Initial Commit with 4.2 Version of Drug Bank Data

drugs.go

@@ -0,0 +1,92 @@
+package drugs
+
+import (
+	"encoding/json"
+	"github.com/sahilm/fuzzy"
+	"io/ioutil"
+	"strings"
+)
+
+type DrugInteraction struct {
+	ID string
+}
+
+type PathWay struct {
+	ID string
+	Drugs []string
+}
+
+type Salt struct {
+	ID string
+	Name string
+}
+
+type DrugDatabase struct {
+	drugs []DrugInfo
+	index map[string]int
+	keys []string
+}
+
+type Classification struct {
+	Description string
+	DirectParent string
+	Kingdom string
+	SuperClass string
+	Class string
+	SubClass string
+}
+
+type DrugInfo struct {
+	ID             string
+	Name           string
+	DrugType       string
+	HalfLife       string
+	Description    string
+	Classification Classification
+	Indication string
+	Toxicity string
+	MechanismOfAction string
+	Pharmacodynamics string
+	Absorption string
+	Interactions   []DrugInteraction
+	Salts          []Salt
+	Groups         map[string]bool
+	Pathways       []PathWay
+}
+
+func (dd * DrugDatabase) generateIndex() {
+	dd.index = make(map[string]int)
+	for i,drug := range dd.drugs {
+		dd.index[strings.ToLower(drug.ID)] = i
+		dd.index[strings.ToLower(drug.Name)] = i
+		dd.keys = append(dd.keys, strings.ToLower(drug.ID))
+		dd.keys = append(dd.keys, strings.ToLower(drug.Name))
+	}
+}
+
+func (dd * DrugDatabase) Lookup(query string) (DrugInfo) {
+	index,ok := dd.index[strings.ToLower(query)]
+	if ok {
+		return dd.drugs[index]
+	}
+	matches := fuzzy.Find(query, dd.keys)
+	for _,match := range matches {
+		return dd.drugs[dd.index[match.Str]]
+	}
+	return DrugInfo{}
+}
+
+func LoadDatabaseJSON(path string) DrugDatabase {
+	data,err := ioutil.ReadFile(path)
+	if err == nil {
+		var db []DrugInfo
+		err := json.Unmarshal(data, &db)
+		if err == nil {
+			var ddb DrugDatabase
+			ddb.drugs = db
+			ddb.generateIndex()
+			return ddb
+		}
+	}
+	return DrugDatabase{}
+}

drugs_test.go

@@ -0,0 +1,20 @@
+package drugs
+
+import (
+	"testing"
+)
+
+func TestQueryDatabase(t *testing.T) {
+	drugsdb := LoadDatabase("./drugbank.xml")
+	t.Logf("Query by ID: %v", drugsdb.QueryDatabaseByID("DB00083"))
+	t.Logf("Query by ID: %v", drugsdb.QueryDatabaseByName("Ibuprofen"))
+	for i := 50; i < 60; i++ {
+		t.Logf("Query by Name: %v", drugsdb.QueryDatabaseByIndex(i))
+	}
+}
+
+func TestQueryJson(t *testing.T) {
+	ddb := LoadDatabaseJSON("./drugs.4.2.db")
+	t.Logf("Query by ID: %v", ddb.Lookup("DB00083"))
+	t.Logf("Query by ID: %v", ddb.Lookup("ibupren"))
+}

go.mod

@@ -0,0 +1,10 @@
+module git.openprivacy.ca/sarah/sigil/cmd/sigilbot/drugs
+
+go 1.12
+
+require (
+	github.com/antchfx/xmlquery v1.1.0
+	github.com/antchfx/xpath v1.1.0 // indirect
+	github.com/sahilm/fuzzy v0.1.0
+	golang.org/x/net v0.0.0-20191027233614-53de4c7853b5 // indirect
+)

go.sum

@@ -0,0 +1,12 @@
+github.com/antchfx/xmlquery v1.1.0 h1:vj0kZ1y3Q6my4AV+a9xbWrMYzubw+84zuiKgvfV8vb8=
+github.com/antchfx/xmlquery v1.1.0/go.mod h1:/+CnyD/DzHRnv2eRxrVbieRU/FIF6N0C+7oTtyUtCKk=
+github.com/antchfx/xpath v1.1.0 h1:mJTvYpiHvxNQRD4Lbfin/FodHVCHh2a5KrOFr4ZxMOI=
+github.com/antchfx/xpath v1.1.0/go.mod h1:Yee4kTMuNiPYJ7nSNorELQMr1J33uOpXDMByNYhvtNk=
+github.com/sahilm/fuzzy v0.1.0 h1:FzWGaw2Opqyu+794ZQ9SYifWv2EIXpwP4q8dY1kDAwI=
+github.com/sahilm/fuzzy v0.1.0/go.mod h1:VFvziUEIMCrT6A6tw2RFIXPXXmzXbOsSHF0DOI8ZK9Y=
+golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
+golang.org/x/net v0.0.0-20191027233614-53de4c7853b5 h1:IX2aat8xHKk1JAYuDPcTTEMfRaGQh2eHrTcrlp3KJi0=
+golang.org/x/net v0.0.0-20191027233614-53de4c7853b5/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
+golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
+golang.org/x/text v0.3.0 h1:g61tztE5qeGQ89tm6NTjjM9VPIm088od1l6aSorWRWg=
+golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=

xmldrugdatabase.go

@@ -0,0 +1,96 @@
+package drugs
+
+import (
+	"github.com/antchfx/xmlquery"
+	"os"
+	"strconv"
+)
+
+
+func LoadDatabase(path string) XMLDrugsDatabase {
+	f, err := os.Open(path)
+	if err == nil {
+		doc, err := xmlquery.Parse(f)
+		if err == nil {
+			return XMLDrugsDatabase{doc}
+		}
+	}
+	return XMLDrugsDatabase{}
+}
+
+
+func populate_druginfo(node *xmlquery.Node) (di DrugInfo) {
+	di.ID = node.SelectElement("drugbank-id").InnerText()
+	di.Name = node.SelectElement("name").InnerText()
+	di.HalfLife = node.SelectElement("half-life").InnerText()
+	di.Description = node.SelectElement("description").InnerText()
+	di.Indication = node.SelectElement("indication").InnerText()
+	di.Pharmacodynamics = node.SelectElement("pharmacodynamics").InnerText()
+	di.Toxicity = node.SelectElement("toxicity").InnerText()
+	di.Absorption = node.SelectElement("absorption").InnerText()
+	di.MechanismOfAction = node.SelectElement("mechanism-of-action").InnerText()
+
+	interactions := node.SelectElement("drug-interactions").SelectElements("drug-interaction")
+	for _, interaction := range interactions {
+		di.Interactions = append(di.Interactions, DrugInteraction{interaction.SelectElement("drugbank-id").InnerText()})
+	}
+
+	di.DrugType = node.SelectAttr("type")
+
+	classification := node.SelectElement("classification")
+	if classification != nil {
+		di.Classification = Classification{
+			classification.SelectElement("description").InnerText(),
+			classification.SelectElement("direct-parent").InnerText(),
+			classification.SelectElement("kingdom").InnerText(),
+			classification.SelectElement("superclass").InnerText(),
+			classification.SelectElement("class").InnerText(),
+			classification.SelectElement("subclass").InnerText()}
+	}
+	groups := node.SelectElement("groups").SelectElements("group")
+	di.Groups = make(map[string]bool)
+	for _, group := range groups {
+		di.Groups[group.InnerText()] = true
+	}
+
+	salts := node.SelectElement("salts").SelectElements("salt")
+	for _, salt := range salts {
+		di.Salts = append(di.Salts, Salt{salt.SelectElement("drugbank-id").InnerText(),
+											  salt.SelectElement("name").InnerText()})
+	}
+
+	pathways := node.SelectElement("pathways").SelectElements("pathway")
+	for _, pathway := range pathways {
+		pathwaysdrugs := []string{}
+		drugs := pathway.SelectElement("drugs").SelectElements("drug")
+		for _,drug := range drugs {
+			pathwaysdrugs = append(pathwaysdrugs, drug.SelectElement("drugbank-id").InnerText())
+		}
+		di.Pathways = append(di.Pathways, PathWay{pathway.SelectElement("smpdb-id").InnerText(), pathwaysdrugs})
+	}
+
+	return
+}
+
+
+type XMLDrugsDatabase struct {
+	root *xmlquery.Node
+}
+
+func (dd XMLDrugsDatabase) QueryDatabaseByID(ID string) (di DrugInfo) {
+	result := xmlquery.FindOne(dd.root, "//drugbank/drug[./drugbank-id='"+ID+"']")
+	return populate_druginfo(result)
+}
+
+func (dd XMLDrugsDatabase) QueryDatabaseByIndex(index int) (di DrugInfo) {
+	result := xmlquery.FindOne(dd.root, "//drugbank/drug["+strconv.Itoa(index)+"]")
+	return populate_druginfo(result)
+}
+
+func (dd XMLDrugsDatabase) QueryDatabaseByName(name string) (di DrugInfo) {
+	result := xmlquery.Find(dd.root, "//drugbank/drug[./name='"+name+"']")
+	if len(result) < 1 {
+		return
+	}
+	return populate_druginfo(result[0])
+}