add pdf2plain ctl

go.mod

@@ -6,4 +6,5 @@ require (
 	github.com/openbiox/ligo v0.0.0-20200119135627-2571ec0d416e
 	github.com/sirupsen/logrus v1.4.2
 	github.com/spf13/cobra v0.0.5
+	github.com/stretchr/testify v1.4.0 // indirect
 )

pdf2plain/README.md

@@ -0,0 +1,45 @@
+## pdf2plain
+
+Can be used to convert pdf to plain text for downstream process of bioextr. 
+
+
+## Installation
+
+Xpdf command line tools (required):
+
+- Linux 32/64-bit: [download](https://xpdfreader-dl.s3.amazonaws.com/xpdf-tools-linux-4.02.tar.gz) ([GPG signature](https://xpdfreader-dl.s3.amazonaws.com/xpdf-tools-linux-4.02.tar.gz.sig))
+- Windows 32/64-bit: [download](https://xpdfreader-dl.s3.amazonaws.com/xpdf-tools-win-4.02.zip) ([GPG signature](https://xpdfreader-dl.s3.amazonaws.com/xpdf-tools-win-4.02.zip.sig))
+- Mac 64-bit: [download](https://xpdfreader-dl.s3.amazonaws.com/xpdf-tools-mac-4.02.tar.gz) ([GPG signature](https://xpdfreader-dl.s3.amazonaws.com/xpdf-tools-mac-4.02.tar.gz.sig))
+
+```bash
+# windows
+wget https://github.com/openbiox/bioextr/releases/download/v0.1.0/pdf2plain.exe
+
+# osx
+wget https://github.com/openbiox/bioextr/releases/download/v0.1.0/pdf2plain_osx
+mv pdf2plain_osx pdf2plain
+chmod a+x pdf2plain
+
+# linux
+wget https://github.com/openbiox/bioextr/releases/download/v0.1.0/pdf2plain_linux64
+mv pdf2plain_linux64 pdf2plain
+chmod a+x pdf2plain
+
+# get latest version
+go get -u github.com/openbiox/bioextr/pdf2plain
+```
+
+## Usage
+
+```
+pdf2plain _examples/Multi-omic_approaches_to_improve_outcome_for_T-cel.pdf -o out.text
+```
+
+## Maintainer
+
+- [@Jianfeng](https://github.com/Miachol)
+
+## License
+
+Academic Free License version 3.0
+

pdf2plain/cmd/root.go

@@ -0,0 +1,85 @@
+package cmd
+
+import (
+	"fmt"
+	"os"
+
+	"code.sajari.com/docconv"
+	"github.com/openbiox/ligo/io"
+	"github.com/spf13/cobra"
+)
+
+// RootClisT is the bioctl global flags
+type RootClisT struct {
+	// version of bioctl
+	Version string
+	Verbose int
+	SaveLog bool
+	TaskID  string
+	LogDir  string
+	Clean   bool
+	Out     string
+
+	HelpFlags bool
+}
+
+var RootClis = RootClisT{
+	Version:   version,
+	Verbose:   1,
+	HelpFlags: true,
+}
+
+var RootCmd = &cobra.Command{
+	Use:   "pdf2plain [input.pdf]",
+	Short: "A wrapper command line tool to convert pdf files to plain text.",
+	Long:  `A wrapper command line tool to convert pdf files to plain text. More see here https://github.com/openbiox/bioextr.`,
+	Run: func(cmd *cobra.Command, args []string) {
+		if RootClis.Clean {
+			RootClis.HelpFlags = false
+		}
+		if len(args) > 0 {
+			initCmd(cmd, args)
+			convertor(cmd, args)
+			RootClis.HelpFlags = false
+		}
+		if RootClis.HelpFlags {
+			cmd.Help()
+		}
+	},
+}
+
+func convertor(cmd *cobra.Command, args []string) {
+	res, err := docconv.ConvertPath(args[0])
+	if err != nil {
+		log.Fatal(err)
+	}
+	if RootClis.Out != "" {
+		if err := io.CreateFileParDir(RootClis.Out); err != nil {
+			log.Warnln(err)
+			return
+		}
+		con, _ := io.Open(RootClis.Out)
+		fmt.Fprintf(con, res.Body)
+		return
+	}
+	fmt.Println(res.Body)
+}
+
+// Execute main interface of bget
+func Execute() {
+	if err := RootCmd.Execute(); err != nil {
+		if !RootCmd.HasFlags() && !RootCmd.HasSubCommands() {
+			RootCmd.Help()
+		} else {
+			fmt.Println(err)
+			os.Exit(1)
+		}
+	}
+}
+
+func init() {
+	wd, _ = os.Getwd()
+	RootCmd.Version = version
+	setGlobalFlag(RootCmd)
+	RootCmd.Example = `  pdf2plain _examples/Multi-omic_approaches_to_improve_outcome_for_T-cel.pdf`
+}

pdf2plain/cmd/utils.go

@@ -0,0 +1,73 @@
+package cmd
+
+import (
+	"fmt"
+	"io"
+	"os"
+	"path"
+	"path/filepath"
+	"strings"
+
+	cvrt "github.com/openbiox/ligo/convert"
+	cio "github.com/openbiox/ligo/io"
+	clog "github.com/openbiox/ligo/log"
+	"github.com/openbiox/ligo/stringo"
+	"github.com/sirupsen/logrus"
+	"github.com/spf13/cobra"
+)
+
+var log = clog.Logger
+var logBash = clog.LoggerBash
+var logEnv = log.WithFields(logrus.Fields{
+	"prefix": "Env"})
+var logPrefix string
+var wd string
+
+func setGlobalFlag(cmd *cobra.Command) {
+	wd, _ = os.Getwd()
+	cmd.PersistentFlags().IntVarP(&(RootClis.Verbose), "verbose", "", 1, "verbose level(0:no output, 1: basic level, 2: with env info")
+	cmd.PersistentFlags().StringVarP(&(RootClis.TaskID), "task-id", "k", stringo.RandString(15), "task ID (default is random).")
+	cmd.PersistentFlags().StringVarP(&(RootClis.LogDir), "log-dir", "", path.Join(wd, "_log"), "log dir.")
+	cmd.PersistentFlags().BoolVarP(&(RootClis.SaveLog), "save-log", "s", false, "save log to file.")
+	cmd.PersistentFlags().BoolVarP(&(RootClis.Clean), "clean", "", false, "remove log dir.")
+	cmd.PersistentFlags().StringVarP(&RootClis.Out, "out", "o", "", "out specifies destination of the returned data (default to stdout or current woring directory).")
+}
+func initCmd(cmd *cobra.Command, args []string) {
+	setLog()
+	if RootClis.Verbose == 2 {
+		logEnv.Infof("Prog: %s", cmd.CommandPath())
+		logEnv.Infof("TaskID: %s", RootClis.TaskID)
+		if RootClis.SaveLog && logPrefix != "" {
+			logEnv.Infof("Log: %s.log", logPrefix)
+		}
+		if len(args) > 0 {
+			logEnv.Infof("Args: %s", strings.Join(args, " "))
+		}
+		logEnv.Infof("Global: %v", cvrt.Struct2Map(RootClis))
+	}
+	if RootClis.Clean {
+		cleanLog()
+	}
+}
+
+func setLog() {
+	var logCon io.Writer
+	var logDir = RootClis.LogDir
+
+	if RootClis.SaveLog {
+		if logDir == "" {
+			logDir = filepath.Join(os.TempDir(), "_log")
+		}
+		logPrefix = fmt.Sprintf("%s/%s", logDir, RootClis.TaskID)
+		cio.CreateDir(logDir)
+		logCon, _ = cio.Open(logPrefix + ".log")
+	}
+	clog.SetLogStream(log, RootClis.Verbose == 0, RootClis.SaveLog, &logCon)
+}
+
+func cleanLog() {
+	RootClis.HelpFlags = false
+	if err := os.RemoveAll(RootClis.LogDir); err != nil {
+		log.Warn(err)
+	}
+}

pdf2plain/cmd/version.go

@@ -0,0 +1,3 @@
+package cmd
+
+var version = "v0.1.0"

pdf2plain/go.mod

@@ -0,0 +1,13 @@
+module github.com/openbiox/bioextr/pdf2plain
+
+go 1.14
+
+require (
+	code.sajari.com/docconv v1.1.0
+	github.com/JalfResi/justext v0.0.0-20170829062021-c0282dea7198 // indirect
+	github.com/advancedlogic/GoOse v0.0.0-20191112112754-e742535969c1 // indirect
+	github.com/levigross/exp-html v0.0.0-20120902181939-8df60c69a8f5 // indirect
+	github.com/openbiox/ligo v0.0.0-20200324043626-a1096f60db64
+	github.com/sirupsen/logrus v1.5.0
+	github.com/spf13/cobra v0.0.6
+)

pdf2plain/main.go

@@ -0,0 +1,23 @@
+// Copyright © 2019 Jianfeng Li lee_jianfeng@openbiox.org
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package main
+
+import (
+    "github.com/openbiox/bioextr/pdf2plain/cmd"
+)
+
+func main() {
+    cmd.Execute()
+}