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feat: allows skipping of specific nextflow files from being cached #414

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feat: allows skipping of specific nextflow files from being cached #414

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d44be29
Adds ability to skip specific nextflow files from being cached, unit …
Apr 20, 2022
4f948c2
commit to ensure all changes have been added
Apr 20, 2022
2fa2234
for rebase
Apr 20, 2022
25e52ce
shrinkwrap added to resolve issues
Apr 20, 2022
9db1d83
updated to fix errors
Apr 20, 2022
9842fd0
updated to fix new errors
Apr 20, 2022
d4b3725
codon172 adding .agcingore file
hnookalaaws Dec 20, 2022
e1249db
Merge pull request #580 from hnookalaaws/codon-172
lingjiekong Dec 20, 2022
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42 changes: 12 additions & 30 deletions packages/cdk/npm-shrinkwrap.json
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3 changes: 3 additions & 0 deletions packages/cli/.agcignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
.nextflow
.snakemake
work
13 changes: 13 additions & 0 deletions packages/cli/go.sum
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ cloud.google.com/go v0.53.0/go.mod h1:fp/UouUEsRkN6ryDKNW/Upv/JBKnv6WDthjR6+vze6
cloud.google.com/go v0.54.0/go.mod h1:1rq2OEkV3YMf6n/9ZvGWI3GWw0VoqH/1x2nd8Is/bPc=
cloud.google.com/go v0.56.0/go.mod h1:jr7tqZxxKOVYizybht9+26Z/gUq7tiRzu+ACVAMbKVk=
cloud.google.com/go v0.57.0/go.mod h1:oXiQ6Rzq3RAkkY7N6t3TcE6jE+CIBBbA36lwQ1JyzZs=
cloud.google.com/go v0.61.0/go.mod h1:XukKJg4Y7QsUu0Hxg3qQKUWR4VuWivmyMK2+rUyxAqw=
cloud.google.com/go v0.62.0/go.mod h1:jmCYTdRCQuc1PHIIJ/maLInMho30T/Y0M4hTdTShOYc=
cloud.google.com/go v0.65.0/go.mod h1:O5N8zS7uWy9vkA9vayVHs65eM1ubvY4h553ofrNHObY=
cloud.google.com/go v0.72.0/go.mod h1:M+5Vjvlc2wnp6tjzE102Dw08nGShTscUx2nZMufOKPI=
Expand All @@ -27,6 +28,7 @@ cloud.google.com/go/bigquery v1.8.0/go.mod h1:J5hqkt3O0uAFnINi6JXValWIb1v0goeZM7
cloud.google.com/go/datastore v1.0.0/go.mod h1:LXYbyblFSglQ5pkeyhO+Qmw7ukd3C+pD7TKLgZqpHYE=
cloud.google.com/go/datastore v1.1.0/go.mod h1:umbIZjpQpHh4hmRpGhH4tLFup+FVzqBi1b3c64qFpCk=
cloud.google.com/go/firestore v1.1.0/go.mod h1:ulACoGHTpvq5r8rxGJ4ddJZBZqakUQqClKRT5SZwBmk=
cloud.google.com/go/firestore v1.3.0/go.mod h1:Qt0gS9Qz9tROrmgFavo36+hdST1FXvmtnGnO0Dr03pU=
cloud.google.com/go/pubsub v1.0.1/go.mod h1:R0Gpsv3s54REJCy4fxDixWD93lHJMoZTyQ2kNxGRt3I=
cloud.google.com/go/pubsub v1.1.0/go.mod h1:EwwdRX2sKPjnvnqCa270oGRyludottCI76h+R3AArQw=
cloud.google.com/go/pubsub v1.2.0/go.mod h1:jhfEVHT8odbXTkndysNHCcx0awwzvfOlguIAii9o8iA=
Expand Down Expand Up @@ -341,6 +343,9 @@ github.com/stretchr/testify v1.6.1/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/
github.com/stretchr/testify v1.7.0 h1:nwc3DEeHmmLAfoZucVR881uASk0Mfjw8xYJ99tb5CcY=
github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
github.com/subosito/gotenv v1.2.0/go.mod h1:N0PQaV/YGNqwC0u51sEeR/aUtSLEXKX9iv69rRypqCw=
github.com/weathersource/go-errors v1.0.1/go.mod h1:6AhTSfdYXpt+kdI9e3N9Beak4vH8Ye/e5+sTazseyPo=
github.com/weathersource/go-gsrv v1.0.1/go.mod h1:yOOB7n+UMhC43FApo/MYhspWrm325uR5aWhTL91tOag=
github.com/weathersource/go-mockfs v1.0.1/go.mod h1:e2mvTTiHoiD/Xj3nPDY5gVqvdW/2uY1vnZWlEflCsNk=
github.com/xeipuuv/gojsonpointer v0.0.0-20180127040702-4e3ac2762d5f h1:J9EGpcZtP0E/raorCMxlFGSTBrsSlaDGf3jU/qvAE2c=
github.com/xeipuuv/gojsonpointer v0.0.0-20180127040702-4e3ac2762d5f/go.mod h1:N2zxlSyiKSe5eX1tZViRH5QA0qijqEDrYZiPEAiq3wU=
github.com/xeipuuv/gojsonreference v0.0.0-20180127040603-bd5ef7bd5415 h1:EzJWgHovont7NscjpAxXsDA8S8BMYve8Y5+7cuRE7R0=
Expand Down Expand Up @@ -441,6 +446,7 @@ golang.org/x/net v0.0.0-20200520182314-0ba52f642ac2/go.mod h1:qpuaurCH72eLCgpAm/
golang.org/x/net v0.0.0-20200625001655-4c5254603344/go.mod h1:/O7V0waA8r7cgGh81Ro3o1hOxt32SMVPicZroKQ2sZA=
golang.org/x/net v0.0.0-20200707034311-ab3426394381/go.mod h1:/O7V0waA8r7cgGh81Ro3o1hOxt32SMVPicZroKQ2sZA=
golang.org/x/net v0.0.0-20200822124328-c89045814202/go.mod h1:/O7V0waA8r7cgGh81Ro3o1hOxt32SMVPicZroKQ2sZA=
golang.org/x/net v0.0.0-20200923182212-328152dc79b1/go.mod h1:/O7V0waA8r7cgGh81Ro3o1hOxt32SMVPicZroKQ2sZA=
golang.org/x/net v0.0.0-20201021035429-f5854403a974/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU=
golang.org/x/net v0.0.0-20201031054903-ff519b6c9102/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU=
golang.org/x/net v0.0.0-20201110031124-69a78807bb2b/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU=
Expand Down Expand Up @@ -577,6 +583,8 @@ golang.org/x/tools v0.0.0-20200512131952-2bc93b1c0c88/go.mod h1:EkVYQZoAsY45+roY
golang.org/x/tools v0.0.0-20200515010526-7d3b6ebf133d/go.mod h1:EkVYQZoAsY45+roYkvgYkIh4xh/qjgUK9TdY2XT94GE=
golang.org/x/tools v0.0.0-20200618134242-20370b0cb4b2/go.mod h1:EkVYQZoAsY45+roYkvgYkIh4xh/qjgUK9TdY2XT94GE=
golang.org/x/tools v0.0.0-20200619180055-7c47624df98f/go.mod h1:EkVYQZoAsY45+roYkvgYkIh4xh/qjgUK9TdY2XT94GE=
golang.org/x/tools v0.0.0-20200713011307-fd294ab11aed/go.mod h1:njjCfa9FT2d7l9Bc6FUM5FLjQPp3cFF28FI3qnDFljA=
golang.org/x/tools v0.0.0-20200727233628-55644ead90ce/go.mod h1:njjCfa9FT2d7l9Bc6FUM5FLjQPp3cFF28FI3qnDFljA=
golang.org/x/tools v0.0.0-20200729194436-6467de6f59a7/go.mod h1:njjCfa9FT2d7l9Bc6FUM5FLjQPp3cFF28FI3qnDFljA=
golang.org/x/tools v0.0.0-20200804011535-6c149bb5ef0d/go.mod h1:njjCfa9FT2d7l9Bc6FUM5FLjQPp3cFF28FI3qnDFljA=
golang.org/x/tools v0.0.0-20200825202427-b303f430e36d/go.mod h1:njjCfa9FT2d7l9Bc6FUM5FLjQPp3cFF28FI3qnDFljA=
Expand Down Expand Up @@ -613,6 +621,7 @@ google.golang.org/api v0.24.0/go.mod h1:lIXQywCXRcnZPGlsd8NbLnOjtAoL6em04bJ9+z0M
google.golang.org/api v0.28.0/go.mod h1:lIXQywCXRcnZPGlsd8NbLnOjtAoL6em04bJ9+z0MncE=
google.golang.org/api v0.29.0/go.mod h1:Lcubydp8VUV7KeIHD9z2Bys/sm/vGKnG1UHuDBSrHWM=
google.golang.org/api v0.30.0/go.mod h1:QGmEvQ87FHZNiUVJkT14jQNYJ4ZJjdRF23ZXz5138Fc=
google.golang.org/api v0.32.0/go.mod h1:/XrVsuzM0rZmrsbjJutiuftIzeuTQcEeaYcSk/mQ1dg=
google.golang.org/api v0.35.0/go.mod h1:/XrVsuzM0rZmrsbjJutiuftIzeuTQcEeaYcSk/mQ1dg=
google.golang.org/api v0.36.0/go.mod h1:+z5ficQTmoYpPn8LCUNVpK5I7hwkpjbcgqA7I34qYtE=
google.golang.org/api v0.40.0/go.mod h1:fYKFpnQN0DsDSKRVRcQSDQNtqWPfM9i+zNPxepjRCQ8=
Expand Down Expand Up @@ -654,10 +663,13 @@ google.golang.org/genproto v0.0.0-20200513103714-09dca8ec2884/go.mod h1:55QSHmfG
google.golang.org/genproto v0.0.0-20200515170657-fc4c6c6a6587/go.mod h1:YsZOwe1myG/8QRHRsmBRE1LrgQY60beZKjly0O1fX9U=
google.golang.org/genproto v0.0.0-20200526211855-cb27e3aa2013/go.mod h1:NbSheEEYHJ7i3ixzK3sjbqSGDJWnxyFXZblF3eUsNvo=
google.golang.org/genproto v0.0.0-20200618031413-b414f8b61790/go.mod h1:jDfRM7FcilCzHH/e9qn6dsT145K34l5v+OpcnNgKAAA=
google.golang.org/genproto v0.0.0-20200711021454-869866162049/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no=
google.golang.org/genproto v0.0.0-20200728010541-3dc8dca74b7b/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no=
google.golang.org/genproto v0.0.0-20200729003335-053ba62fc06f/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no=
google.golang.org/genproto v0.0.0-20200804131852-c06518451d9c/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no=
google.golang.org/genproto v0.0.0-20200825200019-8632dd797987/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no=
google.golang.org/genproto v0.0.0-20200904004341-0bd0a958aa1d/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no=
google.golang.org/genproto v0.0.0-20200924141100-a14c0a98937d/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no=
google.golang.org/genproto v0.0.0-20201109203340-2640f1f9cdfb/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no=
google.golang.org/genproto v0.0.0-20201201144952-b05cb90ed32e/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no=
google.golang.org/genproto v0.0.0-20201210142538-e3217bee35cc/go.mod h1:FWY/as6DDZQgahTzZj3fqbO1CbirC29ZNUFHwi0/+no=
Expand All @@ -681,6 +693,7 @@ google.golang.org/grpc v1.29.1/go.mod h1:itym6AZVZYACWQqET3MqgPpjcuV5QH3BxFS3Iji
google.golang.org/grpc v1.30.0/go.mod h1:N36X2cJ7JwdamYAgDz+s+rVMFjt3numwzf/HckM8pak=
google.golang.org/grpc v1.31.0/go.mod h1:N36X2cJ7JwdamYAgDz+s+rVMFjt3numwzf/HckM8pak=
google.golang.org/grpc v1.31.1/go.mod h1:N36X2cJ7JwdamYAgDz+s+rVMFjt3numwzf/HckM8pak=
google.golang.org/grpc v1.32.0/go.mod h1:N36X2cJ7JwdamYAgDz+s+rVMFjt3numwzf/HckM8pak=
google.golang.org/grpc v1.33.1/go.mod h1:fr5YgcSWrqhRRxogOsw7RzIpsmvOZ6IcH4kBYTpR3n0=
google.golang.org/grpc v1.33.2/go.mod h1:JMHMWHQWaTccqQQlmk3MJZS+GWXOdAesneDmEnv2fbc=
google.golang.org/grpc v1.34.0/go.mod h1:WotjhfgOW/POjDeRt8vscBtXq+2VjORFy659qA51WJ8=
Expand Down
8 changes: 8 additions & 0 deletions packages/cli/internal/pkg/mocks/io/interfaces.go
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Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
package iomocks

import (
"io"
"io/fs"
"os"
"time"

"github.com/aws/amazon-genomics-cli/internal/pkg/cli/spec"
Expand All @@ -17,6 +19,12 @@ type OS interface {
Stat(name string) (fs.FileInfo, error)
MkdirAll(path string, perm fs.FileMode) error
IsNotExist(err error) bool
Create(name string) (*os.File, error)
Open(name string) (*os.File, error)
}

type IO interface {
Copy(dst io.Writer, src io.Reader) (written int64, err error)
}

type FileInfo interface {
Expand Down
70 changes: 70 additions & 0 deletions packages/cli/internal/pkg/mocks/io/mock_interfaces.go
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44 changes: 41 additions & 3 deletions packages/cli/internal/pkg/osutils/utils.go
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package osutils

import (
"bufio"
"fmt"
"io"
"io/fs"
Expand All @@ -20,6 +21,8 @@ var osCreate = os.Create
var ioCopy = io.Copy
var filepathWalkDir = filepath.WalkDir

const agcignore = "./.agcignore"

// DetermineHomeDir returns the file system directory where the AGC files live.
func DetermineHomeDir() (string, error) {
dir, err := osUserHomeDir()
Expand Down Expand Up @@ -63,13 +66,27 @@ func EnsureDirExistence(dirPath string) error {
}

func CopyFileRecursivelyToLocation(absoluteDestinationDir string, absoluteSourceDir string) error {
err := filepathWalkDir(absoluteSourceDir, func(currentPath string, dirEntry fs.DirEntry, err error) error {
err := filepathWalkDir(absoluteSourceDir, getWalkDirFn(absoluteDestinationDir, absoluteSourceDir))
return err
}

func getWalkDirFn(absoluteDestinationDir string, absoluteSourceDir string) fs.WalkDirFunc {
return func(currentPath string, dirEntry fs.DirEntry, err error) error {
if dirEntry == nil {
// There are several use cases when it can happen:
// 1. provided path doesn't exist
// 2. file or sub-directory got deleted after being listed by WalkDir
return fmt.Errorf("file '%s' doesn't exist", currentPath)
}
ignoreDir, err := isDirIgnored(dirEntry.Name())
if err != nil {
return err
}
if ignoreDir ||
strings.HasSuffix(currentPath, ".nextflow.log") {
return filepath.SkipDir
}

if !dirEntry.IsDir() {
srcFile, err := osOpen(currentPath)
if err != nil {
Expand All @@ -91,9 +108,30 @@ func CopyFileRecursivelyToLocation(absoluteDestinationDir string, absoluteSource
}
}
return nil
})
}
}

return err
func isDirIgnored(dirName string) (bool, error) {
if _, err := osStat(agcignore); err != nil {
return false, nil
}
file, err := os.Open(agcignore)
if err != nil {
return false, err
}
defer file.Close()

scanner := bufio.NewScanner(file)
for scanner.Scan() {
if dirName == scanner.Text() {
return true, nil
}
}

if err := scanner.Err(); err != nil {
return false, err
}
return false, nil
}

func getAndCreateRelativePath(currentPath string, sourcePath string, destinationDir string) (string, error) {
Expand Down
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