Merge pull request #49 from kjsanger/feature/migrate-to-wtsi-npg

Relocate repository from github.com/kjsanger to github.com/wtsi-npg

README.md

@@ -14,7 +14,7 @@ therefore baton is required for its operation.
 
 #### Status
 
-[![Build Status](https://travis-ci.org/kjsanger/extendo.svg?branch=devel)](https://travis-ci.org/kjsanger/extendo)
+[![Build Status](https://travis-ci.org/wtsi-npg/extendo.svg?branch=devel)](https://travis-ci.org/wtsi-npg/extendo)
 
 #### Dependencies:
 

client.go

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved.
+ * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved.
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -35,8 +35,8 @@ import (
 	"syscall"
 	"time"
 
-	logs "github.com/kjsanger/logshim"
 	"github.com/pkg/errors"
+	logs "github.com/wtsi-npg/logshim"
 )
 
 const (
@@ -817,7 +817,7 @@ func wrap(operation string, args Args, target RodsItem) *Envelope {
 }
 
 // unwrap removes the envelope from JSON returned by baton-do and returns any
-// RodsItems or error from thre iRODS operation.
+// RodsItems or error from the iRODS operation.
 func unwrap(client *Client, envelope *Envelope) ([]RodsItem, error) {
 	var items []RodsItem
 	if envelope.ErrorMsg != nil {

client_pool.go

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved.
+ * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved.
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -24,10 +24,10 @@ import (
 	"sync"
 	"time"
 
-	logs "github.com/kjsanger/logshim"
 	"github.com/pkg/errors"
+	logs "github.com/wtsi-npg/logshim"
 
-	"github.com/kjsanger/extendo/v2/utilities"
+	"github.com/wtsi-npg/extendo/v2/utilities"
 )
 
 // ClientPool is a pool of iRODS Clients for use by applications. It provides

client_pool_test.go

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved.
+ * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved.
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -26,7 +26,7 @@ import (
 	. "github.com/onsi/ginkgo"
 	. "github.com/onsi/gomega"
 
-	ex "github.com/kjsanger/extendo/v2"
+	ex "github.com/wtsi-npg/extendo/v2"
 )
 
 var _ = Describe("Make a client pool", func() {

client_test.go

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved.
+ * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved.
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -28,7 +28,7 @@ import (
 	. "github.com/onsi/ginkgo"
 	. "github.com/onsi/gomega"
 
-	ex "github.com/kjsanger/extendo/v2"
+	ex "github.com/wtsi-npg/extendo/v2"
 )
 
 var _ = Describe("Find the baton-do executable", func() {

collection.go

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved.
+ * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved.
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -24,8 +24,8 @@ import (
 	"path/filepath"
 	"time"
 
-	logs "github.com/kjsanger/logshim"
 	"github.com/pkg/errors"
+	logs "github.com/wtsi-npg/logshim"
 )
 
 type Collection struct {

collection_test.go

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved.
+ * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved.
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -26,7 +26,7 @@ import (
 	. "github.com/onsi/ginkgo"
 	. "github.com/onsi/gomega"
 
-	ex "github.com/kjsanger/extendo/v2"
+	ex "github.com/wtsi-npg/extendo/v2"
 )
 
 var _ = Describe("Make an existing Collection instance from iRODS", func() {

data_object_test.go

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved.
+ * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved.
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -26,7 +26,7 @@ import (
 	. "github.com/onsi/ginkgo"
 	. "github.com/onsi/gomega"
 
-	ex "github.com/kjsanger/extendo/v2"
+	ex "github.com/wtsi-npg/extendo/v2"
 )
 
 var _ = Describe("Make an existing DataObject instance from iRODS", func() {

extendo_test.go

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2019, 2020 Genome Research Ltd. All rights reserved.
+ * Copyright (C) 2019, 2020, 2021 Genome Research Ltd. All rights reserved.
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -25,10 +25,10 @@ import (
 	"testing"
 	"time"
 
-	logs "github.com/kjsanger/logshim"
-	"github.com/kjsanger/logshim-zerolog/zlog"
 	"github.com/rs/zerolog"
 	"github.com/stretchr/testify/assert"
+	logs "github.com/wtsi-npg/logshim"
+	"github.com/wtsi-npg/logshim-zerolog/zlog"
 )
 
 // These are whitebox Unit tests with access to extendo package internals.

go.mod

@@ -1,13 +1,13 @@
-module github.com/kjsanger/extendo/v2
+module github.com/wtsi-npg/extendo/v2
 
-go 1.13
+go 1.14
 
 require (
-	github.com/kjsanger/logshim v1.1.0
-	github.com/kjsanger/logshim-zerolog v1.1.0
 	github.com/onsi/ginkgo v1.15.0
 	github.com/onsi/gomega v1.10.5
-	github.com/pkg/errors v0.9.1
-	github.com/rs/zerolog v1.20.0
+	github.com/pkg/errors v0.8.1
+	github.com/rs/zerolog v1.19.0
 	github.com/stretchr/testify v1.7.0
+	github.com/wtsi-npg/logshim v1.2.0
+	github.com/wtsi-npg/logshim-zerolog v1.2.0
 )

go.sum

@@ -1,11 +1,8 @@
 github.com/coreos/go-systemd v0.0.0-20190321100706-95778dfbb74e/go.mod h1:F5haX7vjVVG0kc13fIWeqUViNPyEJxv/OmvnBo0Yme4=
-github.com/davecgh/go-spew v1.1.0 h1:ZDRjVQ15GmhC3fiQ8ni8+OwkZQO4DARzQgrnXU1Liz8=
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
-github.com/fsnotify/fsnotify v1.4.7 h1:IXs+QLmnXW2CcXuY+8Mzv/fWEsPGWxqefPtCP5CnV9I=
 github.com/fsnotify/fsnotify v1.4.7/go.mod h1:jwhsz4b93w/PPRr/qN1Yymfu8t87LnFCMoQvtojpjFo=
 github.com/fsnotify/fsnotify v1.4.9 h1:hsms1Qyu0jgnwNXIxa+/V/PDsU6CfLf6CNO8H7IWoS4=
 github.com/fsnotify/fsnotify v1.4.9/go.mod h1:znqG4EE+3YCdAaPaxE2ZRY/06pZUdp0tY4IgpuI1SZQ=
-github.com/golang/protobuf v1.2.0 h1:P3YflyNX/ehuJFLhxviNdFxQPkGK5cDcApsge1SqnvM=
 github.com/golang/protobuf v1.2.0/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
 github.com/golang/protobuf v1.4.0-rc.1/go.mod h1:ceaxUfeHdC40wWswd/P6IGgMaK3YpKi5j83Wpe3EHw8=
 github.com/golang/protobuf v1.4.0-rc.1.0.20200221234624-67d41d38c208/go.mod h1:xKAWHe0F5eneWXFV3EuXVDTCmh+JuBKY0li0aMyXATA=
@@ -16,66 +13,29 @@ github.com/golang/protobuf v1.4.2/go.mod h1:oDoupMAO8OvCJWAcko0GGGIgR6R6ocIYbsSw
 github.com/google/go-cmp v0.3.0/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU=
 github.com/google/go-cmp v0.3.1/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU=
 github.com/google/go-cmp v0.4.0/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE=
-github.com/hpcloud/tail v1.0.0 h1:nfCOvKYfkgYP8hkirhJocXT2+zOD8yUNjXaWfTlyFKI=
 github.com/hpcloud/tail v1.0.0/go.mod h1:ab1qPbhIpdTxEkNHXyeSf5vhxWSCs/tWer42PpOxQnU=
-github.com/kjsanger/logshim v1.0.0 h1:1FMKd0pxtamsXumK1EB9H2twiIf2PnwFwFMV99Ub0BQ=
-github.com/kjsanger/logshim v1.0.0/go.mod h1:a0VpOYrCQgfvQUqympQP5mTuGWz766IAbtPwHeA6PEE=
-github.com/kjsanger/logshim v1.1.0 h1:43+UWmayDVVzTSuDYVeZrCZCwKyE+iahIODsxbtWVvk=
-github.com/kjsanger/logshim v1.1.0/go.mod h1:drKALnhjaOKRtZjagdHMa4k6kgd8k03+rw93ShsNiCI=
-github.com/kjsanger/logshim-zerolog v1.1.0 h1:gwpvOtJd17IE1GbVLgakbZDzNaUrEf96AlZeNdqnCEE=
-github.com/kjsanger/logshim-zerolog v1.1.0/go.mod h1:U5/BO2owB1e49IJn4hTaoSatqnfA91izLrj7mbjXYI4=
 github.com/nxadm/tail v1.4.4 h1:DQuhQpB1tVlglWS2hLQ5OV6B5r8aGxSrPc5Qo6uTN78=
 github.com/nxadm/tail v1.4.4/go.mod h1:kenIhsEOeOJmVchQTgglprH7qJGnHDVpk1VPCcaMI8A=
 github.com/onsi/ginkgo v1.6.0/go.mod h1:lLunBs/Ym6LB5Z9jYTR76FiuTmxDTDusOGeTQH+WWjE=
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+github.com/wtsi-npg/logshim v1.2.0/go.mod h1:1JRn1t/rlx1/oAtv3LOcshcpjDDvHGHCK8p8ua0Hrss=
+github.com/wtsi-npg/logshim-zerolog v1.2.0 h1:b1HpB1h8OO9XBg/m9r6ycmHRUDNZLnpTmfjWrhmeaT4=
+github.com/wtsi-npg/logshim-zerolog v1.2.0/go.mod h1:xyahqnZDG2utxSUAQKYjgEdzQz74wfPY7+JttEie41k=
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 github.com/zenazn/goji v0.9.0/go.mod h1:7S9M489iMyHBNxwZnk9/EHS098H4/F6TATF2mIxtB1Q=
 golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
@@ -84,37 +44,31 @@ golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9/go.mod h1:LzIPMQfyMNhhGPh
 golang.org/x/mod v0.3.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
 golang.org/x/net v0.0.0-20180906233101-161cd47e91fd/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
 golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
-golang.org/x/net v0.0.0-20190620200207-3b0461eec859 h1:R/3boaszxrf1GEUWTVDzSKVwLmSJpwZ1yqXm8j0v2QI=
 golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
 golang.org/x/net v0.0.0-20200520004742-59133d7f0dd7/go.mod h1:qpuaurCH72eLCgpAm/N6yyVIVM9cpaDIP3A8BGJEC5A=
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-golang.org/x/sync v0.0.0-20190423024810-112230192c58 h1:8gQV6CLnAEikrhgkHFbMAEhagSSnXWGV915qUMm9mrU=
 golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
 golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
 golang.org/x/sys v0.0.0-20180909124046-d0be0721c37e/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
-golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a h1:1BGLXjeY4akVXGgbC9HugT3Jv3hCI0z56oJR5vAMgBU=
 golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
 golang.org/x/sys v0.0.0-20190412213103-97732733099d/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/sys v0.0.0-20190904154756-749cb33beabd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/sys v0.0.0-20191005200804-aed5e4c7ecf9/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
-golang.org/x/sys v0.0.0-20191120155948-bd437916bb0e h1:N7DeIrjYszNmSW409R3frPPwglRwMkXSBzwVbkOjLLA=
 golang.org/x/sys v0.0.0-20191120155948-bd437916bb0e/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/sys v0.0.0-20200323222414-85ca7c5b95cd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
-golang.org/x/sys v0.0.0-20200519105757-fe76b779f299 h1:DYfZAGf2WMFjMxbgTjaC+2HC7NkNAQs+6Q8b9WEB/F4=
-golang.org/x/sys v0.0.0-20200519105757-fe76b779f299/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/sys v0.0.0-20200930185726-fdedc70b468f/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20210112080510-489259a85091 h1:DMyOG0U+gKfu8JZzg2UQe9MeaC1X+xQWlAKcRnjxjCw=
 golang.org/x/sys v0.0.0-20210112080510-489259a85091/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
-golang.org/x/text v0.3.0 h1:g61tztE5qeGQ89tm6NTjjM9VPIm088od1l6aSorWRWg=
 golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
-golang.org/x/text v0.3.2/go.mod h1:bEr9sfX3Q8Zfm5fL9x+3itogRgK3+ptLWKqgva+5dAk=
+golang.org/x/text v0.3.3 h1:cokOdA+Jmi5PJGXLlLllQSgYigAEfHXJAERHVMaCc2k=
 golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ=
 golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
 golang.org/x/tools v0.0.0-20190828213141-aed303cbaa74/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
 golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
 golang.org/x/tools v0.0.0-20201224043029-2b0845dc783e/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA=
-golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7 h1:9zdDQZ7Thm29KFXgAX/+yaf3eVbP7djjWp/dXAppNCc=
 golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
 golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
 golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
@@ -125,16 +79,11 @@ google.golang.org/protobuf v0.0.0-20200228230310-ab0ca4ff8a60/go.mod h1:cfTl7dwQ
 google.golang.org/protobuf v1.20.1-0.20200309200217-e05f789c0967/go.mod h1:A+miEFZTKqfCUM6K7xSMQL9OKL/b6hQv+e19PK+JZNE=
 google.golang.org/protobuf v1.21.0/go.mod h1:47Nbq4nVaFHyn7ilMalzfO3qCViNmqZ2kzikPIcrTAo=
 google.golang.org/protobuf v1.23.0/go.mod h1:EGpADcykh3NcUnDUJcl1+ZksZNG86OlYog2l/sGQquU=
-gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405 h1:yhCVgyC4o1eVCa2tZl7eS0r+SDo693bJlVdllGtEeKM=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
-gopkg.in/fsnotify.v1 v1.4.7 h1:xOHLXZwVvI9hhs+cLKq5+I5onOuwQLhQwiu63xxlHs4=
 gopkg.in/fsnotify.v1 v1.4.7/go.mod h1:Tz8NjZHkW78fSQdbUxIjBTcgA1z1m8ZHf0WmKUhAMys=
 gopkg.in/tomb.v1 v1.0.0-20141024135613-dd632973f1e7 h1:uRGJdciOHaEIrze2W8Q3AKkepLTh2hOroT7a+7czfdQ=
 gopkg.in/tomb.v1 v1.0.0-20141024135613-dd632973f1e7/go.mod h1:dt/ZhP58zS4L8KSrWDmTeBkI65Dw0HsyUHuEVlX15mw=
-gopkg.in/yaml.v2 v2.2.2 h1:ZCJp+EgiOT7lHqUV2J862kp8Qj64Jo6az82+3Td9dZw=
-gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
-gopkg.in/yaml.v2 v2.2.4 h1:/eiJrUcujPVeJ3xlSWaiNi3uSVmDGBK1pDHUHAnao1I=
 gopkg.in/yaml.v2 v2.2.4/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
+gopkg.in/yaml.v2 v2.3.0 h1:clyUAQHOM3G0M3f5vQj7LuJrETvjVot3Z5el9nffUtU=
 gopkg.in/yaml.v2 v2.3.0/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
-gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c h1:dUUwHk2QECo/6vqA44rthZ8ie2QXMNeKRTHCNY2nXvo=
 gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=

helpers_test.go

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved.
+ * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved.
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -28,7 +28,7 @@ import (
 
 	. "github.com/onsi/ginkgo"
 
-	ex "github.com/kjsanger/extendo/v2"
+	ex "github.com/wtsi-npg/extendo/v2"
 )
 
 type itemPathTransform func(i []ex.RodsItem) []string

metadata.go

@@ -25,7 +25,7 @@ import (
 	"os/user"
 	"time"
 
-	dcterms "github.com/kjsanger/extendo/v2/dublincore"
+	dcterms "github.com/wtsi-npg/extendo/v2/dublincore"
 )
 
 const ChecksumAttr string = "md5"

rodsitem.go

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved.
+ * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved.
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -26,7 +26,7 @@ import (
 	"strings"
 	"time"
 
-	logs "github.com/kjsanger/logshim"
+	logs "github.com/wtsi-npg/logshim"
 )
 
 // RodsItem represents both collections and data objects in iRODS. It describes