From 6810871b7e289ef636914bc47db677bbcfde51ed Mon Sep 17 00:00:00 2001 From: Stefan Negru Date: Tue, 16 Jan 2024 13:31:54 +0200 Subject: [PATCH] fix wrong assumption to file start Co-authored-by: Alex Aperis <76202622+aaperis@users.noreply.github.com> --- .../tests/common/50_check_endpoint.sh | 6 ++- .../tests/s3notls/52_check_endpoint.sh | 6 ++- api/sda/sda.go | 7 +++ go.mod | 2 +- go.sum | 45 +++++++++++++++---- 5 files changed, 52 insertions(+), 14 deletions(-) diff --git a/.github/integration/tests/common/50_check_endpoint.sh b/.github/integration/tests/common/50_check_endpoint.sh index edbff75..3f21f83 100755 --- a/.github/integration/tests/common/50_check_endpoint.sh +++ b/.github/integration/tests/common/50_check_endpoint.sh @@ -92,7 +92,7 @@ fi curl --cacert certs/ca.pem -H "Authorization: Bearer $token" "https://localhost:8443/files/urn:neic:001-002?startCoordinate=0&endCoordinate=2" --output test-part.txt -echo "TH" > old-part.txt +dd if=old-file.txt ibs=1 skip=0 count=2 > old-part.txt cmp --silent old-part.txt test-part.txt status=$? @@ -100,11 +100,12 @@ if [[ $status = 0 ]]; then echo "Files are the same" else echo "Files are different" + exit 1 fi curl --cacert certs/ca.pem -H "Authorization: Bearer $token" "https://localhost:8443/files/urn:neic:001-002?startCoordinate=7&endCoordinate=14" --output test-part2.txt -echo "LE IS J" > old-part2.txt +dd if=old-file.txt ibs=1 skip=7 count=7 > old-part2.txt cmp --silent old-part2.txt test-part2.txt status=$? @@ -112,6 +113,7 @@ if [[ $status = 0 ]]; then echo "Files are the same" else echo "Files are different" + exit 1 fi # ------------------ diff --git a/.github/integration/tests/s3notls/52_check_endpoint.sh b/.github/integration/tests/s3notls/52_check_endpoint.sh index b49e0c3..67bdff9 100644 --- a/.github/integration/tests/s3notls/52_check_endpoint.sh +++ b/.github/integration/tests/s3notls/52_check_endpoint.sh @@ -88,7 +88,7 @@ fi curl -H "Authorization: Bearer $token" "http://localhost:8080/files/urn:neic:001-002?startCoordinate=0&endCoordinate=2" --output test-part.txt -echo "TH" > old-part.txt +dd if=old-file.txt ibs=1 skip=0 count=2 > old-part.txt cmp --silent old-part.txt test-part.txt status=$? @@ -96,11 +96,12 @@ if [[ $status = 0 ]]; then echo "Files are the same" else echo "Files are different" + exit 1 fi curl -H "Authorization: Bearer $token" "http://localhost:8080/files/urn:neic:001-002?startCoordinate=7&endCoordinate=14" --output test-part2.txt -echo "LE IS J" > old-part2.txt +dd if=old-file.txt ibs=1 skip=7 count=7 > old-part2.txt cmp --silent old-part2.txt test-part2.txt status=$? @@ -108,6 +109,7 @@ if [[ $status = 0 ]]; then echo "Files are the same" else echo "Files are different" + exit 1 fi # ------------------ diff --git a/api/sda/sda.go b/api/sda/sda.go index 4c5c215..2f7b137 100644 --- a/api/sda/sda.go +++ b/api/sda/sda.go @@ -255,6 +255,13 @@ func Download(c *gin.Context) { // used from: https://github.com/neicnordic/crypt4gh/blob/master/examples/reader/main.go#L48C1-L113C1 var sendStream = func(reader *streaming.Crypt4GHReader, writer http.ResponseWriter, start, end int64) error { + if start != 0 { + // We don't want to read from start, skip ahead to where we should be + if _, err := reader.Seek(start, 0); err != nil { + return err + } + } + // Calculate how much we should read (if given) togo := end - start diff --git a/go.mod b/go.mod index 720dbe8..6e3be27 100644 --- a/go.mod +++ b/go.mod @@ -8,7 +8,7 @@ require ( github.com/dgraph-io/ristretto v0.1.1 github.com/gin-gonic/gin v1.9.1 github.com/google/uuid v1.5.0 - github.com/johannesboyne/gofakes3 v0.0.0-20230129080941-f6a8a9ae6fd3 + github.com/johannesboyne/gofakes3 v0.0.0-20230914150226-f005f5cc03aa github.com/lestrrat-go/jwx/v2 v2.0.19 github.com/lib/pq v1.10.9 github.com/neicnordic/crypt4gh v1.8.8 diff --git a/go.sum b/go.sum index 3150420..29df5c8 100644 --- a/go.sum +++ b/go.sum @@ -2,7 +2,7 @@ filippo.io/edwards25519 v1.1.0 h1:FNf4tywRC1HmFuKW5xopWpigGjJKiJSV0Cqo0cJWDaA= filippo.io/edwards25519 v1.1.0/go.mod h1:BxyFTGdWcka3PhytdK4V28tE5sGfRvvvRV7EaN4VDT4= github.com/DATA-DOG/go-sqlmock v1.5.2 h1:OcvFkGmslmlZibjAjaHm3L//6LiuBgolP7OputlJIzU= github.com/DATA-DOG/go-sqlmock v1.5.2/go.mod h1:88MAG/4G7SMwSE3CeA0ZKzrT5CiOU3OJ+JlNzwDqpNU= -github.com/aws/aws-sdk-go v1.33.0/go.mod h1:5zCpMtNQVjRREroY7sYe8lOMRSxkhG6MZveU8YkpAk0= +github.com/aws/aws-sdk-go v1.44.256/go.mod h1:aVsgQcEevwlmQ7qHE9I3h+dtQgpqhFB+i8Phjh7fkwI= github.com/aws/aws-sdk-go v1.49.21 h1:Rl8KW6HqkwzhATwvXhyr7vD4JFUMi7oXGAw9SrxxIFY= github.com/aws/aws-sdk-go v1.49.21/go.mod h1:LF8svs817+Nz+DmiMQKTO3ubZ/6IaTpq3TjupRn3Eqk= github.com/bytedance/sonic v1.5.0/go.mod h1:ED5hyg4y6t3/9Ku1R6dU/4KyJ48DZ4jPhfY1O2AihPM= @@ -49,7 +49,6 @@ github.com/go-playground/universal-translator v0.18.1 h1:Bcnm0ZwsGyWbCzImXv+pAJn github.com/go-playground/universal-translator v0.18.1/go.mod h1:xekY+UJKNuX9WP91TpwSH2VMlDf28Uj24BCp08ZFTUY= github.com/go-playground/validator/v10 v10.15.2 h1:Ra5cll2/eF8X0Ff2+8SMD7euo2nenQ8WEpgqfy4NhHU= github.com/go-playground/validator/v10 v10.15.2/go.mod h1:9iXMNT7sEkjXb0I+enO7QXmzG6QCsPWY4zveKFVRSyU= -github.com/go-sql-driver/mysql v1.5.0/go.mod h1:DCzpHaOWr8IXmIStZouvnhqoel9Qv2LBy8hT2VhHyBg= github.com/goccy/go-json v0.10.2 h1:CrxCmQqYDkv1z7lO7Wbh2HN93uovUHgrECaO5ZrCXAU= github.com/goccy/go-json v0.10.2/go.mod h1:6MelG93GURQebXPDq3khkgXZkazVtN9CRI+MGFi0w8I= github.com/golang/glog v0.0.0-20160126235308-23def4e6c14b/go.mod h1:SBH7ygxi8pfUlaOkMMuAQtPIUF8ecWP5IEl/CR7VP2Q= @@ -63,13 +62,12 @@ github.com/google/uuid v1.5.0 h1:1p67kYwdtXjb0gL0BPiP1Av9wiZPo5A8z2cWkTZ+eyU= github.com/google/uuid v1.5.0/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo= github.com/hashicorp/hcl v1.0.0 h1:0Anlzjpi4vEasTeNFn2mLJgTSwt0+6sfsiTG8qcWGx4= github.com/hashicorp/hcl v1.0.0/go.mod h1:E5yfLk+7swimpb2L/Alb/PJmXilQ/rhwaUYs4T20WEQ= -github.com/jmespath/go-jmespath v0.3.0/go.mod h1:9QtRXoHjLGCJ5IBSaohpXITPlowMeeYCZ7fLUTSywik= github.com/jmespath/go-jmespath v0.4.0 h1:BEgLn5cpjn8UN1mAw4NjwDrS35OdebyEtFe+9YPoQUg= github.com/jmespath/go-jmespath v0.4.0/go.mod h1:T8mJZnbsbmF+m6zOOFylbeCJqk5+pHWvzYPziyZiYoo= github.com/jmespath/go-jmespath/internal/testify v1.5.1 h1:shLQSRRSCCPj3f2gpwzGwWFoC7ycTf1rcQZHOlsJ6N8= github.com/jmespath/go-jmespath/internal/testify v1.5.1/go.mod h1:L3OGu8Wl2/fWfCI6z80xFu9LTZmf1ZRjMHUOPmWr69U= -github.com/johannesboyne/gofakes3 v0.0.0-20230129080941-f6a8a9ae6fd3 h1:aTscQmvmU/1AS3PqVaNtUtJUwyMexxqVErkhwsWoEpw= -github.com/johannesboyne/gofakes3 v0.0.0-20230129080941-f6a8a9ae6fd3/go.mod h1:Cnosl0cRZIfKjTMuH49sQog2LeNsU5Hf4WnPIDWIDV0= +github.com/johannesboyne/gofakes3 v0.0.0-20230914150226-f005f5cc03aa h1:a6Hc6Hlq6MxPNBW53/S/HnVwVXKc0nbdD/vgnQYuxG0= +github.com/johannesboyne/gofakes3 v0.0.0-20230914150226-f005f5cc03aa/go.mod h1:AxgWC4DDX54O2WDoQO1Ceabtn6IbktjU/7bigor+66g= github.com/json-iterator/go v1.1.12 h1:PV8peI4a0ysnczrg+LtxykD8LfKY9ML6u2jnxaEnrnM= github.com/json-iterator/go v1.1.12/go.mod h1:e30LSqwooZae/UwlEbR2852Gd8hjQvJoHmT4TnhNGBo= github.com/kisielk/sqlstruct v0.0.0-20201105191214-5f3e10d3ab46/go.mod h1:yyMNCyc/Ib3bDTKd379tNMpB/7/H5TjM2Y9QJ5THLbE= @@ -124,7 +122,6 @@ github.com/sagikazarmark/slog-shim v0.1.0 h1:diDBnUNK9N/354PgrxMywXnAwEr1QZcOr6g github.com/sagikazarmark/slog-shim v0.1.0/go.mod h1:SrcSrq8aKtyuqEI1uvTDTK1arOWRIczQRv+GVI1AkeQ= github.com/segmentio/asm v1.2.0 h1:9BQrFxC+YOHJlTlHGkTrFWf59nbL3XnCoFLTwDCI7ys= github.com/segmentio/asm v1.2.0/go.mod h1:BqMnlJP91P8d+4ibuonYZw9mfnzI9HfxselHZr5aAcs= -github.com/shabbyrobe/gocovmerge v0.0.0-20180507124511-f6ea450bfb63/go.mod h1:n+VKSARF5y/tS9XFSP7vWDfS+GUC5vs/YT7M5XDTUEM= github.com/shabbyrobe/gocovmerge v0.0.0-20190829150210-3e036491d500 h1:WnNuhiq+FOY3jNj6JXFT+eLN3CQ/oPIsDPRanvwsmbI= github.com/shabbyrobe/gocovmerge v0.0.0-20190829150210-3e036491d500/go.mod h1:+njLrG5wSeoG4Ds61rFgEzKvenR2UHbjMoDHsczxly0= github.com/sirupsen/logrus v1.9.3 h1:dueUQJ1C2q9oE3F7wvmSGAaVtTmUizReu6fjN8uqzbQ= @@ -160,6 +157,7 @@ github.com/twitchyliquid64/golang-asm v0.15.1 h1:SU5vSMR7hnwNxj24w34ZyCi/FmDZTkS github.com/twitchyliquid64/golang-asm v0.15.1/go.mod h1:a1lVb/DtPvCB8fslRZhAngC2+aY1QWCk3Cedj/Gdt08= github.com/ugorji/go/codec v1.2.11 h1:BMaWp1Bb6fHwEtbplGBGJ498wD+LKlNSl25MjdZY4dU= github.com/ugorji/go/codec v1.2.11/go.mod h1:UNopzCgEMSXjBc6AOMqYvWC1ktqTAfzJZUZgYf6w6lg= +github.com/yuin/goldmark v1.4.13/go.mod h1:6yULJ656Px+3vBD8DxQVa3kxgyrAnzto9xy5taEt/CY= go.etcd.io/bbolt v1.3.5/go.mod h1:G5EMThwa9y8QZGBClrRx5EY+Yw9kAhnjy3bSjsnlVTQ= go.uber.org/atomic v1.9.0 h1:ECmE8Bn/WFTYwEW/bpKD3M8VtR/zQVbavAoalC1PYyE= go.uber.org/atomic v1.9.0/go.mod h1:fEN4uk6kAWBTFdckzkM89CLk9XfWZrxpCo0nPH17wJc= @@ -169,30 +167,59 @@ golang.org/x/arch v0.0.0-20210923205945-b76863e36670/go.mod h1:5om86z9Hs0C8fWVUu golang.org/x/arch v0.4.0 h1:A8WCeEWhLwPBKNbFi5Wv5UTCBx5zzubnXDlMOFAzFMc= golang.org/x/arch v0.4.0/go.mod h1:5om86z9Hs0C8fWVUuoMHwpExlXzs5Tkyp9hOrfG7pp8= golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w= +golang.org/x/crypto v0.0.0-20210921155107-089bfa567519/go.mod h1:GvvjBRRGRdwPK5ydBHafDWAxML/pGHZbMvKqRZ5+Abc= golang.org/x/crypto v0.17.0 h1:r8bRNjWL3GshPW3gkd+RpvzWrZAwPS49OmTGZ/uhM4k= golang.org/x/crypto v0.17.0/go.mod h1:gCAAfMLgwOJRpTjQ2zCCt2OcSfYMTeZVSRtQlPC7Nq4= golang.org/x/exp v0.0.0-20240110193028-0dcbfd608b1e h1:723BNChdd0c2Wk6WOE320qGBiPtYx0F0Bbm1kriShfE= golang.org/x/exp v0.0.0-20240110193028-0dcbfd608b1e/go.mod h1:iRJReGqOEeBhDZGkGbynYwcHlctCvnjTYIamk7uXpHI= -golang.org/x/net v0.0.0-20190213061140-3a22650c66bd/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= +golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4/go.mod h1:jJ57K6gSWd91VN4djpZkiMVwK6gcyfeH4XE8wZrZaV4= +golang.org/x/mod v0.8.0/go.mod h1:iBbtSCu2XBx23ZKBPSOrRkjjQPZFPuis4dIYUhu/chs= +golang.org/x/mod v0.10.0/go.mod h1:iBbtSCu2XBx23ZKBPSOrRkjjQPZFPuis4dIYUhu/chs= golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s= -golang.org/x/net v0.0.0-20200202094626-16171245cfb2/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s= +golang.org/x/net v0.0.0-20210226172049-e18ecbb05110/go.mod h1:m0MpNAwzfU5UDzcl9v0D8zg8gWTRqZa9RBIspLL5mdg= +golang.org/x/net v0.0.0-20220722155237-a158d28d115b/go.mod h1:XRhObCWvk6IyKnWLug+ECip1KBveYUHfp+8e9klMJ9c= +golang.org/x/net v0.1.0/go.mod h1:Cx3nUiGt4eDBEyega/BKRp+/AlGL8hYe7U9odMt2Cco= +golang.org/x/net v0.6.0/go.mod h1:2Tu9+aMcznHK/AK1HMvgo6xiTLG5rD5rZLDS+rp2Bjs= +golang.org/x/net v0.9.0/go.mod h1:d48xBJpPfHeWQsugry2m+kC02ZBRGRgulfHnEXEuWns= golang.org/x/net v0.19.0 h1:zTwKpTd2XuCqf8huc7Fo2iSy+4RHPd10s4KzeTnVr1c= golang.org/x/net v0.19.0/go.mod h1:CfAk/cbD4CthTvqiEl8NpboMuiuOYsAr/7NOjZJtv1U= golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= +golang.org/x/sync v0.0.0-20220722155255-886fb9371eb4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= +golang.org/x/sync v0.1.0/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= golang.org/x/sys v0.0.0-20200202164722-d101bd2416d5/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= +golang.org/x/sys v0.0.0-20201119102817-f84b799fce68/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= +golang.org/x/sys v0.0.0-20210615035016-665e8c7367d1/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= +golang.org/x/sys v0.0.0-20220520151302-bc2c85ada10a/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= +golang.org/x/sys v0.0.0-20220722155257-8c9f86f7a55f/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.0.0-20221010170243-090e33056c14/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= +golang.org/x/sys v0.1.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.5.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.6.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= +golang.org/x/sys v0.7.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.16.0 h1:xWw16ngr6ZMtmxDyKyIgsE93KNKz5HKmMa3b8ALHidU= golang.org/x/sys v0.16.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA= +golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo= +golang.org/x/term v0.0.0-20210927222741-03fcf44c2211/go.mod h1:jbD1KX2456YbFQfuXm/mYQcufACuNUgVhRMnK/tPxf8= +golang.org/x/term v0.1.0/go.mod h1:jbD1KX2456YbFQfuXm/mYQcufACuNUgVhRMnK/tPxf8= +golang.org/x/term v0.5.0/go.mod h1:jMB1sMXY+tzblOD4FWmEbocvup2/aLOaQEp7JmGp78k= +golang.org/x/term v0.7.0/go.mod h1:P32HKFT3hSsZrRxla30E9HqToFYAQPCMs/zFMBUFqPY= golang.org/x/term 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