Add cell lines count per tissue

rename tests -> test
update readme
add temp drugs count function with endpoint handler (to be updated in next commit

Author: assefamaru

README.md

@@ -12,8 +12,8 @@ Application currently has two main components: [`api`](./api) and [`web-applicat
 ## Table of Contents
 
 - [**API**](#api)
-  - [Endpoints](#endpoints)
-  - [Running the API Locally](#running-the-api-locally)
+  - [**Endpoints**](#endpoints)
+  - [**Running the API Locally**](#running-the-api-locally)
 - [**Web Application**](#web-application)
 - [**Contributing**](#contributing)
 - [**License**](#license)

api/handlers.go

@@ -648,3 +648,27 @@ func CellDatasetIntersection(c *gin.Context) {
 	}
 	RenderJSON(c, indent, experiments)
 }
+
+// TissueCellStats is a handler for '/stats/cell_tissues' endpoint.
+// Lists all tissues, along with the number of cell lines in each tissue.
+func TissueCellStats(c *gin.Context) {
+	indent, _ := strconv.ParseBool(c.DefaultQuery("indent", "true"))
+	data, err := CountCellsPerTissue()
+	if err != nil {
+		LogInternalServerError(c)
+		return
+	}
+	RenderJSON(c, indent, data)
+}
+
+// DatasetDrugStats is a handler for '/stats/dataset_drugs' endpoint.
+// Lists all datasets, along with the number of drugs tested in each dataset.
+func DatasetDrugStats(c *gin.Context) {
+	indent, _ := strconv.ParseBool(c.DefaultQuery("indent", "true"))
+	data, err := CountDrugsPerDataset()
+	if err != nil {
+		LogInternalServerError(c)
+		return
+	}
+	RenderJSON(c, indent, data)
+}

api/routes.go

@@ -50,4 +50,7 @@ var routes = Routes{
 	Route{GET, "/intersections", IndexIntersection},
 	Route{GET, "/intersections/1/:cell_id/:drug_id", CellDrugIntersection},
 	Route{GET, "/intersections/2/:cell_id/:dataset_id", CellDatasetIntersection},
+
+	Route{GET, "/stats/tissue_cells", TissueCellStats},
+	Route{GET, "/stats/dataset_drugs", DatasetDrugStats},
 }

api/server.go

@@ -21,7 +21,7 @@ func Init(c *Context) {
 
 	router.StaticFile("/favicon.ico", "./static/images/favicon.png")
 
-	v := router.Group(Version())
+	v := router.Group(Version() + "/")
 	for _, route := range routes {
 		v.Handle(route.Method, route.Endpoint, route.Handler)
 	}

api/stats.go

@@ -0,0 +1,97 @@
+package api
+
+import "strconv"
+
+// TissueCellCount models the number of cell lines per tissue.
+type TissueCellCount struct {
+	Tissue Tissue `json:"tissue"`
+	Count  int    `json:"cell_lines_count"`
+}
+
+// TissueCellCounts is a collection of TissueCellsCount.
+type TissueCellCounts []TissueCellCount
+
+// DatasetDrugCount models the number of drugs tested per dataset.
+type DatasetDrugCount struct {
+	Dataset Dataset `json:"dataset"`
+	Count   int     `json:"drugs_count"`
+}
+
+// DatasetDrugCounts is a collection of DatasetDrugCount.
+type DatasetDrugCounts []DatasetDrugCount
+
+// CountCellsPerTissue returns a list of all tissues, along with the number of
+// cell lines of each tissue type.
+func CountCellsPerTissue() (TissueCellCounts, error) {
+	var (
+		tissueCellCount  TissueCellCount
+		tissueCellCounts TissueCellCounts
+	)
+	db, err := InitDB()
+	defer db.Close()
+	if err != nil {
+		return tissueCellCounts, err
+	}
+	query := "SELECT t.tissue_id, t.tissue_name, COUNT(*) AS cell_lines_count FROM tissues t JOIN cells c ON c.tissue_id = t.tissue_id GROUP BY(c.tissue_id);"
+	rows, err := db.Query(query)
+	defer rows.Close()
+	if err != nil {
+		LogPrivateError(err)
+		return tissueCellCounts, err
+	}
+	for rows.Next() {
+		err = rows.Scan(&tissueCellCount.Tissue.ID, &tissueCellCount.Tissue.Name, &tissueCellCount.Count)
+		if err != nil {
+			LogPrivateError(err)
+			return tissueCellCounts, err
+		}
+		tissueCellCounts = append(tissueCellCounts, tissueCellCount)
+	}
+	return tissueCellCounts, nil
+}
+
+// CountDrugsPerDataset returns a list of all datasets, along with the number of
+// drugs tested in each dataset.
+func CountDrugsPerDataset() (DatasetDrugCounts, error) {
+	type DDD struct {
+		ID    int
+		Count int
+	}
+	var (
+		datasetDrugCount  DatasetDrugCount
+		datasetDrugCounts DatasetDrugCounts
+		DD                DDD
+		DDs               []DDD
+	)
+	db, err := InitDB()
+	defer db.Close()
+	if err != nil {
+		return datasetDrugCounts, err
+	}
+	query := "SELECT dataset_id, COUNT(DISTINCT drug_id) AS drugs_count FROM experiments GROUP BY dataset_id;"
+	rows, err := db.Query(query)
+	defer rows.Close()
+	if err != nil {
+		LogPrivateError(err)
+		return datasetDrugCounts, err
+	}
+	for rows.Next() {
+		err = rows.Scan(&DD.ID, &DD.Count)
+		if err != nil {
+			LogPrivateError(err)
+			return datasetDrugCounts, err
+		}
+		DDs = append(DDs, DD)
+	}
+	for _, a := range DDs {
+		var dataset Dataset
+		err = dataset.Find(strconv.Itoa(a.ID), "id")
+		if err != nil {
+			return datasetDrugCounts, err
+		}
+		datasetDrugCount.Dataset = dataset
+		datasetDrugCount.Count = a.Count
+		datasetDrugCounts = append(datasetDrugCounts, datasetDrugCount)
+	}
+	return datasetDrugCounts, nil
+}