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Refactor/use mainline scicatcli #50

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merged 2 commits into from
Jan 7, 2025
Merged

Refactor/use mainline scicatcli #50

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92d8272
use scicat-cli for scicat communication
consolethinks Dec 18, 2024
3146d76
update scicat-cli dependency
consolethinks Dec 18, 2024
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2 changes: 2 additions & 0 deletions api/openapi.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -373,6 +373,8 @@ components:
metaData:
type: string
description: The metadata of the dataset.
required:
- metaData
PostDatasetResponse:
type: object
properties:
Expand Down
14 changes: 7 additions & 7 deletions go.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ require (
github.com/oapi-codegen/gin-middleware v1.0.2
github.com/oapi-codegen/oapi-codegen/v2 v2.3.0
github.com/oapi-codegen/runtime v1.1.1
github.com/paulscherrerinstitute/scicat-cli/v3 v3.0.0-alpha3.0.20240923114554-40b0ae5da12e
github.com/paulscherrerinstitute/scicat-cli/v3 v3.0.0-alpha3.0.20241104135519-f2e1a334d152
github.com/spf13/viper v1.19.0
github.com/swaggo/files v1.0.1
github.com/swaggo/gin-swagger v1.6.0
Expand Down Expand Up @@ -136,14 +136,14 @@ require (
github.com/wailsapp/go-webview2 v1.0.16 // indirect
github.com/wailsapp/mimetype v1.4.1 // indirect
golang.org/x/arch v0.10.0 // indirect
golang.org/x/crypto v0.27.0 // indirect
golang.org/x/exp v0.0.0-20230905200255-921286631fa9 // indirect
golang.org/x/crypto v0.28.0 // indirect
golang.org/x/exp v0.0.0-20241009180824-f66d83c29e7c // indirect
golang.org/x/mod v0.21.0 // indirect
golang.org/x/net v0.29.0 // indirect
golang.org/x/net v0.30.0 // indirect
golang.org/x/sync v0.8.0 // indirect
golang.org/x/sys v0.25.0 // indirect
golang.org/x/text v0.18.0 // indirect
golang.org/x/tools v0.25.0 // indirect
golang.org/x/sys v0.26.0 // indirect
golang.org/x/text v0.19.0 // indirect
golang.org/x/tools v0.26.0 // indirect
google.golang.org/protobuf v1.34.2 // indirect
gopkg.in/yaml.v2 v2.4.0 // indirect
)
Expand Down
16 changes: 16 additions & 0 deletions go.sum
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -266,6 +266,10 @@ github.com/oapi-codegen/runtime v1.1.1 h1:EXLHh0DXIJnWhdRPN2w4MXAzFyE4CskzhNLUmt
github.com/oapi-codegen/runtime v1.1.1/go.mod h1:SK9X900oXmPWilYR5/WKPzt3Kqxn/uS/+lbpREv+eCg=
github.com/paulscherrerinstitute/scicat-cli/v3 v3.0.0-alpha3.0.20240923114554-40b0ae5da12e h1:11aZpGkmjsANwEr3LG3fAhIvySK7rwOyve1IDOH/MhI=
github.com/paulscherrerinstitute/scicat-cli/v3 v3.0.0-alpha3.0.20240923114554-40b0ae5da12e/go.mod h1:MXUPH5xJe/5ZydWzB+UaTwyfNDCxVAG10hXgrTlkRLw=
github.com/paulscherrerinstitute/scicat-cli/v3 v3.0.0-alpha3.0.20241104135519-f2e1a334d152 h1:TOoDq3+wA87HxX42tM62N36ZcWisYinXjdBRLzFHbg4=
github.com/paulscherrerinstitute/scicat-cli/v3 v3.0.0-alpha3.0.20241104135519-f2e1a334d152/go.mod h1:0isvmkPG0GVviHOaTk+PrenP6NaPqzHjaKcJo9J+VYE=
github.com/paulscherrerinstitute/scicat-cli/v3 v3.0.0-alpha3.0.20241104135519-ff8966010bde h1:zdM+5QFYrp+tnRqPxjJ929U0RbBqWT9AnQCc1dBiciY=
github.com/paulscherrerinstitute/scicat-cli/v3 v3.0.0-alpha3.0.20241104135519-ff8966010bde/go.mod h1:MXUPH5xJe/5ZydWzB+UaTwyfNDCxVAG10hXgrTlkRLw=
github.com/pelletier/go-toml/v2 v2.2.3 h1:YmeHyLY8mFWbdkNWwpr+qIL2bEqT0o95WSdkNHvL12M=
github.com/pelletier/go-toml/v2 v2.2.3/go.mod h1:MfCQTFTvCcUyyvvwm1+G6H/jORL20Xlb6rzQu9GuUkc=
github.com/perimeterx/marshmallow v1.1.5 h1:a2LALqQ1BlHM8PZblsDdidgv1mWi1DgC2UmX50IvK2s=
Expand Down Expand Up @@ -370,6 +374,8 @@ golang.org/x/crypto v0.0.0-20191011191535-87dc89f01550/go.mod h1:yigFU9vqHzYiE8U
golang.org/x/crypto v0.0.0-20210921155107-089bfa567519/go.mod h1:GvvjBRRGRdwPK5ydBHafDWAxML/pGHZbMvKqRZ5+Abc=
golang.org/x/crypto v0.27.0 h1:GXm2NjJrPaiv/h1tb2UH8QfgC/hOf/+z0p6PT8o1w7A=
golang.org/x/crypto v0.27.0/go.mod h1:1Xngt8kV6Dvbssa53Ziq6Eqn0HqbZi5Z6R0ZpwQzt70=
golang.org/x/crypto v0.28.0 h1:GBDwsMXVQi34v5CCYUm2jkJvu4cbtru2U4TN2PSyQnw=
golang.org/x/crypto v0.28.0/go.mod h1:rmgy+3RHxRZMyY0jjAJShp2zgEdOqj2AO7U0pYmeQ7U=
golang.org/x/exp v0.0.0-20190121172915-509febef88a4/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
golang.org/x/exp v0.0.0-20190306152737-a1d7652674e8/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
golang.org/x/exp v0.0.0-20190510132918-efd6b22b2522/go.mod h1:ZjyILWgesfNpC6sMxTJOJm9Kp84zZh5NQWvqDGG3Qr8=
Expand All @@ -380,6 +386,8 @@ golang.org/x/exp v0.0.0-20191227195350-da58074b4299/go.mod h1:2RIsYlXP63K8oxa1u0
golang.org/x/exp v0.0.0-20200207192155-f17229e696bd/go.mod h1:J/WKrq2StrnmMY6+EHIKF9dgMWnmCNThgcyBT1FY9mM=
golang.org/x/exp v0.0.0-20230905200255-921286631fa9 h1:GoHiUyI/Tp2nVkLI2mCxVkOjsbSXD66ic0XW0js0R9g=
golang.org/x/exp v0.0.0-20230905200255-921286631fa9/go.mod h1:S2oDrQGGwySpoQPVqRShND87VCbxmc6bL1Yd2oYrm6k=
golang.org/x/exp v0.0.0-20241009180824-f66d83c29e7c h1:7dEasQXItcW1xKJ2+gg5VOiBnqWrJc+rq0DPKyvvdbY=
golang.org/x/exp v0.0.0-20241009180824-f66d83c29e7c/go.mod h1:NQtJDoLvd6faHhE7m4T/1IY708gDefGGjR/iUW8yQQ8=
golang.org/x/image v0.0.0-20190227222117-0694c2d4d067/go.mod h1:kZ7UVZpmo3dzQBMxlp+ypCbDeSB+sBbTgSJuh5dn5js=
golang.org/x/image v0.0.0-20190802002840-cff245a6509b/go.mod h1:FeLwcggjj3mMvU+oOTbSwawSJRM1uh48EjtB4UJZlP0=
golang.org/x/lint v0.0.0-20181026193005-c67002cb31c3/go.mod h1:UVdnD1Gm6xHRNCYTkRU2/jEulfH38KcIWyp/GAMgvoE=
Expand Down Expand Up @@ -419,6 +427,8 @@ golang.org/x/net v0.0.0-20220722155237-a158d28d115b/go.mod h1:XRhObCWvk6IyKnWLug
golang.org/x/net v0.7.0/go.mod h1:2Tu9+aMcznHK/AK1HMvgo6xiTLG5rD5rZLDS+rp2Bjs=
golang.org/x/net v0.29.0 h1:5ORfpBpCs4HzDYoodCDBbwHzdR5UrLBZ3sOnUJmFoHo=
golang.org/x/net v0.29.0/go.mod h1:gLkgy8jTGERgjzMic6DS9+SP0ajcu6Xu3Orq/SpETg0=
golang.org/x/net v0.30.0 h1:AcW1SDZMkb8IpzCdQUaIq2sP4sZ4zw+55h6ynffypl4=
golang.org/x/net v0.30.0/go.mod h1:2wGyMJ5iFasEhkwi13ChkO/t1ECNC4X4eBKkVFyYFlU=
golang.org/x/oauth2 v0.0.0-20180821212333-d2e6202438be/go.mod h1:N/0e6XlmueqKjAGxoOufVs8QHGRruUQn6yWY3a++T0U=
golang.org/x/oauth2 v0.0.0-20190226205417-e64efc72b421/go.mod h1:gOpvHmFTYa4IltrdGE7lF6nIHvwfUNPOp7c8zoXwtLw=
golang.org/x/oauth2 v0.0.0-20190604053449-0f29369cfe45/go.mod h1:gOpvHmFTYa4IltrdGE7lF6nIHvwfUNPOp7c8zoXwtLw=
Expand Down Expand Up @@ -460,6 +470,8 @@ 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 v0.25.0 h1:r+8e+loiHxRqhXVl6ML1nO3l1+oFoWbnlu2Ehimmi34=
golang.org/x/sys v0.25.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
golang.org/x/sys v0.26.0 h1:KHjCJyddX0LoSTb3J+vWpupP9p0oznkqVk/IfjymZbo=
golang.org/x/sys v0.26.0/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 v0.5.0/go.mod h1:jMB1sMXY+tzblOD4FWmEbocvup2/aLOaQEp7JmGp78k=
Expand All @@ -475,6 +487,8 @@ golang.org/x/text v0.3.7/go.mod h1:u+2+/6zg+i71rQMx5EYifcz6MCKuco9NR6JIITiCfzQ=
golang.org/x/text v0.7.0/go.mod h1:mrYo+phRRbMaCq/xk9113O4dZlRixOauAjOtrjsXDZ8=
golang.org/x/text v0.18.0 h1:XvMDiNzPAl0jr17s6W9lcaIhGUfUORdGCNsuLmPG224=
golang.org/x/text v0.18.0/go.mod h1:BuEKDfySbSR4drPmRPG/7iBdf8hvFMuRexcpahXilzY=
golang.org/x/text v0.19.0 h1:kTxAhCbGbxhK0IwgSKiMO5awPoDQ0RpfiVYBfK860YM=
golang.org/x/text v0.19.0/go.mod h1:BuEKDfySbSR4drPmRPG/7iBdf8hvFMuRexcpahXilzY=
golang.org/x/time v0.0.0-20181108054448-85acf8d2951c/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ=
golang.org/x/time v0.0.0-20190308202827-9d24e82272b4/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ=
golang.org/x/time v0.5.0 h1:o7cqy6amK/52YcAKIPlM3a+Fpj35zvRj2TP+e1xFSfk=
Expand Down Expand Up @@ -506,6 +520,8 @@ golang.org/x/tools v0.0.0-20200212150539-ea181f53ac56/go.mod h1:TB2adYChydJhpapK
golang.org/x/tools v0.1.12/go.mod h1:hNGJHUnrk76NpqgfD5Aqm5Crs+Hm0VOH/i9J2+nxYbc=
golang.org/x/tools v0.25.0 h1:oFU9pkj/iJgs+0DT+VMHrx+oBKs/LJMV+Uvg78sl+fE=
golang.org/x/tools v0.25.0/go.mod h1:/vtpO8WL1N9cQC3FN5zPqb//fRXskFHbLKk4OW1Q7rg=
golang.org/x/tools v0.26.0 h1:v/60pFQmzmT9ExmjDv2gGIfi3OqfKoEP6I5+umXlbnQ=
golang.org/x/tools v0.26.0/go.mod h1:TPVVj70c7JJ3WCazhD8OdXcZg/og+b9+tH/KxylGwH0=
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=
Expand Down
42 changes: 22 additions & 20 deletions internal/core/ingestdataset.go
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ import (
"context"
"crypto/tls"
"errors"
"fmt"
"log"
"net/http"
"os"
Expand All @@ -13,12 +14,14 @@ import (
"time"

"github.com/SwissOpenEM/Ingestor/internal/metadataextractor"
"github.com/SwissOpenEM/Ingestor/internal/scicat"
"github.com/SwissOpenEM/Ingestor/internal/task"
"github.com/fatih/color"
"github.com/paulscherrerinstitute/scicat-cli/v3/datasetIngestor"
"github.com/paulscherrerinstitute/scicat-cli/v3/datasetUtils"
)

const MAX_FILES = 400000

func createLocalSymlinkCallbackForFileLister(skipSymlinks *string, skippedLinks *uint) func(symlinkPath string, sourceFolder string) (bool, error) {
scanner := bufio.NewScanner(os.Stdin)
return func(symlinkPath string, sourceFolder string) (bool, error) {
Expand Down Expand Up @@ -129,10 +132,6 @@ func IngestDataset(
user := map[string]string{
"accessToken": config.Scicat.AccessToken,
}
_, accessGroups, err := scicat.ExtractUserInfo(http_client, SCICAT_API_URL, user["accessToken"])
if err != nil {
return "", err
}

datasetFolder := ingestionTask.DatasetFolder.FolderPath

Expand All @@ -152,8 +151,13 @@ func IngestDataset(
}
}

fullUser, accessGroups, err := datasetUtils.GetUserInfoFromToken(http_client, SCICAT_API_URL, config.Scicat.AccessToken)
if err != nil {
return "", err
}

// check if dataset already exists (identified by source folder)
_, _, err = scicat.CheckMetadata(http_client, SCICAT_API_URL, metaDataMap, user, accessGroups)
_, _, err = datasetIngestor.CheckMetadata(http_client, SCICAT_API_URL, metaDataMap, fullUser, accessGroups)
if err != nil {
return "", err
}
Expand All @@ -165,16 +169,19 @@ func IngestDataset(

// collect (local) files
fullFileArray, startTime, endTime, owner, numFiles, totalSize, err := datasetIngestor.GetLocalFileList(datasetFolder, DATASETFILELISTTXT, localSymlinkCallback, localFilepathFilterCallback)
_ = numFiles
_ = totalSize
_ = startTime
_ = endTime
_ = owner
_ = fullFileArray
if err != nil {
log.Printf("")
return "", err
}

// size & filecount checks
if totalSize == 0 {
return "", errors.New("can't ingest: the total size of the dataset is 0")
}
if numFiles > MAX_FILES {
return "", fmt.Errorf("can't ingest: the number of files (%d) exceeds the max. allowed (%d)", numFiles, MAX_FILES)
}

originalMetaDataMap := map[string]string{}
datasetIngestor.UpdateMetaData(http_client, SCICAT_API_URL, user, originalMetaDataMap, metaDataMap, startTime, endTime, owner, TAPECOPIES)

Expand All @@ -188,14 +195,9 @@ func IngestDataset(
metaDataMap["datasetlifecycle"].(map[string]interface{})["archiveStatusMessage"] = "filesNotYetAvailable"
metaDataMap["datasetlifecycle"].(map[string]interface{})["archivable"] = false

datasetId, err := scicat.CreateDataset(http_client, SCICAT_API_URL, metaDataMap, user)
if err != nil {
return "", err
}
err = scicat.CreateOrigDatablocks(http_client, SCICAT_API_URL, fullFileArray, datasetId, user)
if err != nil {
return "", err
}
datasetId, err := datasetIngestor.IngestDataset(http_client, SCICAT_API_URL, metaDataMap, fullFileArray, user)

// TODO: add attachments here if it's going to be needed

switch ingestionTask.TransferMethod {
case task.TransferS3:
Expand Down
5 changes: 0 additions & 5 deletions internal/scicat/consts.go
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60 changes: 0 additions & 60 deletions internal/scicat/datablock.go
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112 changes: 0 additions & 112 deletions internal/scicat/dataset.go
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