dictyBase/modware-annotation

package arangodb

import (
    "fmt"
    "io"

    "github.com/dictyBase/go-obograph/storage"
    ontoarango "github.com/dictyBase/go-obograph/storage/arangodb"
)

func (ar *arangorepository) LoadOboJSON(rde io.Reader) (*storage.UploadInformation, error) {
    dsb, err := ontoarango.NewDataSourceFromDb(ar.database, &ontoarango.CollectionParams{
        OboGraph:     ar.onto.Obog.Name(),
        GraphInfo:    ar.onto.Cv.Name(),
        Relationship: ar.onto.Rel.Name(),
        Term:         ar.onto.Term.Name(),
    })
    if err != nil {
        return &storage.UploadInformation{}, fmt.Errorf("error in creating new data source %s", err)
    }

    info, err := storage.LoadOboJSONFromDataSource(rde, dsb)
    if err != nil {
        return &storage.UploadInformation{}, fmt.Errorf("error in uploading JSON %s", err)
    }

    return info, nil
}

func (ar *arangorepository) termID(onto, term string) (string, error) {
    var tid string
    row, err := ar.database.GetRow(annExistTagQ, map[string]interface{}{
        "@cv_collection":     ar.onto.Cv.Name(),
        "@cvterm_collection": ar.onto.Term.Name(),
        "ontology":           onto,
        "tag":                term,
    })
    if err != nil {
        return tid, fmt.Errorf("error in running obograph retrieving query %s", err)
    }
    if row.IsEmpty() {
        return tid, fmt.Errorf("ontology %s and tag %s does not exist", onto, term)
    }
    if err := row.Read(&tid); err != nil {
        return tid, fmt.Errorf("error in retrieving obograph id %s", err)
    }

    return tid, nil
}

func (ar *arangorepository) termName(tid string) (string, error) {
    var name string
    cvtr, err := ar.database.GetRow(cvtID2LblQ, map[string]interface{}{
        "@cvterm_collection": ar.onto.Term.Name(),
        "id":                 tid,
    })
    if err != nil {
        return name,
            fmt.Errorf("error in running tag retrieving query %s", err)
    }
    if cvtr.IsEmpty() {
        return name, fmt.Errorf("cvterm id %s does not exist", tid)
    }
    if err := cvtr.Read(&name); err != nil {
        return name, fmt.Errorf("error in retrieving tag %s", err)
    }

    return name, nil
}