feature/documentation

.drsconfig

@@ -0,0 +1,9 @@
+{
+  "queryServer": {
+    "baseURL": "https://calypr.ohsu.edu/ga4gh"
+  },
+  "writeServer": {
+    "baseURL": "https://calypr.ohsu.edu/ga4gh"
+  },
+  "gen3Profile": "<calypr-prod-profile-name-here>"
+}

.gitignore

@@ -0,0 +1,3 @@
+.idea/
+.DS_Store
+/tmp

client/README.md

@@ -0,0 +1,14 @@
+# Git DRS Client
+
+## Getting Started
+
+1. Configure gen3 with your credentials ([docs](https://aced-idp.github.io/requirements/#1-download-gen3-client))
+2. Edit platform URL and gen3 profile in `.drsconfig`
+3. Build from source
+    ```bash
+    go build
+    ```
+4. Access through command line
+   ```bash
+   ./git-drs --help
+   ```

client/config.go

@@ -0,0 +1,59 @@
+package client
+
+import (
+	"io"
+	"log"
+	"os"
+	"path/filepath"
+
+	"github.com/bmeg/git-drs/utils"
+	"sigs.k8s.io/yaml"
+)
+
+type Server struct {
+	BaseURL       string `json:"baseURL"`
+	ExtensionType string `json:"type,omitempty"`
+}
+
+type Config struct {
+	QueryServer Server `json:"queryServer"`
+	WriteServer Server `json:"writeServer"`
+	Gen3Profile string `json:"gen3Profile"`
+}
+
+const (
+	DRS_CONFIG = ".drsconfig"
+)
+
+func LoadConfig() (*Config, error) {
+	//look in Git base dir and find .drsconfig file
+
+	topLevel, err := utils.GitTopLevel()
+
+	if err != nil {
+		return nil, err
+	}
+
+	configPath := filepath.Join(topLevel, DRS_CONFIG)
+
+	log.Printf("Looking for %s", configPath)
+	//check if config exists
+	reader, err := os.Open(configPath)
+	if err != nil {
+		return nil, err
+	}
+
+	b, err := io.ReadAll(reader)
+	if err != nil {
+		return nil, err
+	}
+
+	conf := Config{}
+	err = yaml.Unmarshal(b, &conf)
+	if err != nil {
+		return nil, err
+	}
+
+	log.Printf("Config: %s %#v", string(b), conf)
+	return &conf, nil
+}

client/indexd.go

@@ -0,0 +1,166 @@
+package client
+
+import (
+	"encoding/json"
+	"fmt"
+	"io"
+	"net/http"
+	"net/url"
+	"os"
+	"path/filepath"
+
+	"github.com/bmeg/git-drs/drs"
+	"github.com/uc-cdis/gen3-client/gen3-client/jwt"
+)
+
+var conf jwt.Configure
+var profileConfig jwt.Credential
+
+type IndexDClient struct {
+	base    *url.URL
+	profile string
+}
+
+func NewIndexDClient(base string) (ObjectStoreClient, error) {
+	baseURL, err := url.Parse(base)
+	// print baseURL
+	if err != nil {
+		return nil, err
+	}
+
+	cfg, err := LoadConfig()
+	if err != nil {
+		return nil, err
+	}
+
+	// get the gen3Profile from the config
+	profile := cfg.Gen3Profile
+	if profile == "" {
+		return nil, fmt.Errorf("No gen3 profile specified. Please provide a gen3Profile key in your .drsconfig")
+	}
+
+	fmt.Printf("Base URL: %s\n", baseURL.String())
+	fmt.Printf("Profile: %s\n", profile)
+
+	return &IndexDClient{baseURL, profile}, err
+}
+
+// DownloadFile implements ObjectStoreClient
+func (cl *IndexDClient) DownloadFile(id string, access_id string, dstPath string) (*drs.AccessURL, error) {
+	// get file from indexd
+	a := *cl.base
+	a.Path = filepath.Join(a.Path, "drs/v1/objects", id, "access", access_id)
+	// a.Path = filepath.Join("https://calypr.ohsu.edu/user/data/download/", id)
+
+	// unmarshal response
+	req, err := http.NewRequest("GET", a.String(), nil)
+	if err != nil {
+		return nil, err
+	}
+	// extract accessToken from gen3 profile and insert into header of request
+	profileConfig = conf.ParseConfig(cl.profile)
+	if profileConfig.AccessToken == "" {
+		return nil, fmt.Errorf("access token not found in profile config")
+	}
+
+	// Add headers to the request
+	authStr := "Bearer " + profileConfig.AccessToken
+	req.Header.Set("Authorization", authStr)
+
+	client := &http.Client{}
+	response, err := client.Do(req)
+	if err != nil {
+		return nil, err
+	}
+	defer response.Body.Close()
+
+	body, err := io.ReadAll(response.Body)
+	if err != nil {
+		return nil, err
+	}
+
+	out := drs.AccessURL{}
+	err = json.Unmarshal(body, &out)
+	if err != nil {
+		return nil, err
+	}
+
+	// Extract the signed URL from the response
+	signedURL := out.URL
+	if signedURL == "" {
+		return nil, fmt.Errorf("signed URL not found in response.")
+	}
+
+	// Download the file using the signed URL
+	fileResponse, err := http.Get(signedURL)
+	if err != nil {
+		return nil, err
+	}
+	defer fileResponse.Body.Close()
+
+	// Check if the response status is OK
+	if fileResponse.StatusCode != http.StatusOK {
+		return nil, fmt.Errorf("failed to download file using signed URL: %s", fileResponse.Status)
+	}
+
+	// Create the destination directory if it doesn't exist
+	err = os.MkdirAll(filepath.Dir(dstPath), os.ModePerm)
+	if err != nil {
+		return nil, err
+	}
+
+	// Create the destination file
+	dstFile, err := os.Create(dstPath)
+	if err != nil {
+		return nil, err
+	}
+	defer dstFile.Close()
+
+	// Write the file content to the destination file
+	_, err = io.Copy(dstFile, fileResponse.Body)
+	if err != nil {
+		return nil, err
+	}
+
+	fmt.Printf("File written to %s\n", dstFile.Name())
+
+	return &out, nil
+}
+
+// RegisterFile implements ObjectStoreClient.
+func (cl *IndexDClient) RegisterFile(path string, name string) (*drs.DRSObject, error) {
+	panic("unimplemented")
+}
+
+func (cl *IndexDClient) QueryID(id string) (*drs.DRSObject, error) {
+
+	a := *cl.base
+	a.Path = filepath.Join(a.Path, "drs/v1/objects", id)
+
+	req, err := http.NewRequest("GET", a.String(), nil)
+	if err != nil {
+		return nil, err
+	}
+	// Add headers to the request
+	req.Header.Set("Authorization", "Bearer <your-token>")
+	req.Header.Set("Custom-Header", "HeaderValue")
+
+	client := &http.Client{}
+	response, err := client.Do(req)
+	if err != nil {
+		return nil, err
+	}
+	defer response.Body.Close()
+
+	body, err := io.ReadAll(response.Body)
+	if err != nil {
+		return nil, err
+	}
+
+	out := drs.DRSObject{}
+	err = json.Unmarshal(body, &out)
+	if err != nil {
+		return nil, err
+	}
+	return &out, nil
+}

client/interface.go

@@ -0,0 +1,14 @@
+package client
+
+import "github.com/bmeg/git-drs/drs"
+
+type ObjectStoreClient interface {
+	//Given a DRS string ID, retrieve the object describing it
+	QueryID(id string) (*drs.DRSObject, error)
+
+	//Put file into object storage and obtain a DRS record pointing to it
+	RegisterFile(path string, name string) (*drs.DRSObject, error)
+
+	//Download file given a DRS ID
+	DownloadFile(id string, access_id string, dstPath string) (*drs.AccessURL, error)
+}

cmd/add/main.go

@@ -0,0 +1,27 @@
+package add
+
+import (
+	"fmt"
+	"path/filepath"
+
+	"github.com/spf13/cobra"
+)
+
+// Cmd line declaration
+var Cmd = &cobra.Command{
+	Use:   "add",
+	Short: "Add a file",
+	Long:  ``,
+	Args:  cobra.MinimumNArgs(0),
+	RunE: func(cmd *cobra.Command, args []string) error {
+		for _, fileArg := range args {
+			matches, err := filepath.Glob(fileArg)
+			if err == nil {
+				for _, f := range matches {
+					fmt.Printf("Adding %s\n", f)
+				}
+			}
+		}
+		return nil
+	},
+}

cmd/download/main.go

@@ -0,0 +1,57 @@
+package download
+
+import (
+	"github.com/bmeg/git-drs/client"
+	"github.com/bmeg/git-drs/drs"
+	"github.com/spf13/cobra"
+)
+
+var (
+	server  string
+	dstPath string
+	drsObj  *drs.DRSObject
+)
+
+// Cmd line declaration
+// Cmd line declaration
+var Cmd = &cobra.Command{
+	Use:   "download <drsId> <accessId>",
+	Short: "Download file using DRS ID and access ID",
+	Long:  "Download file using DRS ID and access ID. The access ID is the access method used to download the file.",
+	Args:  cobra.ExactArgs(2),
+	RunE: func(cmd *cobra.Command, args []string) error {
+		drsId := args[0]
+		accessId := args[1]
+		cfg, err := client.LoadConfig()
+		if err != nil {
+			return err
+		}
+
+		baseURL := cfg.QueryServer.BaseURL
+
+		client, err := client.NewIndexDClient(baseURL)
+		if err != nil {
+			return err
+		}
+
+		if dstPath == "" {
+
+			drsObj, err = client.QueryID(drsId)
+			if err != nil {
+				return err
+			}
+			dstPath = drsObj.Name
+		}
+
+		_, err = client.DownloadFile(drsId, accessId, dstPath)
+		if err != nil {
+			return err
+		}
+
+		return nil
+	},
+}
+
+func init() {
+	Cmd.Flags().StringVarP(&dstPath, "dstPath", "d", "", "Optional destination file path")
+}