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transmute.go
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transmute.go
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package query
import (
"errors"
"github.com/hscells/cqr"
gpipeline "github.com/hscells/groove/pipeline"
"github.com/hscells/transmute/backend"
"github.com/hscells/transmute/lexer"
"github.com/hscells/transmute/parser"
tpipeline "github.com/hscells/transmute/pipeline"
"io/ioutil"
"log"
"path"
)
var (
// MedlineTransmutePipeline is a default pipeline for Medline queries.
MedlineTransmutePipeline = tpipeline.NewPipeline(
parser.NewMedlineParser(),
backend.NewCQRBackend(),
tpipeline.TransmutePipelineOptions{
LexOptions: lexer.LexOptions{
FormatParenthesis: false,
},
AddRedundantParenthesis: true,
RequiresLexing: true,
})
// PubMedTransmutePipeline is a default pipeline for PubMed queries.
PubMedTransmutePipeline = tpipeline.NewPipeline(
parser.NewPubMedParser(),
backend.NewCQRBackend(),
tpipeline.TransmutePipelineOptions{
LexOptions: lexer.LexOptions{
FormatParenthesis: true,
},
AddRedundantParenthesis: true,
RequiresLexing: false,
})
// PubMedTransmutePipeline is a default pipeline for cqr queries.
CQRTransmutePipeline = tpipeline.NewPipeline(
parser.NewCQRParser(),
backend.NewCQRBackend(),
tpipeline.TransmutePipelineOptions{
LexOptions: lexer.LexOptions{
FormatParenthesis: false,
},
RequiresLexing: false,
})
)
// TransmuteQuerySource is a source for queries.
type TransmuteQuerySource struct {
pipeline tpipeline.TransmutePipeline
queries []gpipeline.Query
}
func (ts TransmuteQuerySource) LoadSingle(file string) (gpipeline.Query, error) {
dir, topic := path.Split(file)
if len(dir) == 0 {
return gpipeline.Query{}, errors.New("query topic cannot be inferred from pathname")
}
source, err := ioutil.ReadFile(file)
if err != nil {
return gpipeline.Query{}, err
}
bq, err := ts.pipeline.Execute(string(source))
if err != nil {
log.Printf("transmute error in topic %s\n", topic)
return gpipeline.Query{}, err
}
repr, err := bq.Representation()
if err != nil {
return gpipeline.Query{}, err
}
return gpipeline.NewQuery(topic, topic, repr.(cqr.CommonQueryRepresentation)), nil
}
// Load takes a directory of queries and parses them using a supplied transmute gpipeline.
func (ts TransmuteQuerySource) Load(directory string) ([]gpipeline.Query, error) {
// First, get a list of files in the directory.
files, err := ioutil.ReadDir(directory)
if err != nil {
return nil, err
}
// Next, use the transmute gpipeline to parse them.
queries := make([]gpipeline.Query, len(files))
for i, f := range files {
if f.IsDir() {
continue
}
if len(f.Name()) == 0 {
continue
}
queries[i], err = ts.LoadSingle(path.Join(directory, f.Name()))
if err != nil {
return nil, err
}
}
// Finally, return the parsed queries.
return queries, nil
}
// NewTransmuteQuerySource creates a new query source from a transmute gpipeline.
func NewTransmuteQuerySource(transmutePipeline tpipeline.TransmutePipeline) TransmuteQuerySource {
return TransmuteQuerySource{
pipeline: transmutePipeline,
}
}