plex create deprecated (#622)

.github/workflows/go.yml

@@ -39,7 +39,7 @@ jobs:
 
       - name: Run Equibind
         run: |
-          result_dir=$(./plex create -t tools/equibind.json -i testdata/binding/pdbbind_processed_size1 --autoRun=true -a test -a ci | grep 'Finished processing, results written to' | sed -n 's/^.*Finished processing, results written to //p' | sed 's/\/io.json//')
+          result_dir=$(./plex init -t tools/equibind.json -i '{"protein": ["testdata/binding/abl/7n9g.pdb"], "small_molecule": ["testdata/binding/abl/ZINC000003986735.sdf"]}' --scatteringMethod=dotProduct --autoRun=true -a test -a ci | grep 'Finished processing, results written to' | sed -n 's/^.*Finished processing, results written to //p' | sed 's/\/io.json//')
           cd "$result_dir/entry-0/outputs"
           if [ "$(find . -name '*docked.sdf' | grep 'docked.sdf')" == "" ]; then
             echo "No docked files found"

.github/workflows/releaser.yml

@@ -59,7 +59,7 @@ jobs:
 
       - name: Run Equibind
         run: |
-          result_dir=$(./plex create -t tools/equibind.json -i testdata/binding/pdbbind_processed_size1 -a test -a ci --autoRun=true | grep 'Finished processing, results written to' | sed -n 's/^.*Finished processing, results written to //p' | sed 's/\/io.json//')
+          result_dir=$(./plex init -t tools/equibind.json -i '{"protein": ["testdata/binding/abl/7n9g.pdb"], "small_molecule": ["testdata/binding/abl/ZINC000003986735.sdf"]}' --scatteringMethod=dotProduct --autoRun=true -a test -a ci | grep 'Finished processing, results written to' | sed -n 's/^.*Finished processing, results written to //p' | sed 's/\/io.json//')
           cd "$result_dir/entry-0/outputs"
           if [ "$(find . -name '*docked.sdf' | grep 'docked.sdf')" == "" ]; then
             echo "No docked files found"

.gitignore

@@ -311,3 +311,6 @@ yarn-error.log
 yarn-debug.log*
 .pnpm-debug.log*
 !./gateway/frontend/lib/
+
+# gorm
+gateway/gorm.db

README.md

@@ -67,7 +67,7 @@ Invoke-Expression (Invoke-WebRequest -Uri "https://raw.githubusercontent.com/lab
 
 2. Submit an example plex job
 ```
-./plex create -t tools/equibind.json -i testdata/binding/abl --autoRun=True
+./plex init -t tools/equibind.json -i '{"protein": ["testdata/binding/abl/7n9g.pdb"], "small_molecule": ["testdata/binding/abl/ZINC000003986735.sdf"]}' --scatteringMethod=dotProduct --autoRun=true 
 ```
 
 ![Getting Started](./readme-getting-started-2x.gif)

cmd/init.go

@@ -6,18 +6,18 @@ import (
 	"io/ioutil"
 	"log"
 	"os"
-	"path/filepath"
-	"strings"
 
 	"github.com/labdao/plex/internal/ipfs"
 	"github.com/labdao/plex/internal/ipwl"
-	"github.com/labdao/plex/internal/web3"
 	"github.com/spf13/cobra"
 )
 
 var (
-	inputs           string
-	scatteringMethod string
+	toolPath              string
+	inputs                string
+	scatteringMethod      string
+	autoRun               bool
+	annotationsForAutoRun *[]string
 )
 
 var initCmd = &cobra.Command{
@@ -34,7 +34,7 @@ var initCmd = &cobra.Command{
 			log.Fatal("Invalid inputs JSON:", err)
 		}
 
-		ioJson, err := InitilizeIo(toolPath, scatteringMethod, kwargs)
+		ioJson, err := ipwl.InitializeIo(toolPath, scatteringMethod, kwargs)
 		if err != nil {
 			log.Fatal(err)
 		}
@@ -69,153 +69,23 @@ var initCmd = &cobra.Command{
 		if err := tempFile.Close(); err != nil {
 			log.Fatalf("Failed to close the temporary file: %v", err)
 		}
-	},
-}
-
-func InitilizeIo(toolPath string, scatteringMethod string, inputVectors map[string][]string) ([]ipwl.IO, error) {
-	// Open the file and load its content
-	tool, toolInfo, err := ipwl.ReadToolConfig(toolPath)
-	if err != nil {
-		return nil, err
-	}
-
-	// Check if all kwargs are in the tool's inputs
-	for inputKey := range inputVectors {
-		if _, exists := tool.Inputs[inputKey]; !exists {
-			log.Printf("The argument %s is not in the tool inputs.\n", inputKey)
-			log.Printf("Available keys: %v\n", tool.Inputs)
-			return nil, fmt.Errorf("the argument %s is not in the tool inputs", inputKey)
-		}
-	}
-
-	// Handle scattering methods and create the inputsList
-	var inputsList [][]string
-	switch scatteringMethod {
-	case "dotProduct":
-		// check if all lists have the same length
-		var vectorLength int
-		for _, v := range inputVectors {
-			if vectorLength == 0 {
-				vectorLength = len(v)
-				continue
-			}
-			if len(v) != vectorLength {
-				return nil, fmt.Errorf("all input arguments must have the same length for dot_product scattering method")
-			}
-			vectorLength = len(v)
-		}
-		for i := 0; i < vectorLength; i++ {
-			tmp := []string{}
-			for _, v := range inputVectors {
-				tmp = append(tmp, v[i])
-			}
-			inputsList = append(inputsList, tmp)
-		}
-	case "crossProduct":
-		cartesian := func(arrs ...[]string) [][]string {
-			result := [][]string{{}}
-
-			for _, arr := range arrs {
-				var temp [][]string
-
-				for _, res := range result {
-					for _, str := range arr {
-						product := append([]string{}, res...)
-						product = append(product, str)
-						temp = append(temp, product)
-					}
-				}
-
-				result = temp
-			}
-
-			return result
-		}
-
-		keys := make([]string, 0, len(inputVectors))
-		for k := range inputVectors {
-			keys = append(keys, k)
-		}
-		arrays := make([][]string, len(inputVectors))
-		for i, k := range keys {
-			arrays[i] = inputVectors[k]
-		}
-		inputsList = cartesian(arrays...)
-	default:
-		return nil, fmt.Errorf("invalid scattering method: %s", scatteringMethod)
-	}
-
-	var userId string
-
-	if web3.IsValidEthereumAddress(os.Getenv("RECIPIENT_WALLET")) {
-		userId = os.Getenv("RECIPIENT_WALLET")
-	} else {
-		fmt.Print("Invalid wallet address detected. Using empty string for user ID.\n")
-		userId = ""
-	}
-
-	// populate ioJSONGraph based on inputsList
-	var ioJSONGraph []ipwl.IO
-	for _, inputs := range inputsList {
-		io := ipwl.IO{
-			Tool:    toolInfo,
-			Inputs:  make(map[string]ipwl.FileInput),
-			Outputs: make(map[string]ipwl.Output),
-			State:   "created",
-			ErrMsg:  "",
-			UserID:  userId,
-		}
 
-		inputKeys := make([]string, 0, len(inputVectors))
-		for k := range inputVectors {
-			inputKeys = append(inputKeys, k)
-		}
-
-		for i, inputValue := range inputs {
-			inputKey := inputKeys[i]
-
-			if strings.Count(inputValue, "/") == 1 {
-				parts := strings.Split(inputValue, "/")
-				cid := parts[0]
-				fileName := parts[1]
-				if !ipfs.IsValidCID(cid) {
-					return nil, fmt.Errorf("invalid CID: %s", cid)
-				}
-				io.Inputs[inputKey] = ipwl.FileInput{
-					Class:    tool.Inputs[inputKey].Type,
-					FilePath: fileName,
-					IPFS:     cid,
-				}
-			} else {
-				cid, err := ipfs.WrapAndPinFile(inputValue) // Pin the file and get the CID
-				if err != nil {
-					return nil, err
-				}
-				io.Inputs[inputKey] = ipwl.FileInput{
-					Class:    tool.Inputs[inputKey].Type,
-					FilePath: filepath.Base(inputValue), // Use the respective input value from inputsList
-					IPFS:     cid,                       // Use the CID returned by WrapAndPinFile
-				}
-			}
-		}
-
-		for outputKey := range tool.Outputs {
-			io.Outputs[outputKey] = ipwl.FileOutput{
-				Class:    tool.Outputs[outputKey].Type,
-				FilePath: "", // Assuming filepath is empty, adapt as needed
-				IPFS:     "", // Assuming IPFS is not provided, adapt as needed
+		if autoRun {
+			_, _, err := PlexRun(cid, outputDir, verbose, showAnimation, concurrency, *annotationsForAutoRun)
+			if err != nil {
+				fmt.Println("Error:", err)
+				os.Exit(1)
 			}
 		}
-		ioJSONGraph = append(ioJSONGraph, io)
-	}
-
-	return ioJSONGraph, nil
+	},
 }
 
 func init() {
 	initCmd.Flags().StringVarP(&toolPath, "toolPath", "t", "", "Path of the Tool config (can be a local path or an IPFS CID)")
 	initCmd.Flags().StringVarP(&inputs, "inputs", "i", "{}", "Inputs in JSON format")
 	initCmd.Flags().StringVarP(&scatteringMethod, "scatteringMethod", "", "{}", "Inputs in JSON format")
+	initCmd.Flags().BoolVarP(&autoRun, "autoRun", "", false, "Auto submit the IO to plex run")
+	annotationsForAutoRun = initCmd.Flags().StringArrayP("annotations", "a", []string{}, "Annotations to add to Bacalhau job")
 
 	rootCmd.AddCommand(initCmd)
 }

cmd/upgrade.go

@@ -31,7 +31,7 @@ var upgradeCmd = &cobra.Command{
 }
 
 const (
-	CurrentPlexVersion = "v0.9.1"
+	CurrentPlexVersion = "v0.10.0"
 	ReleaseURL         = "https://api.github.com/repos/labdao/plex/releases/latest"
 	ToolsURL           = "https://api.github.com/repos/labdao/plex/contents/tools?ref=main"
 )