[mod] Update libgin dependency: 0.3.2

go.mod

@@ -4,7 +4,7 @@ go 1.13
 
 require (
 	github.com/G-Node/git-module v0.8.4-gnode
-	github.com/G-Node/libgin v0.3.1
+	github.com/G-Node/libgin v0.3.2
 	github.com/bgentry/speakeasy v0.1.0 // indirect
 	github.com/denisenkom/go-mssqldb v0.0.0-20191001013358-cfbb681360f0
 	github.com/dustinkirkland/golang-petname v0.0.0-20191129215211-8e5a1ed0cff0
@@ -70,5 +70,3 @@ require (
 	xorm.io/core v0.7.2
 	xorm.io/xorm v0.8.0
 )
-
-// +heroku goVersion go1.13beta1

go.sum

@@ -8,8 +8,8 @@ github.com/G-Node/git-module v0.8.4-gnode h1:BNtyp/2J+zisHObMqrxazJ2fb2ASPu30uN8
 github.com/G-Node/git-module v0.8.4-gnode/go.mod h1:TdKR+8dChXtB7Hw3xS4Bfn5QQenPnihuoWx/vnSnb1k=
 github.com/G-Node/libgin v0.0.0-20191216094436-47f8aadc0067/go.mod h1:2yLXQnNbwjH8mslxnzU8Kb+d7c2Zqo8DIgR6Pgp7lCg=
 github.com/G-Node/libgin v0.3.0/go.mod h1:VjulCBq7k/kgf4Eabk2f4w9SDNowWhLnK+yZvy5Nppk=
-github.com/G-Node/libgin v0.3.1 h1:R6yDRkJ0DlUgD7Y4vZrdKX0DzaTDMYfSbWRm+hw3k3I=
-github.com/G-Node/libgin v0.3.1/go.mod h1:2znNE//YIHBGGXeYCHf0q5+IiOalliAbpG3nGZq9hKY=
+github.com/G-Node/libgin v0.3.2 h1:pbOIm+paF4VqfrTvSu4sPXmo2j5XSOnfxf137uzAHIs=
+github.com/G-Node/libgin v0.3.2/go.mod h1:/2l42QsLZTneVp2LjPoPOWhVjvfbO26atvcbvWA+axI=
 github.com/Shopify/sarama v1.19.0/go.mod h1:FVkBWblsNy7DGZRfXLU0O9RCGt5g3g3yEuWXgklEdEo=
 github.com/Shopify/toxiproxy v2.1.4+incompatible/go.mod h1:OXgGpZ6Cli1/URJOF1DMxUHB2q5Ap20/P/eIdh4G0pI=
 github.com/alecthomas/template v0.0.0-20160405071501-a0175ee3bccc/go.mod h1:LOuyumcjzFXgccqObfd/Ljyb9UuFJ6TxHnclSeseNhc=
@@ -21,6 +21,7 @@ github.com/beorn7/perks v0.0.0-20180321164747-3a771d992973/go.mod h1:Dwedo/Wpr24
 github.com/beorn7/perks v1.0.0/go.mod h1:KWe93zE9D1o94FZ5RNwFwVgaQK1VOXiVxmqh+CedLV8=
 github.com/beorn7/perks v1.0.1 h1:VlbKKnNfV8bJzeqoa4cOKqO6bYr3WgKZxO8Z16+hsOM=
 github.com/beorn7/perks v1.0.1/go.mod h1:G2ZrVWU2WbWT9wwq4/hrbKbnv/1ERSJQ0ibhJ6rlkpw=
+github.com/bgentry/speakeasy v0.1.0 h1:ByYyxL9InA1OWqxJqqp2A5pYHUrCiAL6K3J+LKSsQkY=
 github.com/bgentry/speakeasy v0.1.0/go.mod h1:+zsyZBPWlz7T6j88CTgSN5bM796AkVf0kBD4zp0CCIs=
 github.com/boombuler/barcode v1.0.1-0.20190219062509-6c824513bacc h1:biVzkmvwrH8WK8raXaxBx6fRVTlJILwEwQGL1I/ByEI=
 github.com/boombuler/barcode v1.0.1-0.20190219062509-6c824513bacc/go.mod h1:paBWMcWSl3LHKBqUq+rly7CNSldXjb2rDl3JlRe0mD8=
@@ -36,6 +37,7 @@ github.com/cpuguy83/go-md2man/v2 v2.0.0-20190314233015-f79a8a8ca69d h1:U+s90UTSY
 github.com/cpuguy83/go-md2man/v2 v2.0.0-20190314233015-f79a8a8ca69d/go.mod h1:maD7wRr/U5Z6m/iR4s+kqSMx2CaBsrgA7czyZG/E6dU=
 github.com/cupcake/rdb v0.0.0-20161107195141-43ba34106c76/go.mod h1:vYwsqCOLxGiisLwp9rITslkFNpZD5rz43tf41QFkTWY=
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
+github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/denisenkom/go-mssqldb v0.0.0-20190707035753-2be1aa521ff4/go.mod h1:zAg7JM8CkOJ43xKXIj7eRO9kmWm/TW578qo+oDO6tuM=
 github.com/denisenkom/go-mssqldb v0.0.0-20191001013358-cfbb681360f0 h1:epsH3lb7KVbXHYk7LYGN5EiE0MxcevHU85CKITJ0wUY=
@@ -77,6 +79,7 @@ github.com/go-sql-driver/mysql v1.4.1/go.mod h1:zAC/RDZ24gD3HViQzih4MyKcchzm+sOG
 github.com/go-stack/stack v1.8.0/go.mod h1:v0f6uXyyMGvRgIKkXu+yp6POWl0qKG85gN/melR3HDY=
 github.com/go-xorm/builder v0.3.4 h1:FxkeGB4Cggdw3tPwutLCpfjng2jugfkg6LDMrd/KsoY=
 github.com/go-xorm/builder v0.3.4/go.mod h1:KxkQkNN1DpPKTedxXyTQcmH+rXfvk4LZ9SOOBoZBAxw=
+github.com/go-xorm/sqlfiddle v0.0.0-20180821085327-62ce714f951a h1:9wScpmSP5A3Bk8V3XHWUcJmYTh+ZnlHVyc+A4oZYS3Y=
 github.com/go-xorm/sqlfiddle v0.0.0-20180821085327-62ce714f951a/go.mod h1:56xuuqnHyryaerycW3BfssRdxQstACi0Epw/yC5E2xM=
 github.com/gogo/protobuf v1.1.1/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ=
 github.com/gogo/protobuf v1.2.0/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ=
@@ -103,6 +106,7 @@ github.com/golang/snappy v0.0.0-20180518054509-2e65f85255db/go.mod h1:/XxbfmMg8l
 github.com/golang/snappy v0.0.1/go.mod h1:/XxbfmMg8lxefKM7IXC3fBNl/7bRcc72aCRzEWrmP2Q=
 github.com/google/btree v0.0.0-20180813153112-4030bb1f1f0c/go.mod h1:lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ=
 github.com/google/go-cmp v0.2.0/go.mod h1:oXzfMopK8JAjlY9xF4vHSVASa0yLyX7SntLO5aqRK0M=
+github.com/google/go-cmp v0.3.0 h1:crn/baboCvb5fXaQ0IJ1SGTsTVrWpDsCWC8EGETZijY=
 github.com/google/go-cmp v0.3.0/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU=
 github.com/google/go-github v17.0.0+incompatible h1:N0LgJ1j65A7kfXrZnUDaYCs/Sf4rEjNlfyDHW9dolSY=
 github.com/google/go-github v17.0.0+incompatible/go.mod h1:zLgOLi98H3fifZn+44m+umXrS52loVEgC2AApnigrVQ=
@@ -120,6 +124,7 @@ github.com/gorilla/context v1.1.1/go.mod h1:kBGZzfjB9CEq2AlWe17Uuf7NDRt0dE0s8S51
 github.com/gorilla/mux v1.6.2/go.mod h1:1lud6UwP+6orDFRuTfBEV8e9/aOM/c4fVVCaMa2zaAs=
 github.com/hashicorp/golang-lru v0.5.0/go.mod h1:/m3WP610KZHVQ1SGc6re/UDhFvYD7pJ4Ao+sR/qLZy8=
 github.com/hpcloud/tail v1.0.0/go.mod h1:ab1qPbhIpdTxEkNHXyeSf5vhxWSCs/tWer42PpOxQnU=
+github.com/issue9/assert v1.3.1 h1:L8pRpbnzMIPFJqrMKR/oG03uWrtVeZyYBpI2U2Jx1JE=
 github.com/issue9/assert v1.3.1/go.mod h1:9Ger+iz8X7r1zMYYwEhh++2wMGWcNN2oVI+zIQXxcio=
 github.com/issue9/identicon v1.0.1 h1:pCDfjMDM6xWK0Chxo8Lif+ST/nOEtmXgMITgV1YA9Og=
 github.com/issue9/identicon v1.0.1/go.mod h1:UKNVkUFI68RPz/RlLhsAr1aX6bBSaYEWRHVfdjrMUmk=
@@ -140,8 +145,10 @@ github.com/klauspost/cpuid v1.2.1 h1:vJi+O/nMdFt0vqm8NZBI6wzALWdA2X+egi0ogNyrC/w
 github.com/klauspost/cpuid v1.2.1/go.mod h1:Pj4uuM528wm8OyEC2QMXAi2YiTZ96dNQPGgoMS4s3ek=
 github.com/konsorten/go-windows-terminal-sequences v1.0.1/go.mod h1:T0+1ngSBFLxvqU3pZ+m/2kptfBszLMUkC4ZK/EgS/cQ=
 github.com/kr/logfmt v0.0.0-20140226030751-b84e30acd515/go.mod h1:+0opPa2QZZtGFBFZlji/RkVcI2GknAs/DXo4wKdlNEc=
+github.com/kr/pretty v0.1.0 h1:L/CwN0zerZDmRFUapSPitk6f+Q3+0za1rQkzVuMiMFI=
 github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo=
 github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ=
+github.com/kr/text v0.1.0 h1:45sCR5RtlFHMR4UwH9sdQ5TC8v0qDQCHnXt+kaKSTVE=
 github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI=
 github.com/lib/pq v1.0.0/go.mod h1:5WUZQaWbwv1U+lTReE5YruASi9Al49XbQIvNi/34Woo=
 github.com/lib/pq v1.2.0 h1:LXpIM/LZ5xGFhOpXAQUIMM1HdyqzVYM13zNdjCEEcA0=
@@ -189,6 +196,7 @@ github.com/pelletier/go-toml v1.4.0/go.mod h1:PN7xzY2wHTK0K9p34ErDQMlFxa51Fk0OUr
 github.com/pierrec/lz4 v2.0.5+incompatible/go.mod h1:pdkljMzZIN41W+lC3N2tnIh5sFi+IEE17M5jbnwPHcY=
 github.com/pkg/errors v0.8.0/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
 github.com/pkg/errors v0.8.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
+github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
 github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
 github.com/pquerna/otp v1.2.0 h1:/A3+Jn+cagqayeR3iHs/L62m5ue7710D35zl1zJ1kok=
 github.com/pquerna/otp v1.2.0/go.mod h1:dkJfzwRKNiegxyNb54X/3fLwhCynbMspSyWKnvi1AEg=
@@ -216,6 +224,7 @@ github.com/russross/blackfriday v1.5.2 h1:HyvC0ARfnZBqnXwABFeSZHpKvJHJJfPz81GNue
 github.com/russross/blackfriday v1.5.2/go.mod h1:JO/DiYxRf+HjHt06OyowR9PTA263kcR/rfWxYHBV53g=
 github.com/russross/blackfriday/v2 v2.0.1 h1:lPqVAte+HuHNfhJ/0LC98ESWRz8afy9tM/0RK8m9o+Q=
 github.com/russross/blackfriday/v2 v2.0.1/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=
+github.com/saintfish/chardet v0.0.0-20120816061221-3af4cd4741ca h1:NugYot0LIVPxTvN8n+Kvkn6TrbMyxQiuvKdEwFdR9vI=
 github.com/saintfish/chardet v0.0.0-20120816061221-3af4cd4741ca/go.mod h1:uugorj2VCxiV1x+LzaIdVa9b4S4qGAcH6cbhh4qVxOU=
 github.com/satori/go.uuid v1.2.0 h1:0uYX9dsZ2yD7q2RtLRtPSdGDWzjeM3TbMJP9utgA0ww=
 github.com/satori/go.uuid v1.2.0/go.mod h1:dA0hQrYB0VpLJoorglMZABFdXlWrHn1NEOzdhQKdks0=
@@ -243,6 +252,7 @@ github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+
 github.com/stretchr/objx v0.1.1/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
 github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs=
 github.com/stretchr/testify v1.3.0/go.mod h1:M5WIy9Dh21IEIfnGCwXGc5bZfKNJtfHm1UVUgZn+9EI=
+github.com/stretchr/testify v1.4.0 h1:2E4SXV/wtOkTonXsotYi4li6zVWxYlZuYNCXe9XRJyk=
 github.com/stretchr/testify v1.4.0/go.mod h1:j7eGeouHqKxXV5pUuKE4zz7dFj8WfuZ+81PSLYec5m4=
 github.com/syndtr/goleveldb v1.0.0/go.mod h1:ZVVdQEZoIme9iO1Ch2Jdy24qqXrMMOU6lpPAyBWyWuQ=
 github.com/unknwon/cae v1.0.0 h1:i39lOFaBXZxhGjQOy/RNbi8uzettCs6OQxpR0xXohGU=
@@ -256,6 +266,7 @@ github.com/unknwon/paginater v0.0.0-20170405233947-45e5d631308e h1:Qf3QQl/zmEbWD
 github.com/unknwon/paginater v0.0.0-20170405233947-45e5d631308e/go.mod h1:TBwoao3Q4Eb/cp+dHbXDfRTrZSsj/k7kLr2j1oWRWC0=
 github.com/urfave/cli v1.22.1 h1:+mkCCcOFKPnCmVYVcURKps1Xe+3zP90gSYGNfRkjoIY=
 github.com/urfave/cli v1.22.1/go.mod h1:Gos4lmkARVdJ6EkW0WaNv/tZAAMe9V7XWyB60NtXRu0=
+github.com/ziutek/mymysql v1.5.4 h1:GB0qdRGsTwQSBVYuVShFBKaXSnSnYYC2d9knnE1LHFs=
 github.com/ziutek/mymysql v1.5.4/go.mod h1:LMSpPZ6DbqWFxNCHW77HeMg9I646SAhApZ/wKdgO/C0=
 go.opencensus.io v0.20.1/go.mod h1:6WKK9ahsWS3RSO+PY9ZHZUfv2irvY6gN279GOPZjmmk=
 golang.org/x/crypto v0.0.0-20180904163835-0709b304e793/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4=
@@ -339,6 +350,7 @@ gopkg.in/asn1-ber.v1 v1.0.0-20181015200546-f715ec2f112d/go.mod h1:cuepJuh7vyXfUy
 gopkg.in/bufio.v1 v1.0.0-20140618132640-567b2bfa514e h1:wGA78yza6bu/mWcc4QfBuIEHEtc06xdiU0X8sY36yUU=
 gopkg.in/bufio.v1 v1.0.0-20140618132640-567b2bfa514e/go.mod h1:xsQCaysVCudhrYTfzYWe577fCe7Ceci+6qjO2Rdc0Z4=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127 h1:qIbj1fsPNlZgppZ+VLlY7N33q108Sa+fhmuc+sWQYwY=
 gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/clog.v1 v1.2.0 h1:BHfwHRNQy497iBNsRBassPixSAxRbn2z5KVkdBFbwxc=
 gopkg.in/clog.v1 v1.2.0/go.mod h1:L6fgdpdhFgKX4eGuDvt+N6X2GwZE160NRrIHzvaF8ZM=

vendor/github.com/G-Node/libgin/libgin/doi.go

@@ -1,10 +1,8 @@
 package libgin
 
 import (
-	"bytes"
 	"crypto/md5"
 	"encoding/hex"
-	"encoding/xml"
 	"fmt"
 	"log"
 	"net/http"
@@ -15,9 +13,12 @@ import (
 
 // NOTE: TEMPORARY COPIES FROM gin-doi
 
-// uuidMap is a map between registered repositories and their UUIDs for datasets registered before the new UUID generation method was implemented.
-// This map is required because the current method of computing UUIDs differs from the older method and this lookup is used to handle the old-method UUIDs.
-var uuidMap = map[string]string{
+// UUIDMap is a map between registered repositories and their UUIDs for
+// datasets registered before the new UUID generation method was implemented.
+// This map is required because the current method of computing UUIDs differs
+// from the older method and this lookup is used to handle the old-method
+// UUIDs.
+var UUIDMap = map[string]string{
 	"INT/multielectrode_grasp":                   "f83565d148510fede8a277f660e1a419",
 	"ajkumaraswamy/HB-PAC_disinhibitory_network": "1090f803258557299d287c4d44a541b2",
 	"steffi/Kleineidam_et_al_2017":               "f53069de4c4921a3cfa8f17d55ef98bb",
@@ -27,7 +28,7 @@ var uuidMap = map[string]string{
 
 // RepoPathToUUID computes a UUID from a repository path.
 func RepoPathToUUID(URI string) string {
-	if doi, ok := uuidMap[URI]; ok {
+	if doi, ok := UUIDMap[URI]; ok {
 		return doi
 	}
 	currMd5 := md5.Sum([]byte(URI))
@@ -45,18 +46,21 @@ type DOIRequestData struct {
 
 // DOIRegInfo holds all the metadata and information necessary for a DOI registration request.
 type DOIRegInfo struct {
-	Missing      []string
-	DOI          string
-	UUID         string
-	FileSize     int64
-	Title        string
-	Authors      []Author
-	Description  string
-	Keywords     []string
-	References   []Reference
-	Funding      []string
-	License      *License
-	ResourceType string
+	Missing         []string
+	DOI             string
+	UUID            string
+	FileName        string
+	FileSize        string
+	Title           string
+	Authors         []Author
+	Description     string
+	Keywords        []string
+	References      []Reference
+	Funding         []string
+	License         *License
+	ResourceType    string
+	DateTime        time.Time
+	TemplateVersion string
 }
 
 func (c *DOIRegInfo) GetType() string {
@@ -75,17 +79,15 @@ func (c *DOIRegInfo) GetCitation() string {
 			authors += fmt.Sprintf("%s, ", auth.LastName)
 		}
 	}
-	return fmt.Sprintf("%s (%d) %s. G-Node. doi:%s", authors, time.Now().Year(), c.Title, c.DOI)
+	return fmt.Sprintf("%s (%s) %s. G-Node. doi:%s", authors, c.Year(), c.Title, c.DOI)
 }
 
-func (c *DOIRegInfo) EscXML(txt string) string {
-	buf := new(bytes.Buffer)
-	if err := xml.EscapeText(buf, []byte(txt)); err != nil {
-		log.Printf("Could not escape: %s :: %s", txt, err.Error())
-		return ""
-	}
-	return buf.String()
+func (c *DOIRegInfo) Year() string {
+	return fmt.Sprintf("%d", c.DateTime.Year())
+}
 
+func (c *DOIRegInfo) ISODate() string {
+	return c.DateTime.Format("2006-01-02")
 }
 
 type Author struct {
@@ -119,9 +121,37 @@ type NamedIdentifier struct {
 }
 
 type Reference struct {
-	Reftype string
-	Name    string
-	ID      string
+	Reftype  string
+	Name     string
+	Citation string
+	ID       string
+}
+
+func (ref Reference) GetURL() string {
+	idparts := strings.SplitN(ref.ID, ":", 2)
+	if len(idparts) != 2 {
+		// Malformed ID (no colon)
+		return ""
+	}
+	source := idparts[0]
+	idnum := idparts[1]
+
+	var prefix string
+	switch strings.ToLower(source) {
+	case "doi":
+		prefix = "https://doi.org/"
+	case "arxiv":
+		// https://arxiv.org/help/arxiv_identifier_for_services
+		prefix = "https://arxiv.org/abs/"
+	case "pmid":
+		// https://www.ncbi.nlm.nih.gov/books/NBK3862/#linkshelp.Retrieve_PubMed_Citations
+		prefix = "https://www.ncbi.nlm.nih.gov/pubmed/"
+	default:
+		// Return an empty string to make the reflink inactive
+		return ""
+	}
+
+	return fmt.Sprintf("%s%s", prefix, idnum)
 }
 
 type License struct {

vendor/modules.txt

@@ -1,6 +1,6 @@
 # github.com/G-Node/git-module v0.8.4-gnode
 github.com/G-Node/git-module
-# github.com/G-Node/libgin v0.3.1
+# github.com/G-Node/libgin v0.3.2
 github.com/G-Node/libgin/libgin
 github.com/G-Node/libgin/libgin/annex
 github.com/G-Node/libgin/libgin/gig