Feature/mirror g3t

README.md

@@ -1,47 +1,80 @@
-# Meta
+# Forge
 
-Metadata handling for CALPYR data platform
+FHIR metadata management for CALYPR Gen3 data repositories.
 
-## Workflow -- General Design Paramters
+Forge works alongside [git-drs](https://github.com/calypr/git-drs/blob/main/README.md) to generate and publish FHIR-compliant metadata, making your datasets discoverable on the CALYPR platform.
 
-This repo is designed to produce git hook commands that take care of metadata additions / subtractions that are run before or after certain git commands like commit and push. Draft workflow currently:
+## Quick Start
 
-## Example user workflow
+```bash
+# Verify your connection to CALYPR
+forge ping
 
-```
-git clone repo
-forge init -- exactly same as git-dirs init, just a wrapper around it
-git add files
-git commit -m "test" -- same as git-drs
-git push origin main -- same as git-dirs
-forge publish [github personal access token]
+# Publish metadata to CALYPR
+forge publish ghp_your_github_token
+
+# Monitor the job
+forge list
+forge status <job-uid>
 ```
 
-To generate a personal access token for a github repo check these docs:
-https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens
+## What Forge Does
 
-## Command descriptions
+**1. Manage Project Metadata**
+- `forge publish` - Generate and upload metadata to CALYPR
+- `forge empty` - Remove project metadata
+- `forge meta` - Preview metadata locally
+- `forge validate` - Check metadata validity
 
-### ping
+**2. Monitor Platform State**
+- `forge ping` - Check connection and credentials
+- `forge list` - View all processing jobs
+- `forge status` - Check specific job status
+- `forge output` - View job logs
 
-Same as ping in g3t
+**3. Configure Portal Frontend**
+- `forge config` - Generate a CALYPR explorer template
 
-### meta
+## Installation
+
+```bash
+git clone https://github.com/calypr/forge.git
+cd forge
+go build -o forge
+sudo mv forge /usr/local/bin/
+```
 
-Generates metadata from non checked in .meta files. If .meta files are already checked in you can regen metadata with -r flag. This command is run as part of the pre-commit command
+## Prerequisites
 
-### validate
+- Git DRS installed and configured
+- Data files pushed to CALYPR via git-drs
+- Gen3 credentials (configured through git-drs)
+- GitHub Personal Access Token ([create token](https://github.com/settings/tokens))
 
-Validates metadata against the jsonschema in grip
+## Documentation
 
-### precommit
+- [Getting Started](docs/getting-started.md) - Setup and basic workflows
+- [Command Reference](docs/commands.md) - Detailed command documentation
+- [Configuration Guide](docs/configuration.md) - Git-drs configuration
+- [Metadata Structure](docs/metadata.md) - Understanding FHIR resources
 
-Runs meta init command then locates all .ndjson files in META directory and validates each file.
+## Example Workflow
 
-### publish
+```bash
+# Use git-drs to track and push files
+git lfs track "*.fastq.gz"
+git add data/sample.fastq.gz
+git commit -m "Add sequencing data"
+git push
+
+# Publish metadata to CALYPR
+forge publish ghp_abc123def456
+
+# Monitor the job
+forge list
+# Uid: job-xyz789   Name: fhir_import_export   Status: Succeeded
+```
 
-Validates that your Personal Access token exists and is valid
-Packages together relevent information used to init the git repo in a remote job
-Kicks off a sower job to process the metadata files that you have just pushed up
+## Support
 
-No git hook for publish, users are expected to run that themselves.
+Part of the CALYPR data commons ecosystem.

client/client.go

@@ -1,116 +1,26 @@
 package client
 
 import (
-	"bytes"
-	"fmt"
-	"io"
-	"net/http"
-	"net/url"
-	"path/filepath"
-	"time"
-
-	token "github.com/bmeg/grip-graphql/middleware"
+	"github.com/calypr/git-drs/client"
 	drsConfig "github.com/calypr/git-drs/config"
 
-	"github.com/calypr/data-client/client/commonUtils"
-	"github.com/calypr/data-client/client/jwt"
+	"github.com/calypr/data-client/g3client"
+	"github.com/calypr/data-client/logs"
 )
 
-type Gen3Client struct {
-	Base       *url.URL
-	Cred       jwt.Credential
-	ProjectId  string
-	BucketName string
-}
-
-// load repo-level config and return a new IndexDClient
-func NewGen3Client() (*Gen3Client, error) {
-	var conf jwt.Configure
-
+// NewGen3Client loads repo-level config and return a new DRSClient
+func NewGen3Client(remote drsConfig.Remote, opts ...g3client.Option) (client.DRSClient, func(), error) {
 	cfg, err := drsConfig.LoadConfig()
 	if err != nil {
-		return nil, err
-	}
-
-	profile := cfg.Servers.Gen3.Auth.Profile
-	if profile == "" {
-		return nil, fmt.Errorf("No gen3 profile specified. Please provide a gen3Profile key in your .drsconfig")
-	}
-
-	cred, err := conf.ParseConfig(profile)
-	if err != nil {
-		return nil, err
-	}
-
-	baseUrl, err := url.Parse(cred.APIEndpoint)
-	if err != nil {
-		return nil, fmt.Errorf("error parsing base URL from profile %s: %v", profile, err)
-	}
-
-	// get the gen3Project and gen3Bucket from the config
-	projectId := cfg.Servers.Gen3.Auth.ProjectID
-	if projectId == "" {
-		return nil, fmt.Errorf("No gen3 project specified. Please provide a gen3Project key in your .drsconfig")
-	}
-
-	bucketName := cfg.Servers.Gen3.Auth.Bucket
-	if bucketName == "" {
-		return nil, fmt.Errorf("No gen3 bucket specified. Please provide a gen3Bucket key in your .drsconfig")
-	}
-
-	return &Gen3Client{Base: baseUrl, Cred: cred, ProjectId: projectId, BucketName: bucketName}, err
-}
-
-type Resp struct {
-	Body []byte
-	Err  error
-}
-
-func (cl *Gen3Client) MakeReq(method string, path string, body []byte) *Resp {
-	a := *cl.Base
-	a.Path = filepath.Join(a.Path, path)
-
-	var reqBodyReader io.Reader
-	if body != nil {
-		reqBodyReader = bytes.NewBuffer(body)
-	}
-
-	req, err := http.NewRequest(method, a.String(), reqBodyReader)
-	if err != nil {
-		return &Resp{nil, err}
+		return nil, nil, err
 	}
-	expiration, err := token.GetExpiration(cl.Cred.AccessToken)
-	if err != nil {
-		return &Resp{nil, err}
-	}
-	// Update AccessToken if token is old
-	if expiration.Before(time.Now()) {
-		r := jwt.Request{}
-		err := r.RequestNewAccessToken(cl.Base.String()+commonUtils.FenceAccessTokenEndpoint, &cl.Cred)
-		if err != nil {
-			return &Resp{nil, err}
-		}
-	}
-	if cl.Cred.AccessToken == "" {
-		return &Resp{nil, fmt.Errorf("access token not found in profile config")}
-	}
-	req.Header.Set("Authorization", "bearer "+cl.Cred.AccessToken)
 
-	client := &http.Client{}
-	response, err := client.Do(req)
-	if err != nil {
-		return &Resp{nil, err}
-	}
-	defer response.Body.Close()
-
-	if response.StatusCode != http.StatusOK {
-		return &Resp{nil, fmt.Errorf("failed to check authz, response body: %v", response)}
-	}
+	logger, closer := logs.New(string(remote))
 
-	RespBody, err := io.ReadAll(response.Body)
+	dClient, err := cfg.GetRemoteClient(remote, logger.Logger, opts...)
 	if err != nil {
-		return &Resp{nil, fmt.Errorf("failed to read response Body")}
+		return nil, closer, err
 	}
 
-	return &Resp{RespBody, nil}
+	return dClient, closer, nil
 }