var lifeformService = new LifeformService(lifeformRepository.Object, lifeformIndex.Object);
var plantInfoService = new PlantInfoService(plantInfoRepository.Object, plantLocationRepository.Object, plantInfoIndex.Object);
var synonymService = new SynonymService(synonymRepository.Object);
var taxonService = new TaxonService(taxonRepository.Object, synonymService);
var processor = new PlantInfoProcessor(lifeformService, originService, plantInfoService, taxonService, locationService);
await processor.InitializeOrigin(transformer.Origin);
await processor.InitializeLifeforms();
await processor.InitializeTaxons();
var result = await processor.Process(plantInfos);
result.Count(p => p.ScientificName == "Glandularia quadrangulata").Should().Be(1);
result.Count(p => p.Taxon.Subfamily == null).Should().Be(5);
result.Count(p => p.Taxon.Species == "cremersii").Should().Be(1);
result.Count(p => p.Taxon.Form == "viridifolia").Should().Be(1);
result.Count(p => p.Taxon.Subspecies == "purpurea").Should().Be(1);
result.Count(p => p.Taxon.Variety == "graminea").Should().Be(1);
result.Where(p => p.Locations != null).SelectMany(p => p.Locations).Count().Should().Be(3);
result.Where(p => p.Locations != null).SelectMany(p => p.Locations).Count(l => l.Status == LocationStatus.Native).Should().Be(3);
result.Select(p => p.Origin).DistinctBy(o => o.OriginId).Count().Should().Be(5);
}
public async Task TestITISSynonymProcessor()
{
var transformer = new ITISSynonymTransformer();
var itisData = ITISSynonymData();
var synonyms = new List <Synonym>();
itisData.ForEach(i => synonyms.Add(transformer.Transform(i)));
var originRepository = RepositoryMocks.GetStandardMockOriginRepository(new List <Stores.Origin>());
var locationRepository = RepositoryMocks.GetStandardMockLocationRepository(new List <Stores.Location>());
var synonymRepository = RepositoryMocks.GetStandardMockSynonymRepository(new List <Stores.Synonym>());
var taxonRepository = RepositoryMocks.GetStandardMockTaxonRepository(new List <Stores.Taxon>());
var locationService = new LocationService(locationRepository.Object);
var originService = new OriginService(originRepository.Object, locationService);
var synonymService = new SynonymService(synonymRepository.Object);
var taxonService = new TaxonService(taxonRepository.Object, synonymService);
var processor = new SynonymProcessor(synonymService, originService, taxonService);
await processor.InitializeOrigin(transformer.Origin);
await processor.InitializeTaxons();
var result = await processor.Process(synonyms);
result.Count().Should().Be(16);
result.Count(s => s.Taxon.Kingdom == "Plantae").Should().Be(1);
result.Count(s => s.Language == "English").Should().Be(10);
result.Count(s => s.DateUpdated.Year == 2003).Should().Be(3);
result.Count(s => s.Rank == "Variety").Should().Be(2);
result.Count(s => s.Taxon.Variety != null).Should().Be(2);
result.Count(s => s.Taxon.Variety == "paludicola").Should().Be(1);
result.Select(s => s.Origin).Count().Should().Be(16);
}
//private async Task StoreAssessment(int id, FA4 doc, User user, bool notUpdateChangedBy, bool forceStore = false)
//{
// //var dateTimeFormat = "yyyy-MM-dd HH:mm:ss";
// var now = DateTime.Now;
// doc.LastUpdatedAt = now;
// var assessment = _dbContext.Assessments.SingleOrDefault(x => x.Id == id);
// if (!forceStore && (assessment.LockedForEditBy != null && assessment.LockedForEditBy != user.Brukernavn))
// {
// throw new Exception("IKKE SKRIVETILGANG TIL DENNE VURDERINGEN - Låst av annen bruker");
// }
// // check and update referenceUsages
// var usedReferences = doc.References.Select(x => x.ReferenceId).ToArray();
// if (!forceStore && usedReferences.Any())
// {
// bool ok = await _referenceService.SignalUsage(usedReferences, user.Id);
// }
// var curAss = JsonConvert.DeserializeObject<FA4>(assessment.Doc);
// byte[] zipfile;
// var fileName = "ArtskartData.zip";
// const string name = "Datagrunnlag fra Artskart";
// const string filetype = "application/zip";
// if (!forceStore && doc.ArtskartSistOverført != curAss.ArtskartSistOverført)
// {
// try
// {
// zipfile = await TaskHelper.TimeoutAfter(GetZipDataFromArtskart(doc), TimeSpan.FromSeconds(10));
// }
// catch
// {
// // ok here
// zipfile = Array.Empty<byte>();
// }
// if (zipfile.Length > 0)
// {
// var attach = await _dbContext.Attachments.Where(x =>
// x.AssessmentId == assessment.Id && x.Name == name && x.Type == filetype &&
// x.FileName == fileName).FirstOrDefaultAsync();
// if (attach != null)
// {
// attach.File = zipfile;
// attach.IsDeleted = false;
// attach.Date = DateTime.Now;
// attach.UserId = user.Id;
// }
// else
// {
// attach = new Attachment
// {
// AssessmentId = assessment.Id,
// Date = DateTime.Now,
// File = zipfile,
// FileName = fileName,
// Name = name,
// Type = filetype,
// UserId = user.Id
// };
// _dbContext.Attachments.Add(attach);
// }
// }
// }
// var history = new AssessmentHistory()
// {
// Id = assessment.Id,
// Doc = assessment.Doc,
// HistoryAt = now
// };
// _dbContext.AssessmentHistories.Add(history);
// if (!notUpdateChangedBy)
// {
// doc.EvaluationStatus = "inprogress";
// doc.LastUpdatedOn = now;
// doc.LastUpdatedBy = user.Brukernavn;
// }
// var assessmentString = Newtonsoft.Json.JsonConvert.SerializeObject(doc);
// assessment.Doc = assessmentString;
// await _dbContext.SaveChangesAsync().ConfigureAwait(false);
//}
//private static async Task<byte[]> GetZipDataFromArtskart(FA4 rlRodliste2019)
//{
// // hent datasett fra artskart
// var date = DateTime.Parse(rlRodliste2019.ArtskartSistOverført);
// var kriterier = rlRodliste2019.ArtskartModel;
// var apibase =
// "https://artskart.artsdatabanken.no/PublicApi/api/listhelper/";
// var type =
// kriterier.IncludeObjects == kriterier.IncludeObservations
// ? "all"
// : kriterier.IncludeObjects
// ? "specimen"
// : "observations";
// var region =
// kriterier.IncludeNorge == kriterier.IncludeSvalbard
// ? "all"
// : kriterier.IncludeNorge
// ? "fastland"
// : "svalbard";
// var excludeGbif =
// kriterier.ExcludeGbif ? "&sourcedatabases[]=-40,-211" : "";
// var queryparams =
// $"&fromYear={kriterier.ObservationFromYear}&toYear={kriterier.ObservationToYear}&fromMonth={kriterier.FromMonth}&toMonth={kriterier.ToMonth}&type={type}®ion={region}{excludeGbif}";
// queryparams += $"&scientificNameId={rlRodliste2019.VurdertVitenskapeligNavnId}";
// if (!string.IsNullOrWhiteSpace(rlRodliste2019.ArtskartSelectionGeometry))
// {
// queryparams += $"&geojsonPolygon=";
// dynamic json = JsonConvert.DeserializeObject(rlRodliste2019.ArtskartSelectionGeometry);
// dynamic coordinates = json.geometry.coordinates;
// dynamic items = coordinates[0];
// foreach (dynamic item in items)
// {
// foreach (dynamic o in item)
// {
// string s = o.ToString();
// queryparams += s.Replace(",", ".") + ",";
// }
// }
// queryparams = queryparams.Substring(0, queryparams.Length - 1);
// }
// if (!string.IsNullOrWhiteSpace(rlRodliste2019.ArtskartAdded))
// {
// queryparams += $"&addPoints={rlRodliste2019.ArtskartAdded}";
// }
// if (!string.IsNullOrWhiteSpace(rlRodliste2019.ArtskartRemoved))
// {
// queryparams += $"&removePoints={rlRodliste2019.ArtskartRemoved}";
// }
// var urlen = apibase + rlRodliste2019.TaxonId + "/downloadObservations/?" + queryparams;
// using var client = new HttpClient();
// var zipfile = await client.GetByteArrayAsync(urlen);
// return zipfile ;
//}
private static FA4 CreateNewAssessment(string expertgroup, string userName, int scientificNameId)
{
if (string.IsNullOrWhiteSpace(expertgroup))
{
throw new ArgumentNullException(nameof(expertgroup));
}
if (string.IsNullOrWhiteSpace(userName))
{
throw new ArgumentNullException(nameof(userName));
}
var vurderingscontext = expertgroup.Contains("Svalbard") ? "S" : "N";
var vurderingsår = 2021;
var createdby = "createdbyloading";
var ts = new Prod.Api.Services.TaxonService();
var titask = ts.GetTaxonInfoAsync(scientificNameId);
var ti = titask.GetAwaiter().GetResult();
var(hierarcy, rank) = TaxonService.GetFullPathScientificName(ti);
if (scientificNameId != ti.ValidScientificNameId)
{
throw new ArgumentException("supplied scientificNameId is not ValidScientificNameId");
}
var rl = new FA4();
//rl.Ekspertgruppe = expertgroup;
//rl.VurderingsContext = vurderingscontext;
//rl.Slettet = false;
//rl.LastUpdatedOn = DateTime.Now;
//rl.LastUpdatedBy = userName;
//rl.Vurderingsår = vurderingsår;
//rl.SistVurdertAr = vurderingsår;
//rl.EvaluationStatus = createdby;
//rl.OverordnetKlassifiseringGruppeKode = "rodlisteVurdertArt";
//rl.RodlisteVurdertArt = "etablertBestandINorge";
//rl.VurdertVitenskapeligNavn = ti.ValidScientificName;
//rl.VurdertVitenskapeligNavnId = ti.ValidScientificNameId;
//rl.VurdertVitenskapeligNavnAutor = ti.ValidScientificNameAuthorship;
//rl.VurdertVitenskapeligNavnHierarki = hierarcy;
//rl.TaxonId = ti.TaxonId;
//rl.TaxonRank = rank;
//rl.PopularName = ti.PrefferedPopularname;
////ekstra standardverdier
//rl.ImportInfo.VurderingsId2015 = string.Empty;
//rl.AndelNåværendeBestand = "-";
//rl.A1OpphørtOgReversibel = "-";
//rl.A2Forutgående10År = "-";
//rl.A3Kommende10År = "-";
//rl.A4Intervall10År = "-";
//rl.BA2FåLokaliteterProdukt = "";
//rl.B1BeregnetAreal = "";
//rl.B1UtbredelsesområdeKode = "-";
//rl.B2ForekomstarealKode = "-";
//rl.BA1KraftigFragmenteringKode = "-";
//rl.BA2FåLokaliteterKode = "-";
//rl.CVurdertpopulasjonsstørrelseProdukt = "";
//rl.C1PågåendePopulasjonsreduksjonKode = "-";
//rl.C2A1PågåendePopulasjonsreduksjonKode = "-";
//rl.D1FåReproduserendeIndividKode = "-";
//rl.D2MegetBegrensetForekomstarealKode = "-";
//rl.EKvantitativUtryddingsmodellKode = "-";
////gudene vet om disse har betydning:
//rl.WktPolygon = "";
//rl.SistVurdertAr = 2021;
//rl.C2A2PågåendePopulasjonsreduksjonKode = "-";
//rl.C2BPågåendePopulasjonsreduksjonKode = "-";
//rl.CPopulasjonsstørrelseKode = "-";
//rl.B2ForekomstarealProdukt = "";
//rl.B1UtbredelsesområdeProdukt = "";
//rl.OppsummeringAKriterier = "";
//rl.OppsummeringBKriterier = "";
//rl.OppsummeringCKriterier = "";
//rl.OppsummeringDKriterier = "";
//rl.OppsummeringEKriterier = "";
//rl.B2BeregnetAreal = "";
//if (rl.Ekspertgruppe == "Leddormer") // special case - ville ha LC som standard
//{
// rl.C2A2SannhetsverdiKode = "1";
// rl.OverordnetKlassifiseringGruppeKode = "sikkerBestandLC";
// rl.Kategori = "LC";
//}
//AddFylkeslister(rl);
//rl.NaturtypeHovedenhet = new List<string>();
//SetArtskartImportSettings(rl);
return(rl);
}
/// <summary>
/// Close all clients (connections) to web services.
/// </summary>
public static void CloseClients()
{
if (AnalysisService.IsNotNull())
{
AnalysisService.CloseClients();
}
if (GeoReferenceService.IsNotNull())
{
GeoReferenceService.CloseClients();
}
if (KulService.IsNotNull())
{
KulService.CloseClients();
}
if (MvmService.IsNotNull())
{
MvmService.CloseClients();
}
if (NorsService.IsNotNull())
{
NorsService.CloseClients();
}
if (NorwayTaxonService.IsNotNull())
{
NorwayTaxonService.CloseClients();
}
if (PESINameService.IsNotNull())
{
PESINameService.CloseClients();
}
if (PictureService.IsNotNull())
{
PictureService.CloseClients();
}
if (ReferenceService.IsNotNull())
{
ReferenceService.CloseClients();
}
if (SersService.IsNotNull())
{
SersService.CloseClients();
}
if (SpeciesObservationHarvestService.IsNotNull())
{
SpeciesObservationHarvestService.CloseClients();
}
if (SwedishSpeciesObservationService.IsNotNull())
{
SwedishSpeciesObservationService.CloseClients();
}
if (SwedishSpeciesObservationSOAPService.IsNotNull())
{
SwedishSpeciesObservationSOAPService.CloseClients();
}
if (TaxonAttributeService.IsNotNull())
{
TaxonAttributeService.CloseClients();
}
if (TaxonService.IsNotNull())
{
TaxonService.CloseClients();
}
if (DyntaxaInternalService.IsNotNull())
{
DyntaxaInternalService.CloseClients();
}
if (UserService.IsNotNull())
{
UserService.CloseClients();
}
if (WramService.IsNotNull())
{
WramService.CloseClients();
}
}
