Merge pull request #185 from metrumresearchgroup/develop

release 2.3.0 merging to master

.drone.yml

@@ -22,6 +22,7 @@ steps:
       - if [ -d /tmp/${DRONE_BUILD_NUMBER}/babylontest ] ; then rm -rf /tmp/${DRONE_BUILD_NUMBER}/babylontest; fi
   - name: Build Babylon
     commands:
+      - mkdir -p /tmp/${DRONE_BUILD_NUMBER} ; git rev-parse HEAD > /tmp/${DRONE_BUILD_NUMBER}/bbi_hash
       - go build -o bbi cmd/bbi/main.go
       - ./bbi version
   - name: Get BabylonTest
@@ -30,7 +31,15 @@ steps:
     commands:
       - git clone https://github.com/metrumresearchgroup/babylontest.git /tmp/${DRONE_BUILD_NUMBER}/babylontest
       - cd /tmp/${DRONE_BUILD_NUMBER}/babylontest
+      - mkdir -p /tmp/${DRONE_BUILD_NUMBER} ; git rev-parse HEAD > /tmp/${DRONE_BUILD_NUMBER}/babylontest_hash
       - if [ ! -z $BABYLONTEST_BRANCH ]; then git checkout $BABYLONTEST_BRANCH; fi
+  - name: Copy commit hashes to s3
+    commands:
+      - printf "[\n" > /tmp/${DRONE_BUILD_NUMBER}/commits.json
+      - printf "  {\"repo\":\"metrumresearchgroup/babylon\", \"commit\":\"$(cat /tmp/${DRONE_BUILD_NUMBER}/bbi_hash)\"},\n" >> /tmp/${DRONE_BUILD_NUMBER}/commits.json
+      - printf "  {\"repo\":\"metrumresearchgroup/babylontest\", \"commit\":\"$(cat /tmp/${DRONE_BUILD_NUMBER}/babylontest_hash)\"}\n" >> /tmp/${DRONE_BUILD_NUMBER}/commits.json
+      - printf "]\n" >> /tmp/${DRONE_BUILD_NUMBER}/commits.json
+      - aws s3 cp /tmp/${DRONE_BUILD_NUMBER}/commits.json s3://mrg-validation/babylon/${DRONE_BUILD_NUMBER}/commits.json
   - name: Test
     environment:
       <<: *sge_environment
@@ -57,9 +66,13 @@ steps:
       - cd /tmp/${DRONE_BUILD_NUMBER}/babylontest
       - export ROOT_EXECUTION_DIR=/data/${DRONE_BUILD_NUMBER}
       - export BABYLON_GRID_NAME_PREFIX="drone_${DRONE_BUILD_NUMBER}"
+      #Run test suite and copy results to s3
       - bbi init --dir /opt/NONMEM
-      - go test ./... -v --json --timeout 30m | tee test_output.json
+      - go test ./... -v --json -timeout 30m | tee test_output.json
       - aws s3 cp test_output.json s3://mrg-validation/babylon/${DRONE_BUILD_NUMBER}/results.json
+      #Check for test failures and clean up
+      - chmod +x failure_detector.sh
+      - ./failure_detector.sh test_output.json
       - rm -rf /data/${DRONE_BUILD_NUMBER}
       - rm -rf /tmp/${DRONE_BUILD_NUMBER}/babylontest
   - name: Cleanup on failure
@@ -102,7 +115,8 @@ steps:
       - mkdir testoutput
       - mkdir rendered
       - aws s3 cp s3://mrg-validation/babylon/${DRONE_BUILD_NUMBER}/results.json testoutput/results.json
-      - ./gpv --scenarioFile validation.json --testsDirectory testoutput --outputDirectory rendered
+      - aws s3 cp s3://mrg-validation/babylon/${DRONE_BUILD_NUMBER}/commits.json commits.json
+      - ./gpv --scenarioFile validation.json --commitsFile commits.json --testsDirectory testoutput --outputDirectory rendered
       - aws s3 cp rendered/specification.md s3://mrg-validation/babylon/${DRONE_TAG}/specification.md
       - aws s3 cp rendered/testing_and_validation.md s3://mrg-validation/babylon/${DRONE_TAG}/testing_and_validation.md
       - aws s3 cp rendered/traceability_matrix.md s3://mrg-validation/babylon/${DRONE_TAG}/traceability_matrix.md

.gitignore

@@ -2,4 +2,5 @@
 .idea
 dist
 babylon.log
-babylon.yaml
+babylon.yaml
+main

cmd/covcor.go

@@ -0,0 +1,55 @@
+// Copyright © 2016 Devin Pastoor <[email protected]>
+//
+// 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 cmd
+
+import (
+	"encoding/json"
+	"fmt"
+	parser "github.com/metrumresearchgroup/babylon/parsers/nmparser"
+	log "github.com/sirupsen/logrus"
+
+	"github.com/spf13/cobra"
+	"github.com/spf13/viper"
+)
+
+const covcorLongDescription string = `load .cov and .cor output from model(s), for example: 
+bbi nonmem covcor run001/run001
+bbi nonmem covcor run001/run001.cov
+ `
+// runCmd represents the run command
+var covcorCmd = &cobra.Command{
+	Use:   "covcor",
+	Short: "load .cov and .cor output from a model run",
+	Long: covcorLongDescription,
+	Run: covcor,
+}
+
+func covcor(cmd *cobra.Command, args []string) {
+	if debug {
+		viper.Debug()
+	}
+
+	results, err := parser.GetCovCorOutput(args[0])
+	if err != nil {
+		log.Fatal(err)
+	}
+
+	jsonRes, _ := json.MarshalIndent(results, "", "\t")
+	fmt.Printf("%s\n", jsonRes)
+
+}
+func init() {
+	nonmemCmd.AddCommand(covcorCmd)
+}

cmd/nonmem.go

@@ -167,21 +167,18 @@ type NonMemModel struct {
 	Error error `json:"error"`
 }
 
+var nonmemLongDescription string = fmt.Sprintf("\n%s\n\n%s\n\n%s\n", runLongDescription, summaryLongDescription, covcorLongDescription)
+
 // RunCmd represents the run command
 var nonmemCmd = &cobra.Command{
 	Use:   "nonmem",
 	Short: "nonmem a (set of) models locally or on the grid",
-	Long: `run nonmem model(s), for example: 
-bbi nonmem <local|sge> run001.mod
-bbi nonmem  --clean_lvl=1 <local|sge> run001.mod run002.mod
-bbi nonmem run <local|sge> [001:006].mod // expand to run001.mod run002.mod ... run006.mod local
-bbi nonmem run <local|sge> .// run all models in directory
- `,
+	Long: nonmemLongDescription,
 	Run: nonmem,
 }
 
 func nonmem(cmd *cobra.Command, args []string) {
-	println(runLongDescription)
+	println(nonmemLongDescription)
 }
 
 func init() {

cmd/root.go

@@ -48,11 +48,6 @@ var (
 	//Json indicates whether we should have a JSON tree of output
 	Json               bool
 	preview            bool
-	noExt              bool
-	noGrd              bool
-	noCov              bool
-	noCor              bool
-	noShk              bool
 	executionWaitGroup sync.WaitGroup
 )
 
@@ -98,12 +93,6 @@ func init() {
 	RootCmd.PersistentFlags().BoolVar(&Json, "json", false, "json tree of output, if possible")
 	viper.BindPFlag("json", RootCmd.PersistentFlags().Lookup("json")) //Bind to viper
 	RootCmd.PersistentFlags().BoolVarP(&preview, "preview", "p", false, "preview action, but don't actually run command")
-	//Used for Summary
-	RootCmd.PersistentFlags().BoolVarP(&noExt, "no-ext-file", "", false, "do not use ext file")
-	RootCmd.PersistentFlags().BoolVarP(&noGrd, "no-grd-file", "", false, "do not use grd file")
-	RootCmd.PersistentFlags().BoolVarP(&noCov, "no-cov-file", "", false, "do not use cov file")
-	RootCmd.PersistentFlags().BoolVarP(&noCor, "no-cor-file", "", false, "do not use cor file")
-	RootCmd.PersistentFlags().BoolVarP(&noShk, "no-shk-file", "", false, "do not use shk file")
 }
 
 // initConfig reads in config file and ENV variables if set.

cmd/summary.go

@@ -17,40 +17,153 @@ package cmd
 import (
 	"encoding/json"
 	"fmt"
-
 	parser "github.com/metrumresearchgroup/babylon/parsers/nmparser"
+	log "github.com/sirupsen/logrus"
+	"os"
+	"runtime"
 
 	"github.com/spf13/cobra"
 	"github.com/spf13/viper"
 )
 
-var summaryTree bool
+var (
+	summaryTree bool
+	noExt       bool
+	noGrd       bool
+	noShk       bool
+	extFile     string
+)
+const summaryLongDescription string = `summarize model(s), for example: 
+bbi nonmem summary run001/run001
+bbi nonmem summary run001/run001.lst
+bbi nonmem summary run001/run001.res
+ `
 
 // runCmd represents the run command
 var summaryCmd = &cobra.Command{
 	Use:   "summary",
-	Short: "summarize the output of a model",
-	Long: `run model(s), for example: 
-nmu summarize run001.lst
- `,
+	Short: "summarize the output of model(s)",
+	Long: summaryLongDescription,
 	Run: summary,
 }
 
+type jsonResults struct {
+	Results []parser.SummaryOutput
+	Errors  []error
+}
+
 func summary(cmd *cobra.Command, args []string) {
 	if debug {
 		viper.Debug()
 	}
+	if len(args) == 1 {
+		results, err := parser.GetModelOutput(args[0], parser.NewModelOutputFile(extFile, noExt), !noGrd, !noShk, )
+		if err != nil {
+			log.Fatal(err)
+		}
+		if Json {
+			jsonRes, _ := json.MarshalIndent(results, "", "\t")
+			fmt.Printf("%s\n", jsonRes)
+		} else {
+			results.Summary()
+		}
+		return
+	}
+
+	// if we are going to parse multiple models, we need to reasonably handle failures. The objective
+	// will be to always return a json object if its json, and if not, error as soon as it hits a printed issue.
+	// As such, the idea will be to store results such they can be filtered
+	type result int
+	const (
+		SUCCESS result = 1
+		ERROR          = 2
+	)
+	type modelResult struct {
+		Index   int
+		Outcome result
+		Err     error
+		Result  parser.SummaryOutput
+	}
+
+	workers := runtime.NumCPU()
+	if workers < 4 {
+		workers = 4
+	}
 
-	results := parser.GetModelOutput(args[0], verbose, noExt, noGrd, noCov, noCor, noShk)
+	numModels := len(args)
+	if workers > numModels {
+		workers = numModels
+	}
+	models := make(chan int, numModels)
+	results := make(chan modelResult, numModels)
+	orderedResults := make([]modelResult, numModels)
+	var modelResults jsonResults
 
+	for w := 1; w <= workers; w++ {
+		go func(w int, modIndex <-chan int, results chan<- modelResult) {
+			for i := range modIndex {
+				r, err := parser.GetModelOutput(args[i], parser.NewModelOutputFile(extFile, noExt), !noGrd, !noShk, )
+				if err != nil {
+					results <- modelResult{
+						Index:   i,
+						Outcome: ERROR,
+						Err:     err,
+						Result:  r,
+					}
+				} else {
+					results <- modelResult{
+						Index:   i,
+						Outcome: SUCCESS,
+						Err:     err,
+						Result:  r,
+					}
+				}
+			}
+		}(w, models, results)
+	}
+	for m := 0; m < numModels; m++ {
+		models <- m
+	}
+	close(models)
+	for r := 0; r < numModels; r++ {
+		res := <-results
+		orderedResults[res.Index] = res
+	}
+	for _, res := range orderedResults {
+		if res.Outcome == SUCCESS {
+			modelResults.Results = append(modelResults.Results, res.Result)
+		} else if res.Outcome == ERROR {
+			modelResults.Errors = append(modelResults.Errors, res.Err)
+		}
+	}
 	if Json {
-		jsonRes, _ := json.MarshalIndent(results, "", "\t")
+		jsonRes, _ := json.MarshalIndent(modelResults, "", "\t")
 		fmt.Printf("%s\n", jsonRes)
-	} else {
-		results.Summary()
+		return
 	}
 
+
+	// not json lets print all successful models first then any errors
+	for i, res := range modelResults.Results {
+		res.Summary()
+		// add some spacing between models
+		if i != len(modelResults.Results) -1 {
+			fmt.Println("")
+			fmt.Println("")
+		}
+	}
+	for _, res := range modelResults.Errors {
+		log.Error(res)
+	}
+	if len(modelResults.Errors) > 0 {
+		os.Exit(1)
+	}
 }
 func init() {
 	nonmemCmd.AddCommand(summaryCmd)
+	//Used for Summary
+	summaryCmd.PersistentFlags().BoolVar(&noExt, "no-ext-file", false, "do not use ext file")
+	summaryCmd.PersistentFlags().BoolVar(&noGrd, "no-grd-file", false, "do not use grd file")
+	summaryCmd.PersistentFlags().BoolVar(&noShk, "no-shk-file", false, "do not use shk file")
+	summaryCmd.PersistentFlags().StringVar(&extFile, "ext-file", "", "name of custom ext-file")
 }