Merge pull request #5 from federico-rosatelli/main

SRA Analysis

service/api/analysis.go

@@ -0,0 +1,108 @@
+package api
+
+import (
+	"github.com/BITSapienza/Bio-Server/service/ErrManager"
+	str "github.com/BITSapienza/Bio-Server/service/structures"
+)
+
+func (rt *_router) GetAnalysis() ([]str.SraBioProject, ErrManager.Errors) {
+	var an []str.SraBioProject
+	nProj, err := rt.db.FindAnalysis()
+	if err != nil {
+		return an, err
+	}
+	var sraProjects []str.SraBioProject
+	srr := make(map[string]str.SraBioProject)
+	for _, pro := range nProj {
+		projId := pro["BioProject"].(string)
+		val, ok := srr[projId]
+		if !ok {
+
+			sra := str.SraBioProject{
+				TaxId: pro["TaxId"].(string),
+
+				BioProjectId: pro["BioProject"].(string),
+				BioSamples: []struct {
+					BioSampleId string
+					Experiments []struct {
+						ExperimentId string
+						Runs         []string
+					}
+				}{},
+			}
+			if _, ok := pro["ScientificName"].(string); ok {
+				sra.ScientificName = pro["ScientificName"].(string)
+			}
+			if _, ok := pro["Abstract"].(string); ok {
+				sra.Comment = pro["Abstract"].(string)
+			}
+			sra.BioSamples = append(sra.BioSamples, struct {
+				BioSampleId string
+				Experiments []struct {
+					ExperimentId string
+					Runs         []string
+				}
+			}{
+				BioSampleId: pro["BioSample"].(string),
+			})
+			sra.BioSamples[0].Experiments = append(sra.BioSamples[0].Experiments, struct {
+				ExperimentId string
+				Runs         []string
+			}{ExperimentId: pro["ExperimentCode"].(string)})
+			sra.BioSamples[0].Experiments[0].Runs = append(sra.BioSamples[0].Experiments[0].Runs, pro["Run"].(string))
+			srr[projId] = sra
+		} else {
+			isInsideSample := false
+
+			for k, sample := range val.BioSamples {
+				if sample.BioSampleId == pro["BioSample"].(string) {
+					isInsideSample = true
+					isInsideExample := false
+					for j, expreiment := range sample.Experiments {
+						if expreiment.ExperimentId == pro["ExperimentCode"].(string) {
+							isInsideExample = true
+							srr[projId].BioSamples[k].Experiments[j].Runs = append(srr[projId].BioSamples[k].Experiments[j].Runs, pro["Run"].(string))
+						}
+					}
+					if !isInsideExample {
+						srr[projId].BioSamples[k].Experiments = append(srr[projId].BioSamples[k].Experiments, struct {
+							ExperimentId string
+							Runs         []string
+						}{
+							ExperimentId: pro["ExperimentCode"].(string),
+						})
+						srr[projId].BioSamples[k].Experiments[len(srr[projId].BioSamples[k].Experiments)-1].Runs = append(srr[projId].BioSamples[k].Experiments[len(srr[projId].BioSamples[k].Experiments)-1].Runs, pro["Run"].(string))
+					}
+
+				}
+			}
+			if !isInsideSample {
+				prov := struct {
+					BioSampleId string
+					Experiments []struct {
+						ExperimentId string
+						Runs         []string
+					}
+				}{BioSampleId: pro["BioSample"].(string)}
+
+				prov.Experiments = append(prov.Experiments, struct {
+					ExperimentId string
+					Runs         []string
+				}{ExperimentId: pro["ExperimentCode"].(string)})
+				prov.Experiments[0].Runs = append(prov.Experiments[0].Runs, pro["Run"].(string))
+				value := srr[projId]
+				value.BioSamples = append(value.BioSamples, prov)
+				srr[projId] = value
+			}
+
+		}
+	}
+	for _, key := range srr {
+		sraProjects = append(sraProjects, key)
+	}
+	return sraProjects, nil
+}
+
+// func (a myAnalysis) mutateStruct() (str.SraBioProject, ErrManager.Errors) {
+
+// }

service/api/api-handler.go

@@ -14,5 +14,6 @@ func (rt *_router) Handler() http.Handler {
 	rt.router.GET("/organism/:id/nucleotides/:locus", rt.Get_Nucleotide_From_Locus)
 	rt.router.GET("/organism/:id/proteins", rt.Get_Proteins_Id)
 	rt.router.GET("/organism/:id/proteins/:locus", rt.Get_Protein_From_Locus)
+	rt.router.GET("/analysis", rt.Get_Analysis)
 	return rt.router
 }

service/api/routing-functions.go

@@ -135,3 +135,16 @@ func (rt *_router) Get_Protein_From_Locus(w http.ResponseWriter, r *http.Request
 	}
 
 }
+
+func (rt *_router) Get_Analysis(w http.ResponseWriter, r *http.Request, ps httprouter.Params) {
+	w.Header().Set("content-type", "application/json")
+	c, err := rt.GetAnalysis()
+	if err != nil {
+		http.Error(w, err.Error(), err.Type())
+		return
+	}
+	if errJson := json.NewEncoder(w).Encode(c); errJson != nil {
+		http.Error(w, errJson.Error(), http.StatusBadRequest)
+		return
+	}
+}

service/database/analysis.go

@@ -0,0 +1,61 @@
+package database
+
+import (
+	"context"
+
+	errorM "github.com/BITSapienza/Bio-Server/service/ErrManager"
+
+	"go.mongodb.org/mongo-driver/bson"
+	"go.mongodb.org/mongo-driver/mongo"
+)
+
+// filter = {
+// 	"STUDY.center_name": "BioProject",
+// 	"SAMPLE.IDENTIFIERS.EXTERNAL_ID.namespace": "BioSample",
+// }
+
+// proj = {
+// 	"_id":0,
+// 	"TaxId":"$SAMPLE.SAMPLE_NAME.TAXON_ID.value",
+// 	"BioProject":"$STUDY.alias",
+// 	"BioSample":"$SAMPLE.IDENTIFIERS.EXTERNAL_ID.value",
+// 	"ExperimentCode":"$EXPERIMENT.accession",
+// 	"SRR":"$RUN_SET.RUN.accession",
+// 	"Abstract":"$STUDY.DESCRIPTOR.STUDY_ABSTRACT.value",
+// 	"LinkSRA":"$RUN_SET.RUN.SRAFiles"
+// }
+
+func (db *appDB) FindAnalysis() ([]map[string]interface{}, errorM.Errors) {
+	filter := bson.D{{
+		Key: "$match", Value: bson.M{
+			"STUDY.center_name":                        "BioProject",
+			"SAMPLE.IDENTIFIERS.EXTERNAL_ID.namespace": "BioSample",
+		},
+	}}
+	proj := bson.D{{
+		Key: "$project", Value: bson.M{
+			"_id":            0,
+			"ScientificName": "$SAMPLE.SAMPLE_NAME.SCIENTIFIC_NAME.value",
+			"TaxId":          "$SAMPLE.SAMPLE_NAME.TAXON_ID.value",
+			"BioProject":     "$STUDY.alias",
+			"BioSample":      "$SAMPLE.IDENTIFIERS.EXTERNAL_ID.value",
+			"ExperimentCode": "$EXPERIMENT.accession",
+			"Run":            "$RUN_SET.RUN.accession",
+			"Abstract":       "$STUDY.DESCRIPTOR.STUDY_ABSTRACT.value",
+		},
+	}}
+	dataSeq, errM := db.sequences_data.Aggregate(context.TODO(), mongo.Pipeline{filter, proj})
+	if errM != nil {
+		return nil, errorM.NewError(errM.Error(), errorM.StatusInternalServerError)
+	}
+	var seq_data []map[string]interface{}
+	for dataSeq.Next(context.TODO()) {
+		var seq map[string]interface{}
+		err := dataSeq.Decode(&seq)
+		if err != nil {
+			return nil, errorM.NewError("Can't Decode Result", errorM.StatusInternalServerError)
+		}
+		seq_data = append(seq_data, seq)
+	}
+	return seq_data, nil
+}

service/database/database.go

@@ -24,6 +24,7 @@ type AppDatabase interface {
 	FindProteinsId(taxonId string) (str.TableBasic, errorM.Errors)
 	FindProteinTableByLocus(taxId string, locus string) (str.TableComplete, errorM.Errors)
 	FindProteinByLocus(locus string) (str.Protein, errorM.Errors)
+	FindAnalysis() ([]map[string]interface{}, errorM.Errors)
 }
 
 type appDB struct {
@@ -34,7 +35,7 @@ type appDB struct {
 	table_complete  *mongo.Collection
 	taxonomy_data   *mongo.Collection
 	taxonomy_tree   *mongo.Collection
-	markdown        *mongo.Collection
+	sequences_data  *mongo.Collection
 }
 
 func InitDatabase(client *mongo.Client) (AppDatabase, error) {
@@ -62,8 +63,8 @@ func InitDatabase(client *mongo.Client) (AppDatabase, error) {
 	if collectionTaxonomyTree == nil {
 		return nil, errors.New("error Creating users Collection")
 	}
-	collectionMarkDown := client.Database("Biologia").Collection("markdown")
-	if collectionMarkDown == nil {
+	collectionSequences := client.Database("Biologia").Collection("sequences_data")
+	if collectionSequences == nil {
 		return nil, errors.New("error Creating users Collection")
 	}
 	return &appDB{
@@ -74,6 +75,6 @@ func InitDatabase(client *mongo.Client) (AppDatabase, error) {
 		table_complete:  collectionTableComplete,
 		taxonomy_data:   collectionTaxonomy,
 		taxonomy_tree:   collectionTaxonomyTree,
-		markdown:        collectionMarkDown,
+		sequences_data:  collectionSequences,
 	}, nil
 }

service/structures/structures.go

@@ -124,3 +124,24 @@ type TableComplete struct {
 		CountryName string `bson:"CountryName"`
 	} `bson:"Country"`
 }
+
+type Genome struct {
+	TaxId          string
+	ScientificName string
+	BioProjects    []SraBioProject
+}
+
+type SraBioProject struct {
+	ScientificName string
+	TaxId          string
+	BioProjectId   string
+	Comment        string
+	ImagesPath     []string
+	BioSamples     []struct {
+		BioSampleId string
+		Experiments []struct {
+			ExperimentId string
+			Runs         []string
+		}
+	}
+}