diff --git a/README.md b/README.md index 96c57f7..794811a 100644 --- a/README.md +++ b/README.md @@ -79,3 +79,11 @@ needs to have GRPC install. To install, run: ``` pip install grpcio-tools ``` + +## Go Tests + +Run go tests with +``` +go clean -testcache +go test ./test/... -v +``` \ No newline at end of file diff --git a/cmd/graphmanifest/main.go b/cmd/graphmanifest/main.go deleted file mode 100644 index 7270035..0000000 --- a/cmd/graphmanifest/main.go +++ /dev/null @@ -1,35 +0,0 @@ -package graphmanifest - -import ( - "encoding/json" - "fmt" - - "github.com/spf13/cobra" -) - -var workerCount = 1 - -// Cmd is the declaration of the command line -var Cmd = &cobra.Command{ - Use: "graph-manifest ", - Short: "Build manifest for graph file archive", - Long: `Build manifest for graph file archive. -Only works on .Vertex.json.gz and .Edge.json.gz files`, - Args: cobra.MinimumNArgs(1), - RunE: func(cmd *cobra.Command, args []string) error { - for info := range ScanDir(args[0], workerCount) { - o, _ := json.Marshal(info) - fmt.Printf("%s\n", o) - } - return nil - }, -} - -func init() { - flags := Cmd.Flags() - flags.IntVarP(&workerCount, "workers", "n", workerCount, "Worker Count") - //flags.BoolVar(&runOnce, "run-once", false, "Only Run if database is unintialized") - //flags.StringVar(&graph, "graph", graph, "Destination Graph") - //flags.StringVar(&workDir, "workdir", workDir, "Workdir") - //flags.StringVar(&gripServer, "server", gripServer, "Destination Server") -} diff --git a/cmd/graphmanifest/scan.go b/cmd/graphmanifest/scan.go deleted file mode 100644 index fe057d7..0000000 --- a/cmd/graphmanifest/scan.go +++ /dev/null @@ -1,172 +0,0 @@ -package graphmanifest - -import ( - "bufio" - "compress/gzip" - "encoding/json" - "fmt" - "log" - "os" - "path/filepath" - "strings" - "sync" -) - -func joinMapKeys(s map[string]bool) string { - o := []string{} - for k := range s { - o = append(o, k) - } - return strings.Join(o, ",") -} - -func mapKeys(s map[string]bool) []string { - o := []string{} - for k := range s { - o = append(o, k) - } - return o -} - -type FileInfo struct { - FileType string `json:"fileType"` - Path string `json:"path"` - Gid *string `json:"gid,omitempty"` - FromGid *string `json:"fromGid,omitempty"` - ToGid *string `json:"toGid,omitempty"` - Labels []string `json:"labels"` -} - -func fileScanner(path string) (FileInfo, error) { - if strings.HasSuffix(path, ".Vertex.json.gz") { - log.Printf("Scanning %s", path) - fr, err := os.Open(path) - defer fr.Close() - if err != nil { - return FileInfo{}, err - } - gr, _ := gzip.NewReader(fr) - scanner := bufio.NewScanner(gr) - bufferSize := 32 * 1024 * 1024 - buffer := make([]byte, bufferSize) - scanner.Buffer(buffer, bufferSize) - - labels := map[string]bool{} - gidSubStr := "" - for scanner.Scan() { - d := map[string]interface{}{} - err := json.Unmarshal([]byte(scanner.Text()), &d) - if err == nil { - gid := d["gid"].(string) - label := d["label"].(string) - labels[label] = true - if gidSubStr == "" { - gidSubStr = gid - } else { - i := 0 - for ; i < len(gid) && i < len(gidSubStr) && gid[i] == gidSubStr[i]; i++ { - } - if i > 2 && i != len(gidSubStr) { - gidSubStr = gid[:i] - } - } - } - } - return FileInfo{FileType: "vertex", Path: path, Gid: &gidSubStr, Labels: mapKeys(labels)}, nil - } else if strings.HasSuffix(path, ".Edge.json.gz") { - log.Printf("Scanning %s", path) - fr, err := os.Open(path) - defer fr.Close() - if err != nil { - return FileInfo{}, err - } - gr, _ := gzip.NewReader(fr) - scanner := bufio.NewScanner(gr) - bufferSize := 32 * 1024 * 1024 - buffer := make([]byte, bufferSize) - scanner.Buffer(buffer, bufferSize) - - labels := map[string]bool{} - toGidSubStr := "" - fromGidSubStr := "" - for scanner.Scan() { - d := map[string]interface{}{} - err := json.Unmarshal([]byte(scanner.Text()), &d) - if err == nil { - var toGid, fromGid, label string - if t, ok := d["to"]; ok { - if toGid, ok = t.(string); !ok { - log.Printf("to is not string in %s", d) - } - } else { - log.Printf("to not found in %s", d) - } - fromGid = d["from"].(string) - label = d["label"].(string) - labels[label] = true - if toGidSubStr == "" { - toGidSubStr = toGid - } else { - i := 0 - for ; i < len(toGid) && i < len(toGidSubStr) && toGid[i] == toGidSubStr[i]; i++ { - } - if i > 2 && i != len(toGidSubStr) { - toGidSubStr = toGid[:i] - } - } - if fromGidSubStr == "" { - fromGidSubStr = fromGid - } else { - i := 0 - for ; i < len(fromGid) && i < len(fromGidSubStr) && fromGid[i] == fromGidSubStr[i]; i++ { - } - if i > 2 && i != len(fromGidSubStr) { - fromGidSubStr = fromGid[:i] - } - } - } - } - return FileInfo{FileType: "edge", Path: path, FromGid: &fromGidSubStr, ToGid: &toGidSubStr, Labels: mapKeys(labels)}, nil - } - return FileInfo{}, fmt.Errorf("Unknown file suffix: %s", path) -} - -func ScanDir(path string, workerCount int) chan FileInfo { - if workerCount < 1 { - workerCount = 1 - } - if workerCount > 50 { - workerCount = 50 - } - - out := make(chan FileInfo, workerCount) - fileNames := make(chan string, workerCount) - - wg := &sync.WaitGroup{} - for i := 0; i < workerCount; i++ { - wg.Add(1) - go func() { - for n := range fileNames { - if o, err := fileScanner(n); err == nil { - out <- o - } - } - wg.Done() - }() - } - - go func() { - wg.Wait() - close(out) - }() - - go func() { - defer close(fileNames) - filepath.Walk(path, func(path string, info os.FileInfo, err error) error { - fileNames <- path - return nil - }) - }() - - return out -} diff --git a/cmd/manifest/main.go b/cmd/manifest/main.go deleted file mode 100644 index d307d6d..0000000 --- a/cmd/manifest/main.go +++ /dev/null @@ -1,88 +0,0 @@ -package manifest - -import ( - "fmt" - //"log" - //"io/ioutil" - - //"github.com/bmeg/sifter/steps" - "github.com/bmeg/sifter/manifest" - - "github.com/spf13/cobra" -) - -// CheckCmd is the declaration of the command line -var CheckCmd = &cobra.Command{ - Use: "check", - Short: "Check files against manifest", - Args: cobra.MinimumNArgs(1), - RunE: func(cmd *cobra.Command, args []string) error { - - man, err := manifest.Load(args[0]) - if err != nil { - return err - } - for _, ent := range man.Entries { - state := "MISSING" - fileMD5 := "" - if ent.Exists() { - state = "OK" - if m, err := ent.CalcMD5(); err == nil { - fileMD5 = m - } else { - fileMD5 = "ERROR" - } - } - manMD5 := ent.MD5 - if ent.MD5 == "" { - manMD5 = "NoMD5" - } - if state == "OK" { - if manMD5 != fileMD5 { - state = "MD5-Change" - } - } - fmt.Printf("%s\t%s\t%s\t%s\n", ent.Path, state, fileMD5, manMD5) - } - return nil - }, -} - -var SumCmd = &cobra.Command{ - Use: "sum", - Short: "Compute and update checksums for manifest", - Args: cobra.MinimumNArgs(1), - RunE: func(cmd *cobra.Command, args []string) error { - man, err := manifest.Load(args[0]) - if err != nil { - return err - } - changed := false - for i := range man.Entries { - if man.Entries[i].Exists() { - if m, err := man.Entries[i].CalcMD5(); err == nil { - if m != man.Entries[i].MD5 { - fmt.Printf("Updating %s\n", man.Entries[i].Path) - man.Entries[i].MD5 = m - changed = true - } - } - } - } - if changed { - fmt.Printf("Saving results\n") - } - return nil - }, -} - -var Cmd = &cobra.Command{ - Use: "manifest", - SilenceErrors: true, - SilenceUsage: true, -} - -func init() { - Cmd.AddCommand(CheckCmd) - Cmd.AddCommand(SumCmd) -} diff --git a/cmd/root.go b/cmd/root.go index 252bccc..d23161c 100644 --- a/cmd/root.go +++ b/cmd/root.go @@ -3,9 +3,7 @@ package cmd import ( "os" - "github.com/bmeg/sifter/cmd/graphmanifest" "github.com/bmeg/sifter/cmd/inspect" - "github.com/bmeg/sifter/cmd/manifest" "github.com/bmeg/sifter/cmd/run" "github.com/spf13/cobra" ) @@ -20,8 +18,6 @@ var RootCmd = &cobra.Command{ func init() { RootCmd.AddCommand(run.Cmd) RootCmd.AddCommand(inspect.Cmd) - RootCmd.AddCommand(manifest.Cmd) - RootCmd.AddCommand(graphmanifest.Cmd) } var genBashCompletionCmd = &cobra.Command{ diff --git a/cmd/run/proxy.go b/cmd/run/proxy.go deleted file mode 100644 index 20d8f0d..0000000 --- a/cmd/run/proxy.go +++ /dev/null @@ -1,56 +0,0 @@ -package run - -import ( - "fmt" - "net/http" - "net/http/httputil" - "net/url" - "sync" -) - -type LoadProxyServer struct { - port int - destURL string - waitScreen bool - count uint64 - group *sync.WaitGroup - proxy *httputil.ReverseProxy -} - -func NewLoadProxyServer(port int, proxyURL string) *LoadProxyServer { - rpURL, _ := url.Parse(proxyURL) - - return &LoadProxyServer{port: port, destURL: proxyURL, group: &sync.WaitGroup{}, waitScreen: true, proxy: httputil.NewSingleHostReverseProxy(rpURL)} -} - -func (lp *LoadProxyServer) ServeHTTP(res http.ResponseWriter, req *http.Request) { - if lp.waitScreen { - res.Header().Set("Content-Type", "text/html; charset=utf-8") - page := fmt.Sprintf(`
Sifter Loading Data
%d elements loaded
`, lp.count) - data := []byte(page) - res.Write(data) - } else { - lp.proxy.ServeHTTP(res, req) - } -} - -func (lp *LoadProxyServer) UpdateCount(count uint64) { - lp.count = count -} - -func (lp *LoadProxyServer) Start() error { - // create a new handler - lp.group.Add(1) - go func() { - s := fmt.Sprintf(":%d", lp.port) - http.ListenAndServe(s, lp) - lp.group.Done() - }() - return nil -} - -func (lp *LoadProxyServer) StartProxy() error { - lp.waitScreen = false - lp.group.Wait() - return nil -} diff --git a/datastore/mongo.go b/datastore/mongo.go deleted file mode 100644 index c4a1a15..0000000 --- a/datastore/mongo.go +++ /dev/null @@ -1,115 +0,0 @@ -package datastore - -import ( - "context" - "log" - "time" - - "go.mongodb.org/mongo-driver/bson" - "go.mongodb.org/mongo-driver/mongo" - "go.mongodb.org/mongo-driver/mongo/options" -) - -// Config describes the configuration for the mongodb driver. -type Config struct { - URL string - Database string - Collection string - Username string - Password string - BatchSize int -} - -type DataStore interface { - HasRecordStream(key string) bool - GetRecordStream(key string) chan map[string]interface{} - SetRecordStream(key string, data chan map[string]interface{}) error -} - -type mongoStore struct { - client *mongo.Client - database string - collection string -} - -func GetMongoStore(conf Config) (DataStore, error) { - log.Printf("Starting Mongo DataStore connection") - - clientOpts := options.Client() - clientOpts.SetAppName("sifter") - clientOpts.SetConnectTimeout(1 * time.Minute) - if conf.Username != "" || conf.Password != "" { - cred := options.Credential{Username: conf.Username, Password: conf.Password} - clientOpts.SetAuth(cred) - } - clientOpts.SetRetryReads(true) - clientOpts.SetRetryWrites(true) - clientOpts.SetMaxPoolSize(4096) - clientOpts.SetMaxConnIdleTime(10 * time.Minute) - clientOpts.ApplyURI(conf.URL) - - client, err := mongo.NewClient(clientOpts) - if err != nil { - return nil, err - } - - ctx, cancel := context.WithTimeout(context.Background(), 10*time.Second) - defer cancel() - err = client.Connect(ctx) - if err != nil { - return nil, err - } - - return mongoStore{client: client, database: conf.Database, collection: conf.Collection}, nil -} - -func (ms mongoStore) SetRecordStream(key string, data chan map[string]interface{}) error { - coll := ms.client.Database(ms.database).Collection(ms.collection) - _, err := coll.InsertOne(context.Background(), bson.M{"_id": key}) - if err != nil { - log.Printf("Cache Insert Error: %s", err) - } - conColl := ms.client.Database(ms.database).Collection(ms.collection + "_contents") - for i := range data { - tmp := bson.M{} - for k, v := range i { - tmp[k] = v - } - tmp["_srcid"] = key - _, err := conColl.InsertOne(context.Background(), tmp) - if err != nil { - log.Printf("Cache Insert Error: %s", err) - } - } - return nil -} - -func (ms mongoStore) HasRecordStream(key string) bool { - coll := ms.client.Database(ms.database).Collection(ms.collection) - result := coll.FindOne(context.Background(), bson.M{"_id": key}) - return result.Err() == nil -} - -func (ms mongoStore) GetRecordStream(key string) chan map[string]interface{} { - coll := ms.client.Database(ms.database).Collection(ms.collection + "_contents") - - out := make(chan map[string]interface{}, 10) - - go func() { - defer close(out) - cursor, err := coll.Find(context.TODO(), bson.M{"_srcid": key}) - if err != nil { - log.Printf("Errors: %s", err) - } - result := map[string]interface{}{} - for cursor.Next(context.TODO()) { - if nil == cursor.Decode(&result) { - out <- result - } - } - if err := cursor.Close(context.TODO()); err != nil { - log.Printf("MongoDB: Record stream error") - } - }() - return out -} diff --git a/download/download.go b/download/download.go deleted file mode 100644 index 391e814..0000000 --- a/download/download.go +++ /dev/null @@ -1,77 +0,0 @@ -package download - -import ( - "fmt" - "io" - "log" - "net/url" - "os" - "path/filepath" - "strings" - "time" - - "github.com/hashicorp/go-getter" - "github.com/jlaffaye/ftp" -) - -func ToFile(src string, dest string) (string, error) { - - var err error - dest, err = filepath.Abs(dest) - if err != nil { - return "", err - } - - if strings.HasPrefix(src, "ftp:") { - u, err := url.Parse(src) - if err != nil { - return "", err - } - c, err := ftp.Dial(u.Host+":21", ftp.DialWithTimeout(5*time.Second)) - if err != nil { - return "", err - } - err = c.Login("anonymous", "anonymous") - if err != nil { - return "", err - } - r, err := c.Retr(u.Path) - if err != nil { - return "", err - } - defer r.Close() - - log.Printf("Saving to %s", dest) - f, err := os.Create(dest) - if err != nil { - return "", err - } - defer f.Close() - - downloadSize, _ := io.Copy(f, r) - log.Printf("Downloaded %d bytes", downloadSize) - return dest, nil - } - - if strings.HasPrefix(src, "s3:") { - s3Key := os.Getenv("AWS_ACCESS_KEY_ID") - s3Secret := os.Getenv("AWS_SECRET_ACCESS_KEY") - s3Endpoint := os.Getenv("AWS_ENDPOINT") - if s3Endpoint != "" { - u, err := url.Parse(src) - if err != nil { - return "", err - } - //"s3::http://127.0.0.1:9000/test-bucket/hello.txt?aws_access_key_id=KEYID&aws_access_key_secret=SECRETKEY®ion=us-east-2" - src = fmt.Sprintf("s3::%s/%s%s", s3Endpoint, u.Host, u.Path) - } - if s3Key != "" && s3Secret != "" { - src = src + fmt.Sprintf("?aws_access_key_id=%s&aws_access_key_secret=%s", s3Key, s3Secret) - } - src = src + "&archive=false" - } else { - src = src + "?archive=false" - } - - return dest, getter.GetFile(dest, src) -} diff --git a/download/util.go b/download/util.go deleted file mode 100644 index ed3ad0b..0000000 --- a/download/util.go +++ /dev/null @@ -1,21 +0,0 @@ -package download - -import ( - "strings" -) - -func IsURL(s string) bool { - if strings.HasPrefix(s, "http://") { - return true - } - if strings.HasPrefix(s, "https://") { - return true - } - if strings.HasPrefix(s, "s3://") { - return true - } - if strings.HasPrefix(s, "ftp://") { - return true - } - return false -} diff --git a/go.mod b/go.mod index 160f355..ddb9760 100644 --- a/go.mod +++ b/go.mod @@ -17,13 +17,10 @@ require ( github.com/golang/protobuf v1.5.3 github.com/google/shlex v0.0.0-20191202100458-e7afc7fbc510 github.com/google/uuid v1.3.0 - github.com/hashicorp/go-getter v1.7.0 - github.com/jlaffaye/ftp v0.0.0-20200602180915-5563613968bf github.com/linkedin/goavro/v2 v2.10.0 github.com/mattn/go-sqlite3 v1.14.16 github.com/santhosh-tekuri/jsonschema/v5 v5.3.0 github.com/spf13/cobra v1.6.1 - go.mongodb.org/mongo-driver v1.7.5 google.golang.org/grpc v1.56.3 google.golang.org/protobuf v1.30.0 sigs.k8s.io/yaml v1.3.0 @@ -31,11 +28,6 @@ require ( ) require ( - cloud.google.com/go v0.110.0 // indirect - cloud.google.com/go/compute v1.19.1 // indirect - cloud.google.com/go/compute/metadata v0.2.3 // indirect - cloud.google.com/go/iam v0.13.0 // indirect - cloud.google.com/go/storage v1.29.0 // indirect github.com/DataDog/datadog-agent/pkg/obfuscate v0.42.0 // indirect github.com/DataDog/datadog-agent/pkg/remoteconfig/state v0.42.0 // indirect github.com/DataDog/datadog-go/v5 v5.2.0 // indirect @@ -44,9 +36,7 @@ require ( github.com/DataDog/zstd v1.4.5 // indirect github.com/Microsoft/go-winio v0.6.0 // indirect github.com/Workiva/go-datastructures v1.0.52 // indirect - github.com/aws/aws-sdk-go v1.44.192 // indirect github.com/beorn7/perks v1.0.1 // indirect - github.com/bgentry/go-netrc v0.0.0-20140422174119-9fd32a8b3d3d // indirect github.com/bitly/go-simplejson v0.5.0 // indirect github.com/cespare/xxhash v1.1.0 // indirect github.com/cespare/xxhash/v2 v2.2.0 // indirect @@ -58,29 +48,20 @@ require ( github.com/dgryski/go-farm v0.0.0-20190423205320-6a90982ecee2 // indirect github.com/dustin/go-humanize v1.0.1 // indirect github.com/fatih/color v1.14.1 // indirect - github.com/go-stack/stack v1.8.0 // indirect github.com/gogo/protobuf v1.3.2 // indirect github.com/golang/glog v1.1.0 // indirect - github.com/golang/groupcache v0.0.0-20210331224755-41bb18bfe9da // indirect github.com/golang/snappy v0.0.4 // indirect - github.com/google/go-cmp v0.5.9 // indirect - github.com/googleapis/enterprise-certificate-proxy v0.2.3 // indirect - github.com/googleapis/gax-go/v2 v2.7.1 // indirect github.com/grpc-ecosystem/go-grpc-middleware v1.3.0 // indirect github.com/grpc-ecosystem/go-grpc-prometheus v1.2.0 // indirect github.com/grpc-ecosystem/grpc-gateway/v2 v2.5.0 // indirect github.com/hashicorp/errwrap v1.1.0 // indirect - github.com/hashicorp/go-cleanhttp v0.5.2 // indirect github.com/hashicorp/go-hclog v1.4.0 // indirect github.com/hashicorp/go-multierror v1.1.1 // indirect github.com/hashicorp/go-plugin v1.4.3 // indirect - github.com/hashicorp/go-safetemp v1.0.0 // indirect - github.com/hashicorp/go-version v1.6.0 // indirect github.com/hashicorp/yamux v0.0.0-20180604194846-3520598351bb // indirect github.com/iancoleman/orderedmap v0.0.0-20190318233801-ac98e3ecb4b0 // indirect github.com/inconshreveable/mousetrap v1.1.0 // indirect github.com/influxdata/tdigest v0.0.1 // indirect - github.com/jmespath/go-jmespath v0.4.0 // indirect github.com/jmoiron/sqlx v1.2.1-0.20190826204134-d7d95172beb5 // indirect github.com/kennygrant/sanitize v1.2.4 // indirect github.com/klauspost/compress v1.15.15 // indirect @@ -90,7 +71,6 @@ require ( github.com/mattn/go-colorable v0.1.13 // indirect github.com/mattn/go-isatty v0.0.17 // indirect github.com/matttproud/golang_protobuf_extensions v1.0.4 // indirect - github.com/mitchellh/go-homedir v1.1.0 // indirect github.com/mitchellh/go-testing-interface v1.14.1 // indirect github.com/oklog/run v1.0.0 // indirect github.com/opentracing-contrib/go-grpc v0.0.0-20210225150812-73cb765af46e // indirect @@ -110,12 +90,6 @@ require ( github.com/tinylib/msgp v1.1.8 // indirect github.com/uber/jaeger-client-go v2.30.0+incompatible // indirect github.com/uber/jaeger-lib v2.4.1+incompatible // indirect - github.com/ulikunitz/xz v0.5.10 // indirect - github.com/xdg-go/pbkdf2 v1.0.0 // indirect - github.com/xdg-go/scram v1.0.2 // indirect - github.com/xdg-go/stringprep v1.0.2 // indirect - github.com/youmark/pkcs8 v0.0.0-20201027041543-1326539a0a0a // indirect - go.opencensus.io v0.24.0 // indirect go.uber.org/atomic v1.10.0 // indirect go4.org/intern v0.0.0-20220617035311-6925f38cc365 // indirect go4.org/unsafe/assume-no-moving-gc v0.0.0-20220617031537-928513b29760 // indirect @@ -123,7 +97,6 @@ require ( golang.org/x/exp v0.0.0-20230131160201-f062dba9d201 // indirect golang.org/x/mod v0.8.0 // indirect golang.org/x/net v0.17.0 // indirect - golang.org/x/oauth2 v0.7.0 // indirect golang.org/x/sync v0.1.0 // indirect golang.org/x/sys v0.13.0 // indirect golang.org/x/term v0.13.0 // indirect @@ -131,8 +104,6 @@ require ( golang.org/x/time v0.3.0 // indirect golang.org/x/tools v0.6.0 // indirect golang.org/x/xerrors v0.0.0-20220907171357-04be3eba64a2 // indirect - google.golang.org/api v0.114.0 // indirect - google.golang.org/appengine v1.6.7 // indirect google.golang.org/genproto v0.0.0-20230410155749-daa745c078e1 // indirect gopkg.in/DataDog/dd-trace-go.v1 v1.47.0 // indirect gopkg.in/yaml.v2 v2.4.0 // indirect diff --git a/go.sum b/go.sum index 204574d..c7ec999 100644 --- a/go.sum +++ b/go.sum @@ -13,179 +13,24 @@ cloud.google.com/go v0.56.0/go.mod h1:jr7tqZxxKOVYizybht9+26Z/gUq7tiRzu+ACVAMbKV cloud.google.com/go v0.57.0/go.mod h1:oXiQ6Rzq3RAkkY7N6t3TcE6jE+CIBBbA36lwQ1JyzZs= 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= -cloud.google.com/go v0.74.0/go.mod h1:VV1xSbzvo+9QJOxLDaJfTjx5e+MePCpCWwvftOeQmWk= -cloud.google.com/go v0.78.0/go.mod h1:QjdrLG0uq+YwhjoVOLsS1t7TW8fs36kLs4XO5R5ECHg= -cloud.google.com/go v0.79.0/go.mod h1:3bzgcEeQlzbuEAYu4mrWhKqWjmpprinYgKJLgKHnbb8= 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h1:duJ4Jxv5lDcvg4QuQr0oowTf7dz4/CR8NtyCooz9HL8= @@ -401,7 +230,6 @@ github.com/go-sourcemap/sourcemap v2.1.2+incompatible/go.mod h1:F8jJfvm2KbVjc5Nq github.com/go-sql-driver/mysql v1.4.0/go.mod h1:zAC/RDZ24gD3HViQzih4MyKcchzm+sOG5ZlKdlhCg5w= github.com/go-sql-driver/mysql v1.5.0/go.mod h1:DCzpHaOWr8IXmIStZouvnhqoel9Qv2LBy8hT2VhHyBg= github.com/go-sql-driver/mysql v1.7.0 h1:ueSltNNllEqE3qcWBTD0iQd3IpL/6U+mJxLkazJ7YPc= -github.com/go-stack/stack v1.8.0 h1:5SgMzNM5HxrEjV0ww2lTmX6E2Izsfxas4+YHWRs3Lsk= github.com/go-stack/stack v1.8.0/go.mod h1:v0f6uXyyMGvRgIKkXu+yp6POWl0qKG85gN/melR3HDY= github.com/go-task/slim-sprig v0.0.0-20210107165309-348f09dbbbc0/go.mod h1:fyg7847qk6SyHyPtNmDHnmrv/HOrqktSC+C9fM+CJOE= github.com/go-toolsmith/astcast v1.0.0/go.mod h1:mt2OdQTeAQcY4DQgPSArJjHCcOwlX+Wl/kwN+LbLGQ4= @@ -464,8 +292,6 @@ github.com/golang/groupcache v0.0.0-20190129154638-5b532d6fd5ef/go.mod h1:cIg4er github.com/golang/groupcache v0.0.0-20190702054246-869f871628b6/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc= github.com/golang/groupcache v0.0.0-20191227052852-215e87163ea7/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc= github.com/golang/groupcache v0.0.0-20200121045136-8c9f03a8e57e/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc= -github.com/golang/groupcache v0.0.0-20210331224755-41bb18bfe9da h1:oI5xCqsCo564l8iNU+DwB5epxmsaqB+rhGL0m5jtYqE= -github.com/golang/groupcache v0.0.0-20210331224755-41bb18bfe9da/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc= github.com/golang/mock v1.1.1/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A= github.com/golang/mock v1.2.0/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A= github.com/golang/mock v1.3.1/go.mod h1:sBzyDLLjw3U8JLTeZvSv8jJB+tU5PVekmnlKIyFUx0Y= @@ -473,7 +299,6 @@ github.com/golang/mock v1.4.0/go.mod h1:UOMv5ysSaYNkG+OFQykRIcU/QvvxJf3p21QfJ2Bt github.com/golang/mock v1.4.1/go.mod h1:UOMv5ysSaYNkG+OFQykRIcU/QvvxJf3p21QfJ2Bt3cw= github.com/golang/mock v1.4.3/go.mod h1:UOMv5ysSaYNkG+OFQykRIcU/QvvxJf3p21QfJ2Bt3cw= github.com/golang/mock v1.4.4/go.mod h1:l3mdAwkq5BuhzHwde/uurv3sEJeZMXNpwsxVWU71h+4= -github.com/golang/mock v1.5.0/go.mod h1:CWnOUgYIOo4TcNZ0wHX3YZCqsaM1I1Jvs6v3mP3KVu8= github.com/golang/mock v1.6.0/go.mod h1:p6yTPP+5HYm5mzsMV8JkE6ZKdX+/wYM6Hr+LicevLPs= github.com/golang/protobuf v1.2.0/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U= github.com/golang/protobuf v1.3.1/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U= @@ -490,7 +315,6 @@ github.com/golang/protobuf v1.4.1/go.mod h1:U8fpvMrcmy5pZrNK1lt4xCsGvpyWQ/VVv6QD github.com/golang/protobuf v1.4.2/go.mod h1:oDoupMAO8OvCJWAcko0GGGIgR6R6ocIYbsSw735rRwI= github.com/golang/protobuf v1.4.3/go.mod h1:oDoupMAO8OvCJWAcko0GGGIgR6R6ocIYbsSw735rRwI= github.com/golang/protobuf v1.5.0/go.mod h1:FsONVRAS9T7sI+LIUmWTfcYkHO4aIWwzhcaSAoJOfIk= -github.com/golang/protobuf v1.5.1/go.mod h1:DopwsBzvsk0Fs44TXzsVbJyPhcCPeIwnvohx4u74HPM= github.com/golang/protobuf v1.5.2/go.mod h1:XVQd3VNwM+JqD3oG2Ue2ip4fOMUkwXdXDdiuN0vRsmY= github.com/golang/protobuf v1.5.3 h1:KhyjKVUg7Usr/dYsdSqoFveMYd5ko72D+zANwlG1mmg= github.com/golang/protobuf v1.5.3/go.mod h1:XVQd3VNwM+JqD3oG2Ue2ip4fOMUkwXdXDdiuN0vRsmY= @@ -531,19 +355,12 @@ github.com/google/go-cmp v0.5.3/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/ github.com/google/go-cmp v0.5.4/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= github.com/google/go-cmp v0.5.5/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= github.com/google/go-cmp v0.5.6/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= -github.com/google/go-cmp v0.5.7/go.mod h1:n+brtR0CgQNWTVd5ZUFpTBC8YFBDLK/h/bpaJ8/DtOE= -github.com/google/go-cmp v0.5.8/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY= github.com/google/go-cmp v0.5.9 h1:O2Tfq5qg4qc4AmwVlvv0oLiVAGB7enBSJ2x2DqQFi38= -github.com/google/go-cmp v0.5.9/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY= github.com/google/go-querystring v1.0.0/go.mod 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github.com/google/pprof v0.0.0-20191218002539-d4f498aebedc/go.mod h1:ZgVRPoUq/hfqzAqh7sHMqb3I9Rq5C59dIz2SbBwJ4eM= @@ -551,14 +368,7 @@ github.com/google/pprof v0.0.0-20200212024743-f11f1df84d12/go.mod h1:ZgVRPoUq/hf github.com/google/pprof v0.0.0-20200229191704-1ebb73c60ed3/go.mod h1:ZgVRPoUq/hfqzAqh7sHMqb3I9Rq5C59dIz2SbBwJ4eM= github.com/google/pprof v0.0.0-20200430221834-fc25d7d30c6d/go.mod h1:ZgVRPoUq/hfqzAqh7sHMqb3I9Rq5C59dIz2SbBwJ4eM= github.com/google/pprof v0.0.0-20200708004538-1a94d8640e99/go.mod h1:ZgVRPoUq/hfqzAqh7sHMqb3I9Rq5C59dIz2SbBwJ4eM= -github.com/google/pprof v0.0.0-20201023163331-3e6fc7fc9c4c/go.mod h1:kpwsk12EmLew5upagYY7GY0pfYCcupk39gWOCRROcvE= -github.com/google/pprof v0.0.0-20201203190320-1bf35d6f28c2/go.mod h1:kpwsk12EmLew5upagYY7GY0pfYCcupk39gWOCRROcvE= -github.com/google/pprof v0.0.0-20210122040257-d980be63207e/go.mod h1:kpwsk12EmLew5upagYY7GY0pfYCcupk39gWOCRROcvE= -github.com/google/pprof v0.0.0-20210226084205-cbba55b83ad5/go.mod h1:kpwsk12EmLew5upagYY7GY0pfYCcupk39gWOCRROcvE= github.com/google/pprof v0.0.0-20210407192527-94a9f03dee38/go.mod h1:kpwsk12EmLew5upagYY7GY0pfYCcupk39gWOCRROcvE= -github.com/google/pprof v0.0.0-20210601050228-01bbb1931b22/go.mod h1:kpwsk12EmLew5upagYY7GY0pfYCcupk39gWOCRROcvE= -github.com/google/pprof v0.0.0-20210609004039-a478d1d731e9/go.mod h1:kpwsk12EmLew5upagYY7GY0pfYCcupk39gWOCRROcvE= -github.com/google/pprof v0.0.0-20210720184732-4bb14d4b1be1/go.mod h1:kpwsk12EmLew5upagYY7GY0pfYCcupk39gWOCRROcvE= github.com/google/renameio v0.1.0/go.mod h1:KWCgfxg9yswjAJkECMjeO8J8rahYeXnNhOm40UhjYkI= github.com/google/shlex v0.0.0-20191202100458-e7afc7fbc510 h1:El6M4kTTCOh6aBiKaUGG7oYTSPP8MxqL4YI3kZKwcP4= github.com/google/shlex v0.0.0-20191202100458-e7afc7fbc510/go.mod h1:pupxD2MaaD3pAXIBCelhxNneeOaAeabZDe5s4K6zSpQ= @@ -566,23 +376,8 @@ github.com/google/uuid v1.0.0/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+ github.com/google/uuid v1.1.2/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo= github.com/google/uuid v1.3.0 h1:t6JiXgmwXMjEs8VusXIJk2BXHsn+wx8BZdTaoZ5fu7I= github.com/google/uuid v1.3.0/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo= -github.com/googleapis/enterprise-certificate-proxy v0.0.0-20220520183353-fd19c99a87aa/go.mod h1:17drOmN3MwGY7t0e+Ei9b45FFGA3fBs3x36SsCg1hq8= -github.com/googleapis/enterprise-certificate-proxy v0.1.0/go.mod h1:17drOmN3MwGY7t0e+Ei9b45FFGA3fBs3x36SsCg1hq8= -github.com/googleapis/enterprise-certificate-proxy v0.2.0/go.mod h1:8C0jb7/mgJe/9KK8Lm7X9ctZC2t60YyIpYEI16jx0Qg= -github.com/googleapis/enterprise-certificate-proxy v0.2.3 h1:yk9/cqRKtT9wXZSsRH9aurXEpJX+U6FLtpYTdC3R06k= -github.com/googleapis/enterprise-certificate-proxy v0.2.3/go.mod h1:AwSRAtLfXpU5Nm3pW+v7rGDHp09LsPtGY9MduiEsR9k= github.com/googleapis/gax-go/v2 v2.0.4/go.mod h1:0Wqv26UfaUD9n4G6kQubkQ+KchISgw+vpHVxEJEs9eg= github.com/googleapis/gax-go/v2 v2.0.5/go.mod h1:DWXyrwAJ9X0FpwwEdw+IPEYBICEFu5mhpdKc/us6bOk= 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v0.0.0-20181017120253-0766667cb4d1/go.mod h1:wJfORRmW1u3UXTncJ5qlYoELFm8eSnnEO6hX4iZ3EWY= github.com/gopherjs/gopherjs v0.0.0-20190430165422-3e4dfb77656c/go.mod h1:wJfORRmW1u3UXTncJ5qlYoELFm8eSnnEO6hX4iZ3EWY= github.com/gordonklaus/ineffassign v0.0.0-20200309095847-7953dde2c7bf/go.mod h1:cuNKsD1zp2v6XfE/orVX2QE1LC+i254ceGcVeDT3pTU= @@ -598,7 +393,6 @@ github.com/grpc-ecosystem/go-grpc-middleware v1.3.0/go.mod h1:z0ButlSOZa5vEBq9m2 github.com/grpc-ecosystem/go-grpc-prometheus v1.2.0 h1:Ovs26xHkKqVztRpIrF/92BcuyuQ/YW4NSIpoGtfXNho= github.com/grpc-ecosystem/go-grpc-prometheus v1.2.0/go.mod h1:8NvIoxWQoOIhqOTXgfV/d3M/q6VIi02HzZEHgUlZvzk= github.com/grpc-ecosystem/grpc-gateway v1.9.0/go.mod h1:vNeuVxBJEsws4ogUvrchl83t/GYV9WGTSLVdBhOQFDY= -github.com/grpc-ecosystem/grpc-gateway v1.16.0/go.mod h1:BDjrQk3hbvj6Nolgz8mAMFbcEtjT1g+wF4CSlocrBnw= github.com/grpc-ecosystem/grpc-gateway/v2 v2.5.0 h1:ajue7SzQMywqRjg2fK7dcpc0QhFGpTR2plWfV4EZWR4= github.com/grpc-ecosystem/grpc-gateway/v2 v2.5.0/go.mod h1:r1hZAcvfFXuYmcKyCJI9wlyOPIZUJl6FCB8Cpca/NLE= github.com/grpc-ecosystem/grpc-opentracing v0.0.0-20180507213350-8e809c8a8645/go.mod h1:6iZfnjpejD4L/4DwD7NryNaJyCQdzwWwH2MWhCA90Kw= @@ -608,10 +402,6 @@ github.com/hashicorp/errwrap v1.0.0/go.mod h1:YH+1FKiLXxHSkmPseP+kNlulaMuP3n2brv github.com/hashicorp/errwrap v1.1.0 h1:OxrOeh75EUXMY8TBjag2fzXGZ40LB6IKw45YeGUDY2I= github.com/hashicorp/errwrap v1.1.0/go.mod h1:YH+1FKiLXxHSkmPseP+kNlulaMuP3n2brvKWEqk/Jc4= github.com/hashicorp/go-cleanhttp v0.5.1/go.mod h1:JpRdi6/HCYpAwUzNwuwqhbovhLtngrth3wmdIIUrZ80= -github.com/hashicorp/go-cleanhttp v0.5.2 h1:035FKYIWjmULyFRBKPs8TBQoi0x6d9G4xc9neXJWAZQ= -github.com/hashicorp/go-cleanhttp v0.5.2/go.mod h1:kO/YDlP8L1346E6Sodw+PrpBSV4/SoxCXGY6BqNFT48= -github.com/hashicorp/go-getter v1.7.0 h1:bzrYP+qu/gMrL1au7/aDvkoOVGUJpeKBgbqRHACAFDY= -github.com/hashicorp/go-getter v1.7.0/go.mod h1:W7TalhMmbPmsSMdNjD0ZskARur/9GJ17cfHTRtXV744= github.com/hashicorp/go-hclog v0.14.1/go.mod 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github.com/hashicorp/go-uuid v1.0.0/go.mod h1:6SBZvOh/SIDV7/2o3Jml5SYk/TvGqwFJ/bN7x4byOro= github.com/hashicorp/go-uuid v1.0.1/go.mod h1:6SBZvOh/SIDV7/2o3Jml5SYk/TvGqwFJ/bN7x4byOro= github.com/hashicorp/go-version v1.2.0/go.mod h1:fltr4n8CU8Ke44wwGCBoEymUuxUHl09ZGVZPK5anwXA= -github.com/hashicorp/go-version v1.6.0 h1:feTTfFNnjP967rlCxM/I9g701jU+RN74YKx2mOkIeek= -github.com/hashicorp/go-version v1.6.0/go.mod h1:fltr4n8CU8Ke44wwGCBoEymUuxUHl09ZGVZPK5anwXA= github.com/hashicorp/go.net v0.0.1/go.mod h1:hjKkEWcCURg++eb33jQU7oqQcI9XDCnUzHA0oac0k90= github.com/hashicorp/golang-lru v0.5.0/go.mod h1:/m3WP610KZHVQ1SGc6re/UDhFvYD7pJ4Ao+sR/qLZy8= github.com/hashicorp/golang-lru v0.5.1/go.mod h1:/m3WP610KZHVQ1SGc6re/UDhFvYD7pJ4Ao+sR/qLZy8= @@ -665,12 +451,8 @@ github.com/jessevdk/go-flags v1.4.0/go.mod h1:4FA24M0QyGHXBuZZK/XkWh8h0e1EYbRYJS github.com/jhump/protoreflect v1.6.0/go.mod h1:eaTn3RZAmMBcV0fifFvlm6VHNz3wSkYyXYWUh7ymB74= github.com/jhump/protoreflect v1.8.1 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github.com/microcosm-cc/bluemonday v1.0.2/go.mod h1:iVP4YcDBq+n/5fb23BhYFvIMq/le github.com/miekg/dns v1.0.14/go.mod h1:W1PPwlIAgtquWBMBEV9nkV9Cazfe8ScdGz/Lj7v3Nrg= github.com/mitchellh/cli v1.0.0/go.mod h1:hNIlj7HEI86fIcpObd7a0FcrxTWetlwJDGcceTlRvqc= github.com/mitchellh/go-homedir v1.0.0/go.mod h1:SfyaCUpYCn1Vlf4IUYiD9fPX4A5wJrkLzIz1N1q0pr0= -github.com/mitchellh/go-homedir v1.1.0 h1:lukF9ziXFxDFPkA1vsr5zpc1XuPDn/wFntq5mG+4E0Y= github.com/mitchellh/go-homedir v1.1.0/go.mod h1:SfyaCUpYCn1Vlf4IUYiD9fPX4A5wJrkLzIz1N1q0pr0= github.com/mitchellh/go-ps v0.0.0-20190716172923-621e5597135b/go.mod h1:r1VsdOzOPt1ZSrGZWFoNhsAedKnEd6r9Np1+5blZCWk= github.com/mitchellh/go-testing-interface v0.0.0-20171004221916-a61a99592b77/go.mod h1:kRemZodwjscx+RGhAo8eIhFbs2+BFgRtFPeD/KE+zxI= @@ -954,7 +733,6 @@ github.com/subosito/gotenv v1.2.0/go.mod h1:N0PQaV/YGNqwC0u51sEeR/aUtSLEXKX9iv69 github.com/syndtr/goleveldb v1.0.0/go.mod h1:ZVVdQEZoIme9iO1Ch2Jdy24qqXrMMOU6lpPAyBWyWuQ= github.com/syndtr/goleveldb v1.0.1-0.20210819022825-2ae1ddf74ef7/go.mod h1:q4W45IWZaF22tdD+VEXcAWRA037jwmWEB5VWYORlTpc= github.com/tidwall/pretty v1.0.0/go.mod h1:XNkn88O1ChpSDQmQeStsy+sBenx6DDtFZJxhVysOjyk= -github.com/tidwall/pretty v1.2.0 h1:RWIZEg2iJ8/g6fDDYzMpobmaoGh5OLl4AXtGUGPcqCs= github.com/timakin/bodyclose v0.0.0-20190930140734-f7f2e9bca95e/go.mod h1:Qimiffbc6q9tBWlVV6x0P9sat/ao1xEkREYPPj9hphk= github.com/tinylib/msgp v1.1.8 h1:FCXC1xanKO4I8plpHGH2P7koL/RzZs12l/+r7vakfm0= github.com/tinylib/msgp v1.1.8/go.mod h1:qkpG+2ldGg4xRFmx+jfTvZPxfGFhi64BcnL9vkCm/Tw= @@ -967,8 +745,6 @@ github.com/uber/jaeger-lib v2.4.1+incompatible h1:td4jdvLcExb4cBISKIpHuGoVXh+dVK github.com/uber/jaeger-lib v2.4.1+incompatible/go.mod h1:ComeNDZlWwrWnDv8aPp0Ba6+uUTzImX/AauajbLI56U= github.com/ugorji/go v1.1.4/go.mod h1:uQMGLiO92mf5W77hV/PUCpI3pbzQx3CRekS0kk+RGrc= github.com/ugorji/go/codec v0.0.0-20181204163529-d75b2dcb6bc8/go.mod h1:VFNgLljTbGfSG7qAOspJ7OScBnGdDN/yBr0sguwnwf0= -github.com/ulikunitz/xz v0.5.10 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h1:VXEWRZ6URJIkUq2SCAyapmhH0ZLRBP+FT4xhp5Zvxng= go.opencensus.io v0.21.0/go.mod h1:mSImk1erAIZhrmZN+AvHh14ztQfjbGwt4TtuofqLduU= go.opencensus.io v0.22.0/go.mod h1:+kGneAE2xo2IficOXnaByMWTGM9T73dGwxeWcUqIpI8= go.opencensus.io v0.22.2/go.mod h1:yxeiOL68Rb0Xd1ddK5vPZ/oVn4vY4Ynel7k9FzqtOIw= go.opencensus.io v0.22.3/go.mod h1:yxeiOL68Rb0Xd1ddK5vPZ/oVn4vY4Ynel7k9FzqtOIw= go.opencensus.io v0.22.4/go.mod h1:yxeiOL68Rb0Xd1ddK5vPZ/oVn4vY4Ynel7k9FzqtOIw= -go.opencensus.io v0.22.5/go.mod h1:5pWMHQbX5EPX2/62yrJeAkowc+lfs/XD7Uxpq3pI6kk= go.opencensus.io v0.22.6/go.mod h1:XItmlyltB5F7CS4xOC1DcqMoFqwtC6OG2xF7mCv7P7E= -go.opencensus.io v0.23.0/go.mod h1:XItmlyltB5F7CS4xOC1DcqMoFqwtC6OG2xF7mCv7P7E= -go.opencensus.io v0.24.0 h1:y73uSU6J157QMP2kn2r30vwW1A2W2WFwSCGnAVxeaD0= -go.opencensus.io v0.24.0/go.mod h1:vNK8G9p7aAivkbmorf4v+7Hgx+Zs0yY+0fOtgBfjQKo= -go.opentelemetry.io/proto/otlp v0.7.0/go.mod h1:PqfVotwruBrMGOCsRd/89rSnXhoiJIqeYNgFYFoEGnI= go.uber.org/atomic v1.4.0/go.mod h1:gD2HeocX3+yG+ygLZcrzQJaqmWj9AIm7n08wl/qW/PE= go.uber.org/atomic v1.6.0/go.mod h1:sABNBOSYdrvTF6hTgEIbc7YasKWGhgEQZyfxyTvoXHQ= go.uber.org/atomic v1.7.0/go.mod h1:fEN4uk6kAWBTFdckzkM89CLk9XfWZrxpCo0nPH17wJc= @@ -1084,7 +849,6 @@ golang.org/x/lint v0.0.0-20190930215403-16217165b5de/go.mod h1:6SW0HCj/g11FgYtHl golang.org/x/lint v0.0.0-20191125180803-fdd1cda4f05f/go.mod h1:5qLYkcX4OjUUV8bRuDixDT3tpyyb+LUpUlRWLxfhWrs= golang.org/x/lint v0.0.0-20200130185559-910be7a94367/go.mod h1:3xt1FjdF8hUf6vQPIChWIBhFzV8gjjsPE/fR3IyQdNY= golang.org/x/lint v0.0.0-20200302205851-738671d3881b/go.mod h1:3xt1FjdF8hUf6vQPIChWIBhFzV8gjjsPE/fR3IyQdNY= -golang.org/x/lint v0.0.0-20201208152925-83fdc39ff7b5/go.mod h1:3xt1FjdF8hUf6vQPIChWIBhFzV8gjjsPE/fR3IyQdNY= golang.org/x/lint v0.0.0-20210508222113-6edffad5e616/go.mod h1:3xt1FjdF8hUf6vQPIChWIBhFzV8gjjsPE/fR3IyQdNY= golang.org/x/mobile v0.0.0-20190312151609-d3739f865fa6/go.mod h1:z+o9i4GpDbdi3rU15maQ/Ox0txvL9dWGYEHz965HBQE= golang.org/x/mobile v0.0.0-20190719004257-d2bd2a29d028/go.mod h1:E/iHnbuqvinMTCcRqshq8CkpyQDoeVncDDYHnLhea+o= @@ -1094,8 +858,6 @@ golang.org/x/mod v0.1.1-0.20191105210325-c90efee705ee/go.mod h1:QqPTAvyqsEbceGzB golang.org/x/mod v0.1.1-0.20191107180719-034126e5016b/go.mod h1:QqPTAvyqsEbceGzBzNggFXnrqF1CaUcvgkdR5Ot7KZg= golang.org/x/mod v0.2.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA= golang.org/x/mod v0.3.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA= -golang.org/x/mod v0.4.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA= -golang.org/x/mod v0.4.1/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA= golang.org/x/mod v0.4.2/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA= golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4/go.mod h1:jJ57K6gSWd91VN4djpZkiMVwK6gcyfeH4XE8wZrZaV4= golang.org/x/mod v0.7.0/go.mod h1:iBbtSCu2XBx23ZKBPSOrRkjjQPZFPuis4dIYUhu/chs= @@ -1143,28 +905,14 @@ golang.org/x/net v0.0.0-20200707034311-ab3426394381/go.mod h1:/O7V0waA8r7cgGh81R golang.org/x/net v0.0.0-20200813134508-3edf25e44fcc/go.mod h1:/O7V0waA8r7cgGh81Ro3o1hOxt32SMVPicZroKQ2sZA= golang.org/x/net v0.0.0-20200822124328-c89045814202/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= -golang.org/x/net v0.0.0-20201209123823-ac852fbbde11/go.mod h1:m0MpNAwzfU5UDzcl9v0D8zg8gWTRqZa9RBIspLL5mdg= golang.org/x/net v0.0.0-20210119194325-5f4716e94777/go.mod h1:m0MpNAwzfU5UDzcl9v0D8zg8gWTRqZa9RBIspLL5mdg= golang.org/x/net v0.0.0-20210226172049-e18ecbb05110/go.mod h1:m0MpNAwzfU5UDzcl9v0D8zg8gWTRqZa9RBIspLL5mdg= -golang.org/x/net v0.0.0-20210316092652-d523dce5a7f4/go.mod h1:RBQZq4jEuRlivfhVLdyRGr576XBO4/greRjx4P4O3yc= golang.org/x/net v0.0.0-20210405180319-a5a99cb37ef4/go.mod h1:p54w0d4576C0XHj96bSt6lcn1PtDYWL6XObtHCRCNQM= golang.org/x/net v0.0.0-20210428140749-89ef3d95e781/go.mod h1:OJAsFXCWl8Ukc7SiCT/9KSuxbyM7479/AVlXFRxuMCk= -golang.org/x/net v0.0.0-20210503060351-7fd8e65b6420/go.mod h1:9nx3DQGgdP8bBQD5qxJ1jj9UTztislL4KSBs9R2vV5Y= golang.org/x/net v0.0.0-20211112202133-69e39bad7dc2/go.mod h1:9nx3DQGgdP8bBQD5qxJ1jj9UTztislL4KSBs9R2vV5Y= golang.org/x/net v0.0.0-20220127200216-cd36cc0744dd/go.mod h1:CfG3xpIq0wQ8r1q4Su4UZFWDARRcnwPjda9FqA0JpMk= -golang.org/x/net v0.0.0-20220225172249-27dd8689420f/go.mod h1:CfG3xpIq0wQ8r1q4Su4UZFWDARRcnwPjda9FqA0JpMk= -golang.org/x/net v0.0.0-20220325170049-de3da57026de/go.mod h1:CfG3xpIq0wQ8r1q4Su4UZFWDARRcnwPjda9FqA0JpMk= -golang.org/x/net v0.0.0-20220412020605-290c469a71a5/go.mod h1:CfG3xpIq0wQ8r1q4Su4UZFWDARRcnwPjda9FqA0JpMk= -golang.org/x/net v0.0.0-20220425223048-2871e0cb64e4/go.mod h1:CfG3xpIq0wQ8r1q4Su4UZFWDARRcnwPjda9FqA0JpMk= -golang.org/x/net v0.0.0-20220607020251-c690dde0001d/go.mod h1:XRhObCWvk6IyKnWLug+ECip1KBveYUHfp+8e9klMJ9c= -golang.org/x/net v0.0.0-20220617184016-355a448f1bc9/go.mod h1:XRhObCWvk6IyKnWLug+ECip1KBveYUHfp+8e9klMJ9c= -golang.org/x/net v0.0.0-20220624214902-1bab6f366d9e/go.mod h1:XRhObCWvk6IyKnWLug+ECip1KBveYUHfp+8e9klMJ9c= golang.org/x/net v0.0.0-20220722155237-a158d28d115b/go.mod h1:XRhObCWvk6IyKnWLug+ECip1KBveYUHfp+8e9klMJ9c= -golang.org/x/net v0.0.0-20220909164309-bea034e7d591/go.mod h1:YDH+HFinaLZZlnHAfSS6ZXJJ9M9t4Dl22yv3iI2vPwk= -golang.org/x/net v0.0.0-20221014081412-f15817d10f9b/go.mod h1:YDH+HFinaLZZlnHAfSS6ZXJJ9M9t4Dl22yv3iI2vPwk= -golang.org/x/net v0.1.0/go.mod h1:Cx3nUiGt4eDBEyega/BKRp+/AlGL8hYe7U9odMt2Cco= golang.org/x/net v0.3.0/go.mod h1:MBQ8lrhLObU/6UmLb4fmbmk5OcyYmqtbGd/9yIeKjEE= golang.org/x/net v0.17.0 h1:pVaXccu2ozPjCXewfr1S7xza/zcXTity9cCdXQYSjIM= golang.org/x/net v0.17.0/go.mod h1:NxSsAGuq816PNPmqtQdLE42eU2Fs7NoRIZrHJAlaCOE= @@ -1173,29 +921,7 @@ golang.org/x/oauth2 v0.0.0-20190226205417-e64efc72b421/go.mod h1:gOpvHmFTYa4Iltr golang.org/x/oauth2 v0.0.0-20190604053449-0f29369cfe45/go.mod h1:gOpvHmFTYa4IltrdGE7lF6nIHvwfUNPOp7c8zoXwtLw= golang.org/x/oauth2 v0.0.0-20191202225959-858c2ad4c8b6/go.mod h1:gOpvHmFTYa4IltrdGE7lF6nIHvwfUNPOp7c8zoXwtLw= golang.org/x/oauth2 v0.0.0-20200107190931-bf48bf16ab8d/go.mod h1:gOpvHmFTYa4IltrdGE7lF6nIHvwfUNPOp7c8zoXwtLw= -golang.org/x/oauth2 v0.0.0-20200902213428-5d25da1a8d43/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20201109201403-9fd604954f58/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20201208152858-08078c50e5b5/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20210218202405-ba52d332ba99/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20210220000619-9bb904979d93/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20210313182246-cd4f82c27b84/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20210514164344-f6687ab2804c/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= golang.org/x/oauth2 v0.0.0-20210615190721-d04028783cf1/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20210628180205-a41e5a781914/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20210805134026-6f1e6394065a/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20210819190943-2bc19b11175f/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20211104180415-d3ed0bb246c8/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A= -golang.org/x/oauth2 v0.0.0-20220223155221-ee480838109b/go.mod h1:DAh4E804XQdzx2j+YRIaUnCqCV2RuMz24cGBJ5QYIrc= -golang.org/x/oauth2 v0.0.0-20220309155454-6242fa91716a/go.mod h1:DAh4E804XQdzx2j+YRIaUnCqCV2RuMz24cGBJ5QYIrc= -golang.org/x/oauth2 v0.0.0-20220411215720-9780585627b5/go.mod h1:DAh4E804XQdzx2j+YRIaUnCqCV2RuMz24cGBJ5QYIrc= -golang.org/x/oauth2 v0.0.0-20220608161450-d0670ef3b1eb/go.mod h1:jaDAt6Dkxork7LmZnYtzbRWj0W47D86a3TGe0YHBvmE= -golang.org/x/oauth2 v0.0.0-20220622183110-fd043fe589d2/go.mod h1:jaDAt6Dkxork7LmZnYtzbRWj0W47D86a3TGe0YHBvmE= -golang.org/x/oauth2 v0.0.0-20220822191816-0ebed06d0094/go.mod h1:h4gKUeWbJ4rQPri7E0u6Gs4e9Ri2zaLxzw5DI5XGrYg= -golang.org/x/oauth2 v0.0.0-20220909003341-f21342109be1/go.mod h1:h4gKUeWbJ4rQPri7E0u6Gs4e9Ri2zaLxzw5DI5XGrYg= -golang.org/x/oauth2 v0.0.0-20221014153046-6fdb5e3db783/go.mod h1:h4gKUeWbJ4rQPri7E0u6Gs4e9Ri2zaLxzw5DI5XGrYg= -golang.org/x/oauth2 v0.1.0/go.mod h1:G9FE4dLTsbXUu90h/Pf85g4w1D+SSAgR+q46nJZ8M4A= -golang.org/x/oauth2 v0.7.0 h1:qe6s0zUXlPX80/dITx3440hWZ7GwMwgDDyrSGTPJG/g= -golang.org/x/oauth2 v0.7.0/go.mod h1:hPLQkd9LyjfXTiRohC/41GhcFqxisoUQ99sCUOHO9x4= golang.org/x/sync v0.0.0-20180314180146-1d60e4601c6f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20181108010431-42b317875d0f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20181221193216-37e7f081c4d4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= @@ -1206,11 +932,8 @@ golang.org/x/sync v0.0.0-20190911185100-cd5d95a43a6e/go.mod h1:RxMgew5VJxzue5/jJ golang.org/x/sync v0.0.0-20200317015054-43a5402ce75a/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20200625203802-6e8e738ad208/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= -golang.org/x/sync v0.0.0-20201207232520-09787c993a3a/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20210220032951-036812b2e83c/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= -golang.org/x/sync v0.0.0-20220601150217-0de741cfad7f/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 v0.0.0-20220929204114-8fcdb60fdcc0/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.1.0 h1:wsuoTGHzEhffawBOhz5CYhcrV4IdKZbEyZjBMuTp12o= golang.org/x/sync v0.1.0/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sys v0.0.0-20171026204733-164713f0dfce/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= @@ -1263,56 +986,29 @@ golang.org/x/sys v0.0.0-20200519105757-fe76b779f299/go.mod h1:h1NjWce9XRLGQEsW7w golang.org/x/sys v0.0.0-20200523222454-059865788121/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20200803210538-64077c9b5642/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20200814200057-3d37ad5750ed/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20200905004654-be1d3432aa8f/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20200930185726-fdedc70b468f/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20201119102817-f84b799fce68/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20201201145000-ef89a241ccb3/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20210104204734-6f8348627aad/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20210112080510-489259a85091/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20210119212857-b64e53b001e4/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20210124154548-22da62e12c0c/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20210220050731-9a76102bfb43/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20210305230114-8fe3ee5dd75b/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys 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v0.0.0-20220128215802-99c3d69c2c27/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= -golang.org/x/sys v0.0.0-20220209214540-3681064d5158/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= -golang.org/x/sys v0.0.0-20220227234510-4e6760a101f9/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= -golang.org/x/sys v0.0.0-20220328115105-d36c6a25d886/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= -golang.org/x/sys v0.0.0-20220412211240-33da011f77ad/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= -golang.org/x/sys v0.0.0-20220502124256-b6088ccd6cba/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.0.0-20220503163025-988cb79eb6c6/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.0.0-20220520151302-bc2c85ada10a/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= -golang.org/x/sys v0.0.0-20220610221304-9f5ed59c137d/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= -golang.org/x/sys v0.0.0-20220615213510-4f61da869c0c/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= -golang.org/x/sys v0.0.0-20220624220833-87e55d714810/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.0.0-20220722155257-8c9f86f7a55f/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= -golang.org/x/sys v0.0.0-20220728004956-3c1f35247d10/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.0.0-20220811171246-fbc7d0a398ab/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 v0.3.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.13.0 h1:Af8nKPmuFypiUBjVoU9V20FiaFXOcuZI21p0ycVYYGE= golang.org/x/sys v0.13.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= 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 v0.3.0/go.mod h1:q750SLmJuPmVoN1blW3UFBPREJfb1KmY3vwxfr+nFDA= golang.org/x/term v0.13.0 h1:bb+I9cTfFazGW51MZqBVmZy7+JEJMouUHTUSKVQLBek= golang.org/x/term v0.13.0/go.mod h1:LTmsnFJwVN6bCy1rVCoS+qHT1HhALEFxKncY3WNNh4U= @@ -1322,11 +1018,9 @@ golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= golang.org/x/text v0.3.1-0.20180807135948-17ff2d5776d2/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/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= -golang.org/x/text v0.3.4/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= golang.org/x/text v0.3.5/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= golang.org/x/text v0.3.6/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= golang.org/x/text v0.3.7/go.mod h1:u+2+/6zg+i71rQMx5EYifcz6MCKuco9NR6JIITiCfzQ= -golang.org/x/text v0.4.0/go.mod h1:mrYo+phRRbMaCq/xk9113O4dZlRixOauAjOtrjsXDZ8= golang.org/x/text v0.5.0/go.mod h1:mrYo+phRRbMaCq/xk9113O4dZlRixOauAjOtrjsXDZ8= golang.org/x/text v0.13.0 h1:ablQoSUd0tRdKxZewP80B+BaqeKJuVhuRxj/dkrun3k= golang.org/x/text v0.13.0/go.mod h1:TvPlkZtksWOMsz7fbANvkp4WM8x/WCo/om8BMLbz+aE= @@ -1402,19 +1096,11 @@ golang.org/x/tools v0.0.0-20200717024301-6ddee64345a6/go.mod h1:njjCfa9FT2d7l9Bc 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= -golang.org/x/tools v0.0.0-20200904185747-39188db58858/go.mod h1:Cj7w3i3Rnn0Xh82ur9kSqwfTHTeVxaDqrfMjpcNT6bE= -golang.org/x/tools v0.0.0-20201110124207-079ba7bd75cd/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= -golang.org/x/tools v0.0.0-20201201161351-ac6f37ff4c2a/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= -golang.org/x/tools v0.0.0-20201208233053-a543418bbed2/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= golang.org/x/tools v0.0.0-20201224043029-2b0845dc783e/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= -golang.org/x/tools v0.0.0-20210105154028-b0ab187a4818/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= golang.org/x/tools v0.0.0-20210106214847-113979e3529a/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= golang.org/x/tools v0.1.0/go.mod h1:xkSsbof2nBLbhDlRMhhhyNLN/zl3eTqcnHD5viDpcZ0= golang.org/x/tools v0.1.1/go.mod h1:o0xws9oXOQQZyjljx8fwUC0k7L1pTE6eaCbjGeHmOkk= -golang.org/x/tools v0.1.2/go.mod h1:o0xws9oXOQQZyjljx8fwUC0k7L1pTE6eaCbjGeHmOkk= golang.org/x/tools v0.1.3/go.mod h1:o0xws9oXOQQZyjljx8fwUC0k7L1pTE6eaCbjGeHmOkk= -golang.org/x/tools v0.1.4/go.mod h1:o0xws9oXOQQZyjljx8fwUC0k7L1pTE6eaCbjGeHmOkk= -golang.org/x/tools v0.1.5/go.mod h1:o0xws9oXOQQZyjljx8fwUC0k7L1pTE6eaCbjGeHmOkk= golang.org/x/tools v0.1.12/go.mod h1:hNGJHUnrk76NpqgfD5Aqm5Crs+Hm0VOH/i9J2+nxYbc= golang.org/x/tools v0.4.0/go.mod h1:UE5sM2OK9E/d67R0ANs2xJizIymRP5gJU295PvKXxjQ= golang.org/x/tools v0.6.0 h1:BOw41kyTf3PuCW1pVQf8+Cyg8pMlkYB1oo9iJ6D/lKM= @@ -1423,9 +1109,6 @@ golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8T 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= golang.org/x/xerrors v0.0.0-20200804184101-5ec99f83aff1/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= -golang.org/x/xerrors v0.0.0-20220411194840-2f41105eb62f/go.mod 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-google.golang.org/genproto v0.0.0-20220815135757-37a418bb8959/go.mod h1:dbqgFATTzChvnt+ujMdZwITVAJHFtfyN1qUhDqEiIlk= -google.golang.org/genproto v0.0.0-20220817144833-d7fd3f11b9b1/go.mod h1:dbqgFATTzChvnt+ujMdZwITVAJHFtfyN1qUhDqEiIlk= -google.golang.org/genproto v0.0.0-20220822174746-9e6da59bd2fc/go.mod h1:dbqgFATTzChvnt+ujMdZwITVAJHFtfyN1qUhDqEiIlk= -google.golang.org/genproto v0.0.0-20220829144015-23454907ede3/go.mod h1:dbqgFATTzChvnt+ujMdZwITVAJHFtfyN1qUhDqEiIlk= -google.golang.org/genproto v0.0.0-20220829175752-36a9c930ecbf/go.mod h1:dbqgFATTzChvnt+ujMdZwITVAJHFtfyN1qUhDqEiIlk= -google.golang.org/genproto v0.0.0-20220913154956-18f8339a66a5/go.mod h1:0Nb8Qy+Sk5eDzHnzlStwW3itdNaWoZA5XeSG+R3JHSo= -google.golang.org/genproto v0.0.0-20220914142337-ca0e39ece12f/go.mod h1:0Nb8Qy+Sk5eDzHnzlStwW3itdNaWoZA5XeSG+R3JHSo= -google.golang.org/genproto v0.0.0-20220915135415-7fd63a7952de/go.mod h1:0Nb8Qy+Sk5eDzHnzlStwW3itdNaWoZA5XeSG+R3JHSo= -google.golang.org/genproto v0.0.0-20220916172020-2692e8806bfa/go.mod h1:0Nb8Qy+Sk5eDzHnzlStwW3itdNaWoZA5XeSG+R3JHSo= -google.golang.org/genproto v0.0.0-20220919141832-68c03719ef51/go.mod h1:0Nb8Qy+Sk5eDzHnzlStwW3itdNaWoZA5XeSG+R3JHSo= -google.golang.org/genproto v0.0.0-20220920201722-2b89144ce006/go.mod h1:ht8XFiar2npT/g4vkk7O0WYS1sHOHbdujxbEp7CJWbw= -google.golang.org/genproto v0.0.0-20220926165614-551eb538f295/go.mod h1:woMGP53BroOrRY3xTxlbr8Y3eB/nzAvvFM83q7kG2OI= -google.golang.org/genproto v0.0.0-20220926220553-6981cbe3cfce/go.mod h1:woMGP53BroOrRY3xTxlbr8Y3eB/nzAvvFM83q7kG2OI= -google.golang.org/genproto v0.0.0-20221010155953-15ba04fc1c0e/go.mod h1:3526vdqwhZAwq4wsRUaVG555sVgsNmIjRtO7t/JH29U= -google.golang.org/genproto v0.0.0-20221014173430-6e2ab493f96b/go.mod h1:1vXfmgAz9N9Jx0QA82PqRVauvCz1SGSz739p0f183jM= -google.golang.org/genproto v0.0.0-20221014213838-99cd37c6964a/go.mod h1:1vXfmgAz9N9Jx0QA82PqRVauvCz1SGSz739p0f183jM= -google.golang.org/genproto v0.0.0-20221025140454-527a21cfbd71/go.mod h1:9qHF0xnpdSfF6knlcsnpzUu5y+rpwgbvsyGAZPBMg4s= google.golang.org/genproto v0.0.0-20230410155749-daa745c078e1 h1:KpwkzHKEF7B9Zxg18WzOa7djJ+Ha5DzthMyZYQfEn2A= google.golang.org/genproto v0.0.0-20230410155749-daa745c078e1/go.mod h1:nKE/iIaLqn2bQwXBg8f1g2Ylh6r5MN5CmZvuzZCgsCU= google.golang.org/grpc v1.8.0/go.mod h1:yo6s7OP7yaDglbqo1J04qKzAhqBH6lvTonzMVmEdcZw= @@ -1613,30 +1188,9 @@ google.golang.org/grpc v1.28.0/go.mod h1:rpkK4SK4GF4Ach/+MFLZUBavHOvF2JJB5uozKKa google.golang.org/grpc v1.29.1/go.mod h1:itym6AZVZYACWQqET3MqgPpjcuV5QH3BxFS3IjizoKk= 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 v1.33.1/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= google.golang.org/grpc v1.35.0-dev.0.20201218190559-666aea1fb34c/go.mod h1:qjiiYl8FncCW8feJPdyg3v6XW24KsRHe+dy9BAGRRjU= -google.golang.org/grpc v1.35.0/go.mod h1:qjiiYl8FncCW8feJPdyg3v6XW24KsRHe+dy9BAGRRjU= -google.golang.org/grpc v1.36.0/go.mod h1:qjiiYl8FncCW8feJPdyg3v6XW24KsRHe+dy9BAGRRjU= -google.golang.org/grpc v1.36.1/go.mod h1:qjiiYl8FncCW8feJPdyg3v6XW24KsRHe+dy9BAGRRjU= -google.golang.org/grpc v1.37.0/go.mod h1:NREThFqKR1f3iQ6oBuvc5LadQuXVGo9rkm5ZGrQdJfM= -google.golang.org/grpc v1.37.1/go.mod h1:NREThFqKR1f3iQ6oBuvc5LadQuXVGo9rkm5ZGrQdJfM= google.golang.org/grpc v1.38.0/go.mod h1:NREThFqKR1f3iQ6oBuvc5LadQuXVGo9rkm5ZGrQdJfM= -google.golang.org/grpc v1.39.0/go.mod h1:PImNr+rS9TWYb2O4/emRugxiyHZ5JyHW5F+RPnDzfrE= -google.golang.org/grpc v1.39.1/go.mod h1:PImNr+rS9TWYb2O4/emRugxiyHZ5JyHW5F+RPnDzfrE= -google.golang.org/grpc v1.40.0/go.mod h1:ogyxbiOoUXAkP+4+xa6PZSE9DZgIHtSpzjDTB9KAK34= -google.golang.org/grpc v1.40.1/go.mod h1:ogyxbiOoUXAkP+4+xa6PZSE9DZgIHtSpzjDTB9KAK34= -google.golang.org/grpc v1.44.0/go.mod h1:k+4IHHFw41K8+bbowsex27ge2rCb65oeWqe4jJ590SU= -google.golang.org/grpc v1.45.0/go.mod h1:lN7owxKUQEqMfSyQikvvk5tf/6zMPsrK+ONuO11+0rQ= -google.golang.org/grpc v1.46.0/go.mod h1:vN9eftEi1UMyUsIF80+uQXhHjbXYbm0uXoFCACuMGWk= -google.golang.org/grpc v1.46.2/go.mod h1:vN9eftEi1UMyUsIF80+uQXhHjbXYbm0uXoFCACuMGWk= -google.golang.org/grpc v1.47.0/go.mod h1:vN9eftEi1UMyUsIF80+uQXhHjbXYbm0uXoFCACuMGWk= -google.golang.org/grpc v1.48.0/go.mod h1:vN9eftEi1UMyUsIF80+uQXhHjbXYbm0uXoFCACuMGWk= -google.golang.org/grpc v1.49.0/go.mod h1:ZgQEeidpAuNRZ8iRrlBKXZQP1ghovWIVhdJRyCDK+GI= -google.golang.org/grpc v1.50.0/go.mod h1:ZgQEeidpAuNRZ8iRrlBKXZQP1ghovWIVhdJRyCDK+GI= -google.golang.org/grpc v1.50.1/go.mod h1:ZgQEeidpAuNRZ8iRrlBKXZQP1ghovWIVhdJRyCDK+GI= google.golang.org/grpc v1.56.3 h1:8I4C0Yq1EjstUzUJzpcRVbuYA2mODtEmpWiQoN/b2nc= google.golang.org/grpc v1.56.3/go.mod h1:I9bI3vqKfayGqPUAwGdOSu7kt6oIJLixfffKrpXqQ9s= google.golang.org/grpc/cmd/protoc-gen-go-grpc v1.1.0/go.mod h1:6Kw0yEErY5E/yWrBtf03jp27GLLJujG4z/JK95pnjjw= @@ -1657,7 +1211,6 @@ google.golang.org/protobuf v1.26.0-rc.1/go.mod h1:jlhhOSvTdKEhbULTjvd4ARK9grFBp0 google.golang.org/protobuf v1.26.0/go.mod h1:9q0QmTI4eRPtz6boOQmLYwt+qCgq0jsYwAQnmE0givc= google.golang.org/protobuf v1.27.1/go.mod h1:9q0QmTI4eRPtz6boOQmLYwt+qCgq0jsYwAQnmE0givc= google.golang.org/protobuf v1.28.0/go.mod h1:HV8QOd/L58Z+nl8r43ehVNZIU/HEI6OcFqwMG9pJV4I= -google.golang.org/protobuf v1.28.1/go.mod h1:HV8QOd/L58Z+nl8r43ehVNZIU/HEI6OcFqwMG9pJV4I= google.golang.org/protobuf v1.30.0 h1:kPPoIgf3TsEvrm0PFe15JQ+570QVxYzEvvHqChK+cng= google.golang.org/protobuf v1.30.0/go.mod h1:HV8QOd/L58Z+nl8r43ehVNZIU/HEI6OcFqwMG9pJV4I= gopkg.in/DataDog/dd-trace-go.v1 v1.47.0 h1:w3mHEgOR1o52mkyCbkTM+El8DG732+Fnug4FAGhIpsk= @@ -1669,7 +1222,6 @@ gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8 gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c h1:Hei/4ADfdWqJk1ZMxUNpqntNwaWcugrBjAiHlqqRiVk= gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q= -gopkg.in/cheggaaa/pb.v1 v1.0.27/go.mod h1:V/YB90LKu/1FcN3WVnfiiE5oMCibMjukxqG/qStrOgw= gopkg.in/errgo.v2 v2.1.0/go.mod h1:hNsd1EY+bozCKY1Ytp96fpM3vjJbqLJn88ws8XvfDNI= gopkg.in/fsnotify.v1 v1.4.7/go.mod h1:Tz8NjZHkW78fSQdbUxIjBTcgA1z1m8ZHf0WmKUhAMys= gopkg.in/gemnasium/logrus-airbrake-hook.v2 v2.1.2/go.mod h1:Xk6kEKp8OKb+X14hQBKWaSkCsqBpgog8nAV2xsGOxlo= @@ -1685,7 +1237,6 @@ gopkg.in/tomb.v2 v2.0.0-20140626144623-14b3d72120e8/go.mod h1:BHsqpu/nsuzkT5BpiH gopkg.in/yaml.v2 v2.0.0-20170812160011-eb3733d160e7/go.mod h1:JAlM8MvJe8wmxCU4Bli9HhUf9+ttbYbLASfIpnQbh74= gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= -gopkg.in/yaml.v2 v2.2.3/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v2 v2.2.4/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v2 v2.2.5/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v2 v2.2.7/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= diff --git a/test/command_line_test.go b/test/command_line_test.go index dde18b2..69da65f 100644 --- a/test/command_line_test.go +++ b/test/command_line_test.go @@ -2,11 +2,14 @@ package test import ( "bytes" + "compress/gzip" "fmt" "io" "io/ioutil" "os" "os/exec" + "path/filepath" + "strings" "testing" "sigs.k8s.io/yaml" @@ -34,11 +37,17 @@ func lineCounter(r io.Reader) (int, error) { } type CommandLineConfig struct { - Playbook string `json:"playbook"` - Checks []string `json:"checks"` - Outputs []string `json:"outputs"` + LineCount []int `json:"linecount"` + Playbook string `json:"playbook"` + Outputs []string `json:"outputs"` } +/* +This test checks three things: +1. The file exists in the expected place in config.yaml +2. The file contains the expercted number of data lines +3. The file's name is the expected name. Tests useName option added in this PR +*/ func TestCommandLines(t *testing.T) { raw, err := ioutil.ReadFile(tPath) if err != nil { @@ -48,44 +57,47 @@ func TestCommandLines(t *testing.T) { if err := yaml.UnmarshalStrict(raw, &conf); err != nil { t.Error(fmt.Errorf("failed to read config %s %s", tPath, err)) } - + // read in conf, ie config.yaml in this case for _, c := range conf { cmd := exec.Command("../sifter", "run", c.Playbook) - //cmd.Stdout = os.Stdout - //cmd.Stderr = os.Stderr fmt.Printf("Running: %s\n", c.Playbook) err = cmd.Run() if err != nil { t.Errorf("Failed running %s: %s", c.Playbook, err) } else { - /* - for f, chk := range c.Outputs { - path := filepath.Join("out", f) - if _, err := os.Stat(path); err == nil { - if chk.LineCount != 0 { - file, err := os.Open(path) - var reader io.Reader - if strings.HasSuffix(path, ".gz") { - reader, _ = gzip.NewReader(file) - } else { - reader = file - } - defer file.Close() - if err == nil { - count, _ := lineCounter(reader) - if count != chk.LineCount { - t.Errorf("Incorrect number of lines: %d != %d", count, chk.LineCount) - } - } else { - t.Errorf("failed to open %s", f) + for i, chk := range c.Outputs { + // iterate through expected output paths + path := filepath.Join(filepath.Dir(c.Playbook), chk) + fmt.Printf("Checking %s \n", path) + if stat, err := os.Stat(path); err == nil { + if stat.Size() > 0 { + file, err := os.Open(path) + var reader io.Reader + if strings.HasSuffix(path, ".gz") { + reader, _ = gzip.NewReader(file) + } else { + reader = file + } + defer file.Close() + if err == nil { + // count of data lines of each expected output file and compare to expected value in config + count, _ := lineCounter(reader) + + if count != c.LineCount[i] { + t.Errorf("Incorrect number of lines: %d != %d", count, c.LineCount[i]) } + } else { + t.Errorf("failed to open %s", path) } - } else if os.IsNotExist(err) { - t.Errorf("Output %s missing", f) } + } else if os.IsNotExist(err) { + t.Errorf("Output %s missing", path) } - */ + + // remove test files when done testing + os.RemoveAll(path) + } } - os.RemoveAll("./out") + } } diff --git a/test/config.yaml b/test/config.yaml index c12b240..19024a9 100644 --- a/test/config.yaml +++ b/test/config.yaml @@ -1,18 +1,45 @@ -- playbook: examples/gdc/gdc-convert.yaml - checks: - - exists - - non-zero-lines - outputs: - - out/GDCConvert.aliquot.json.gz - - out/GDCConvert.case.json.gz - - out/GDCConvert.sample.json.gz - - playbook: examples/pathwaycommons/pathway_commons.yaml + LineCount: + - 200 + - 192 + outputs: + - output/pathway_commons.edges.edge.json.gz + - output/pathway_commons.nodes.node.json.gz - playbook: examples/pathwaycommons/gene_collect.yaml - + LineCount: + - 3 + # UseName Test, actual file name would've been sifter.newpip.sifout.json.gz without the flag + outputs: + - output_gene/sifout.json.gz - playbook: examples/gene-table/gene-table.yaml + LineCount: + - 20 + outputs: + - output/gene.table - playbook: examples/lookup/inline-table.yaml + LineCount: + - 10 + outputs: + - output/sifter.transform.test.json.gz - playbook: examples/lookup/tsv-table-replace.yaml + LineCount: + - 10 + outputs: + - output-tsv/gdc-projects.tranform.case-mondo.json.gz - playbook: examples/gdc/gdc-convert.yaml + LineCount: + - 256444 + - 106521 + - 106521 + outputs: + - output/gdc.caseGraph.edge.json.gz + - output/gdc.caseGraph.vertex.json.gz + - output/gdc.caseObject.case.json.gz - playbook: examples/pfb/transform.yaml + LineCount: + - 1138 + - 873 + outputs: + - output/sifter.edge.edge.json.gz + - output/sifter.vertex.vertex.json.gz diff --git a/test/examples/gdc/gdc-convert.yaml b/test/examples/gdc/gdc-convert.yaml index b9ae9e9..b882814 100644 --- a/test/examples/gdc/gdc-convert.yaml +++ b/test/examples/gdc/gdc-convert.yaml @@ -1,9 +1,9 @@ name: gdc -outdir: ../../out +outdir: output/ config: - cases: ../../resources/case.json + cases: ../../resources/gdc-case.json.gz schema: ../../resources/schemas inputs: @@ -23,68 +23,12 @@ pipelines: title: Case schema: "{{config.schema}}" - emit: + # Testing that this doesn't do anything + useName: False name: case - + caseGraph: - from: caseObject - graphBuild: schema: "{{config.schema}}" - #idPrefix: Case - title: Case - - sampleData: - - from: caseData - - fieldProcess: - field: samples - mapping: - cases: "{{row.id}}" - - sampleObject: - - from: sampleData - - project: - mapping: - type: sample - id: "{{row.sample_id}}" - - objectValidate: - title: Sample - schema: "{{config.schema}}" - - emit: - name: sample - - sampleGraph: - - from: sampleObject - - graphBuild: - schema: "{{config.schema}}" - #idPrefix: Sample - title: Sample - - aliquotObject: - - from: sampleData - - fieldProcess: - field: portions - mapping: - samples: "{{row.id}}" - - fieldProcess: - field: analytes - mapping: - samples: "{{row.samples}}" - - fieldProcess: - field: aliquots - mapping: - samples: "{{row.samples}}" - - project: - mapping: - type: aliquot - id: "{{row.aliquot_id}}" - - objectValidate: - title: Aliquot - schema: "{{config.schema}}" - - emit: - name: aliquot - - aliquotGraph: - - from: aliquotObject - - graphBuild: - schema: "{{config.schema}}" - #idPrefix: Aliquot - title: Aliquot + title: Case \ No newline at end of file diff --git a/test/examples/gdc/out-graph/Aliquot.Aliquot.Vertex.json.gz b/test/examples/gdc/out-graph/Aliquot.Aliquot.Vertex.json.gz deleted file mode 100644 index 0d61a5a..0000000 Binary files a/test/examples/gdc/out-graph/Aliquot.Aliquot.Vertex.json.gz and /dev/null differ diff --git a/test/examples/gdc/out-graph/Aliquot_Sample.derived_from.Edge.json.gz b/test/examples/gdc/out-graph/Aliquot_Sample.derived_from.Edge.json.gz deleted file mode 100644 index efd0fdb..0000000 Binary files a/test/examples/gdc/out-graph/Aliquot_Sample.derived_from.Edge.json.gz and /dev/null differ diff --git a/test/examples/gdc/out-graph/Case.Case.Vertex.json.gz b/test/examples/gdc/out-graph/Case.Case.Vertex.json.gz deleted file mode 100644 index 841985a..0000000 Binary files a/test/examples/gdc/out-graph/Case.Case.Vertex.json.gz and /dev/null differ diff --git a/test/examples/gdc/out-graph/Case_Project.member_of.Edge.json.gz b/test/examples/gdc/out-graph/Case_Project.member_of.Edge.json.gz deleted file mode 100644 index 1119839..0000000 Binary files a/test/examples/gdc/out-graph/Case_Project.member_of.Edge.json.gz and /dev/null differ diff --git a/test/examples/gdc/out-graph/Case_Sample.samples.Edge.json.gz b/test/examples/gdc/out-graph/Case_Sample.samples.Edge.json.gz deleted file mode 100644 index b77b9fe..0000000 Binary files a/test/examples/gdc/out-graph/Case_Sample.samples.Edge.json.gz and /dev/null differ diff --git a/test/examples/gdc/out-graph/Project_Case.cases.Edge.json.gz b/test/examples/gdc/out-graph/Project_Case.cases.Edge.json.gz deleted file mode 100644 index 43a0150..0000000 Binary files a/test/examples/gdc/out-graph/Project_Case.cases.Edge.json.gz and /dev/null differ diff --git a/test/examples/gdc/out-graph/Sample.Sample.Vertex.json.gz b/test/examples/gdc/out-graph/Sample.Sample.Vertex.json.gz deleted file mode 100644 index e9bee87..0000000 Binary files a/test/examples/gdc/out-graph/Sample.Sample.Vertex.json.gz and /dev/null differ diff --git a/test/examples/gdc/out-graph/Sample_Aliquot.aliquots.Edge.json.gz b/test/examples/gdc/out-graph/Sample_Aliquot.aliquots.Edge.json.gz deleted file mode 100644 index 602b5e2..0000000 Binary files a/test/examples/gdc/out-graph/Sample_Aliquot.aliquots.Edge.json.gz and /dev/null differ diff --git a/test/examples/gdc/out-graph/Sample_Case.derived_from.Edge.json.gz b/test/examples/gdc/out-graph/Sample_Case.derived_from.Edge.json.gz deleted file mode 100644 index 8f9bc7d..0000000 Binary files a/test/examples/gdc/out-graph/Sample_Case.derived_from.Edge.json.gz and /dev/null differ diff --git a/test/examples/gdc/out/GDCConvert.aliquot.json.gz b/test/examples/gdc/out/GDCConvert.aliquot.json.gz deleted file mode 100644 index 430d77d..0000000 Binary files a/test/examples/gdc/out/GDCConvert.aliquot.json.gz and /dev/null differ diff --git a/test/examples/gdc/out/GDCConvert.case.json.gz b/test/examples/gdc/out/GDCConvert.case.json.gz deleted file mode 100644 index 6246dc2..0000000 Binary files a/test/examples/gdc/out/GDCConvert.case.json.gz and /dev/null differ diff --git a/test/examples/gdc/out/GDCConvert.sample.json.gz b/test/examples/gdc/out/GDCConvert.sample.json.gz deleted file mode 100644 index 2716d88..0000000 Binary files a/test/examples/gdc/out/GDCConvert.sample.json.gz and /dev/null differ diff --git a/test/examples/gene-table/gene-table.yaml b/test/examples/gene-table/gene-table.yaml index e1d28a9..0df1f11 100644 --- a/test/examples/gene-table/gene-table.yaml +++ b/test/examples/gene-table/gene-table.yaml @@ -1,6 +1,6 @@ name: geneTable -outdir: ../../out +outdir: output/ docs: > This takes a Gene TSV, filters rows, selects columns and outputs a 2 diff --git a/test/examples/gene-table/out/gene.table b/test/examples/gene-table/out/gene.table deleted file mode 100644 index 56b234f..0000000 --- a/test/examples/gene-table/out/gene.table +++ /dev/null @@ -1 +0,0 @@ -GeneID Ensembl_gene_identifier diff --git a/test/examples/lookup/inline-table.yaml b/test/examples/lookup/inline-table.yaml index 06f17de..2bcae4f 100644 --- a/test/examples/lookup/inline-table.yaml +++ b/test/examples/lookup/inline-table.yaml @@ -1,9 +1,9 @@ -outdir: ../../out +outdir: output/ config: json: ../../resources/projects.json - + inputs: jsonData: diff --git a/test/examples/lookup/tsv-table-replace.yaml b/test/examples/lookup/tsv-table-replace.yaml index d9ea5af..1d38d73 100644 --- a/test/examples/lookup/tsv-table-replace.yaml +++ b/test/examples/lookup/tsv-table-replace.yaml @@ -1,7 +1,7 @@ name: gdc-projects -outdir: ../../out/ +outdir: output-tsv/ config: cases: ../../resources/case.json diff --git a/test/examples/pathwaycommons/gene_collect.yaml b/test/examples/pathwaycommons/gene_collect.yaml index 94b6e68..85fb3ab 100644 --- a/test/examples/pathwaycommons/gene_collect.yaml +++ b/test/examples/pathwaycommons/gene_collect.yaml @@ -1,5 +1,5 @@ -outdir: ../../out +outdir: output_gene config: sifFile: ../../resources/pathways.sif @@ -19,9 +19,13 @@ pipelines: init: { "_to" : [] } method: merge gpython: | - def merge(x,y): y["_from"] = x["_from"] y["_to"].append(x["_to"]) return y - - debug: {} + newpip: + - from: geneReduce + - emit: + useName: True + name: sifout + diff --git a/test/examples/pathwaycommons/pathway_commons.yaml b/test/examples/pathwaycommons/pathway_commons.yaml index 799b300..d8d2c52 100644 --- a/test/examples/pathwaycommons/pathway_commons.yaml +++ b/test/examples/pathwaycommons/pathway_commons.yaml @@ -1,6 +1,6 @@ name: pathway_commons -outdir: ../../out +outdir: output config: sifFile: ../../resources/pathways.sif @@ -17,7 +17,7 @@ pipelines: - from: sifFile - project: mapping: - nodes: + nodes: - { "_gid" : "{{row._from}}" } - { "_gid" : "{{row._to}}" } - fieldProcess: diff --git a/test/examples/pfb/transform.yaml b/test/examples/pfb/transform.yaml index f66cca5..5847205 100644 --- a/test/examples/pfb/transform.yaml +++ b/test/examples/pfb/transform.yaml @@ -2,7 +2,7 @@ config: file: ../../resources/1000G.pfb.avro -outdir: ../../out +outdir: output/ inputs: pfb: @@ -21,7 +21,7 @@ pipelines: # undo the "key" : {"string" : "value" } pattern uses for multi-type fields method: transform gpython: | - + def transform(x): if x is None: return x @@ -46,14 +46,14 @@ pipelines: vertex: - from: transform - - map: + - map: method: transform gpython: | def transform(x): o = x["object"][x["name"]] return { "gid" : x["name"] + ":" + x["id"], "label" : x["name"], "data" : o } - + - emit: name: vertex @@ -72,5 +72,5 @@ pipelines: - to - from - label - - emit: + - emit: name: edge \ No newline at end of file diff --git a/test/resources/gdc-case.json.gz b/test/resources/gdc-case.json.gz new file mode 100644 index 0000000..1bfe660 Binary files /dev/null and b/test/resources/gdc-case.json.gz differ diff --git a/test/resources/gene2ensembl.gz b/test/resources/gene2ensembl.gz index b1b764e..726d398 100644 Binary files a/test/resources/gene2ensembl.gz and b/test/resources/gene2ensembl.gz differ diff --git a/test/resources/schemas/_definitions.yaml b/test/resources/schemas/_definitions.yaml index 5308ae2..e807d83 100644 --- a/test/resources/schemas/_definitions.yaml +++ b/test/resources/schemas/_definitions.yaml @@ -22,7 +22,8 @@ foreign_key_project: # which is the user defined ID for project properties: id: - $ref: "#/UUID" + type: string + #$ref: "#/UUID" code: type: string @@ -52,7 +53,8 @@ foreign_key: # which are user defined IDs ("submitter IDs in the backend") properties: id: - $ref: "#/UUID" + type: string + #$ref: "#/UUID" submitter_id: type: string @@ -276,3 +278,33 @@ ubiquitous_properties: $ref: "#/datetime" updated_datetime: $ref: "#/datetime" + +chromosome: + type: string + description: "Reference to a chromosome" + pattern: "^(chr).*$" + +strand: + type: string + description: "Reference to a chromosome strand" + enum: + - "+" + - "-" + +genome: + type: string + description: "Reference to a genome build" + enum: + - "GRCh37" + - "GRCh38" + +expression_metric: + type: string + description: "Expression metric" + enum: + - "TPM" + - "TPM_GENE" + - "RPKM" + - "FPKM" + - "RAW_COUNT" + - "RMA" diff --git a/test/resources/schemas/_settings.yaml b/test/resources/schemas/_settings.yaml new file mode 100644 index 0000000..d7e2171 --- /dev/null +++ b/test/resources/schemas/_settings.yaml @@ -0,0 +1,6 @@ +# Global settings for the graph + +# Is the graph case centric, that we want +# to create a link between all children to case +# to expedite case filter on nodes +enable_case_cache: false diff --git a/test/resources/schemas/_terms.yaml b/test/resources/schemas/_terms.yaml index 0ca296b..e69de29 100644 --- a/test/resources/schemas/_terms.yaml +++ b/test/resources/schemas/_terms.yaml @@ -1,1841 +0,0 @@ -id: _terms - -28s_16s_ribosomal_rna_ratio: - description: > - The 28S/18S ribosomal RNA band ratio used to assess the quality of total RNA. - termDef: - term: "28s/18s Ribosomal RNA Ratio" - source: null - cde_id: null - cde_version: null - term_url: null - -a260_a280_ratio: - description: > - Numeric value that represents the sample ratio of nucleic acid absorbance at 260 nm and 280 nm, - used to determine a measure of DNA purity. - termDef: - term: Nucleic Acid Absorbance at 260 And Absorbance at 280 DNA Purity Ratio Value - source: caDSR - cde_id: 5432595 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432595&version=1.0" - -adapter_name: # TOREVIEW - description: > - Name of the sequencing adapter. - -adapter_sequence: # TOREVIEW - description: > - Base sequence of the sequencing adapter. - -age_at_diagnosis: - description: > - Age at the time of diagnosis expressed in number of days since birth. - termDef: - term: Patient Diagnosis Age Day Value - source: caDSR - cde_id: 3225640 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" - -ajcc_clinical_m: - description: > - Extent of the distant metastasis for the cancer based on evidence obtained from clinical - assessment parameters determined prior to treatment. - termDef: - term: Neoplasm American Joint Committee on Cancer Clinical Distant Metastasis M Stage - source: caDSR - cde_id: 3440331 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440331&version=1.0" - -ajcc_clinical_n: - description: > - Extent of the regional lymph node involvement for the cancer based on evidence obtained from - clinical assessment parameters determined prior to treatment. - termDef: - term: Neoplasm American Joint Committee on Cancer Clinical Regional Lymph Node N Stage - source: caDSR - cde_id: 3440330 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440330&version=1.0" - -ajcc_clinical_stage: - description: > - Stage group determined from clinical information on the tumor (T), regional node (N) and - metastases (M) and by grouping cases with similar prognosis for cancer. - termDef: - term: Neoplasm American Joint Committee on Cancer Clinical Group Stage - source: caDSR - cde_id: 3440332 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440332&version=1.0" - -ajcc_clinical_t: - description: > - Extent of the primary cancer based on evidence obtained from clinical assessment parameters - determined prior to treatment. - termDef: - term: Neoplasm American Joint Committee on Cancer Clinical Primary Tumor T Stage - source: caDSR - cde_id: 3440328 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440328&version=1.0" - -ajcc_pathologic_m: - description: > - Code to represent the defined absence or presence of distant spread or metastases (M) to - locations via vascular channels or lymphatics beyond the regional lymph nodes, using - criteria established by the American Joint Committee on Cancer (AJCC). - termDef: - term: American Joint Committee on Cancer Metastasis Stage Code - source: caDSR - cde_id: 3045439 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045439&version=1.0" - -ajcc_pathologic_n: - description: > - The codes that represent the stage of cancer based on the nodes present (N stage) according - to criteria based on multiple editions of the AJCC's Cancer Staging Manual. - termDef: - term: Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code - source: caDSR - cde_id: 3203106 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203106&version=1.0" - -ajcc_pathologic_stage: - description: > - The extent of a cancer, especially whether the disease has spread from the original site to - other parts of the body based on AJCC staging criteria. - termDef: - term: Neoplasm Disease Stage American Joint Committee on Cancer Code - source: caDSR - cde_id: 3203222 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203222&version=1.0" - -ajcc_pathologic_t: - description: > - Code of pathological T (primary tumor) to define the size or contiguous extension of the - primary tumor (T), using staging criteria from the American Joint Committee on Cancer - (AJCC). - termDef: - term: American Joint Committee on Cancer Tumor Stage Code - source: caDSR - cde_id: 3045435 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045435&version=1.0" - -alcohol_history: - description: > - A response to a question that asks whether the participant has consumed at least 12 drinks of - any kind of alcoholic beverage in their lifetime. - termDef: - term: Alcohol Lifetime History Indicator - source: caDSR - cde_id: 2201918 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2201918&version=1.0" - -alcohol_intensity: - description: > - Category to describe the patient's current level of alcohol use as self-reported by the patient. - termDef: - term: Person Self-Report Alcoholic Beverage Exposure Category - source: caDSR - cde_id: 3457767 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3457767&version=1.0" - -aliquot_quantity: - description: > - The quantity in micrograms (ug) of the aliquot(s) derived from the analyte(s) shipped for - sequencing and characterization. - termDef: - term: Biospecimen Aliquot Quantity - source: null - cde_id: null - cde_version: null - term_url: null - -aliquot_volume: - description: > - The volume in microliters (ml) of the aliquot(s) derived from the analyte(s) shipped for - sequencing and characterization. - termDef: - term: Biospecimen Aliquot Volume - source: null - cde_id: null - cde_version: null - term_url: null - -amount: # TOREVIEW - description: > - Weight in grams or volume in mL. - -analyte_quantity: - description: > - The quantity in micrograms (ug) of the analyte(s) derived from the analyte(s) shipped for - sequencing and characterization. - termDef: - term: Biospecimen Analyte Quantity - source: null - cde_id: null - cde_version: null - term_url: null - -analyte_type: - description: > - Text term that represents the kind of molecular specimen analyte. - termDef: - term: Molecular Specimen Type Text Name - source: caDSR - cde_id: 2513915 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2513915&version=2.0" - -analyte_type_id: - description: > - A single letter code used to identify a type of molecular analyte. - termDef: - term: Molecular Analyte Identification Code - source: caDSR - cde_id: 5432508 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432508&version=1.0" - -analyte_volume: - description: > - The volume in microliters (ml) of the analyte(s) derived from the analyte(s) shipped for - sequencing and characterization. - termDef: - term: Biospecimen Analyte Volume - source: null - cde_id: null - cde_version: null - term_url: null - -ann_arbor_b_symptoms: - description: > - Text term to signify whether lymphoma B-symptoms are present as noted in the patient's medical - record. - termDef: - term: Lymphoma B-Symptoms Medical Record Documented Indicator - source: caDSR - cde_id: 2902402 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2902402&version=1.0" - -ann_arbor_clinical_stage: - description: > - The classification of the clinically confirmed anatomic disease extent of lymphoma (Hodgkin's - and Non-Hodgkins) based on the Ann Arbor Staging System. - termDef: - term: Ann Arbor Clinical Stage - source: null - cde_id: null - cde_version: null - term_url: null - -ann_arbor_extranodal_involvement: - description: > - Indicator that identifies whether a patient with malignant lymphoma has lymphomatous involvement - of an extranodal site. - termDef: - term: Lymphomatous Extranodal Site Involvement Indicator - source: caDSR - cde_id: 3364582 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3364582&version=1.0" - -ann_arbor_pathologic_stage: - description: > - The classification of the pathologically confirmed anatomic disease extent of lymphoma - (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System. - termDef: - term: Ann Arbor Pathologic Stage - source: null - cde_id: null - cde_version: null - term_url: null - -ann_arbor_tumor_stage: - description: > - The classification of the anatomic disease extent of lymphoma (Hodgkin's and Non-Hodgkins) based - on the Ann Arbor Staging System. - termDef: - term: Ann Arbor Tumor Stage - source: null - cde_id: null - cde_version: null - term_url: null - -base_caller_name: # TOREVIEW - description: > - Name of the base caller. - -base_caller_version: # TOREVIEW - description: > - Version of the base caller. - -biomarker_name: - description: > - The name of the biomarker being tested for this specimen and set of test results. - termDef: - term: Biomarker Name - source: caDSR - cde_id: 5473 - cde_version: 11.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5473&version=2.31" - -biomarker_result: - description: > - Text term to define the results of genetic testing. - termDef: - term: Laboratory Procedure Genetic Abnormality Test Result Type - source: caDSR - cde_id: 3234680 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3234680&version=1.0" - -biomarker_test_method: - description: > - Text descriptor of a molecular analysis method used for an individual. - termDef: - term: Disease Detection Molecular Analysis Method Type - source: caDSR - cde_id: 3121575 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121575&version=1.0" - -biospecimen_anatomic_site: - description: > - Text term that represents the name of the primary disease site of the submitted tumor sample. - termDef: - term: Submitted Tumor Sample Primary Anatomic Site - source: caDSR - cde_id: 4742851 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4742851&version=1.0" - -bmi: - description: > - The body mass divided by the square of the body height expressed in units of kg/m^2. - termDef: - term: Body Mass Index (BMI) - source: caDSR - cde_id: 4973892 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4973892&version=1.0" - -burkitt_lymphoma_clinical_variant: - description: > - Burkitt's lymphoma categorization based on clinical features that differ from other forms of the - same disease. - termDef: - term: Burkitt Lymphoma Clinical Variant Type - source: caDSR - cde_id: 3770421 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3770421&version=1.0" - -cause_of_death: - description: > - Text term to identify the cause of death for a patient. - termDef: - term: Patient Death Reason - source: caDSR - cde_id: 2554674 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2554674&version=3.0" - -cea_level_preoperative: - description: > - Numeric value of the Carcinoembryonic antigen or CEA at the time before surgery. [Manually- - curated] - termDef: - term: Preoperative Carcinoembryonic Antigen Result Value - source: caDSR - cde_id: 2716510 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2716510&version=1.0" - -cigarettes_per_day: - description: > - The average number of cigarettes smoked per day. - termDef: - term: Smoking Use Average Number - source: caDSR - cde_id: 2001716 - cde_version: 4.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2001716&version=4.0" - -circumferential_resection_margin: - description: > - A value in millimeters indicating the measured length between a malignant lesion of the - colon or rectum and the nearest radial (or circumferential) border of tissue removed during - cancer surgery. - termDef: - term: Colorectal Surgical Margin Circumferential Distance Measurement - source: caDSR - cde_id: 64202 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64202&version=3.0" - -classification_of_tumor: - description: > - Text that describes the kind of disease present in the tumor specimen as related to a specific - timepoint. - termDef: - term: Tumor Tissue Disease Description Type - source: caDSR - cde_id: 3288124 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" - -colon_polyps_history: - description: > - Yes/No indicator to describe if the subject had a previous history of colon polyps as noted - in the history/physical or previous endoscopic report (s). - termDef: - term: Colon Carcinoma Polyp Occurrence Indicator - source: caDSR - cde_id: 3107197 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3107197&version=1.0" - -composition: - description: > - Text term that represents the cellular composition of the sample. - termDef: - term: Biospecimen Cellular Composition Type - source: caDSR - cde_id: 5432591 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432591&version=1.0" - -concentration: - description: > - Numeric value that represents the concentration of an analyte or aliquot extracted from the - sample or sample portion, measured in milligrams per milliliter. - termDef: - term: Biospecimen Analyte or Aliquot Extracted Concentration Milligram per Milliliter Value - source: caDSR - cde_id: 5432594 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432594&version=1.0" - -creation_datetime: - description: > - The datetime of portion creation encoded as seconds from epoch. - termDef: - term: Biospecimen Portion Creation Seconds Date/Time - source: caDSR - cde_id: 5432592 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432592&version=1.0" - -current_weight: - description: > - Numeric value that represents the current weight of the sample, measured in milligrams. - termDef: - term: Tissue Sample Current Weight Milligram Value - source: caDSR - cde_id: 5432606 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432606&version=1.0" - -data_category: # TOREVIEW - description: > - Broad categorization of the contents of the data file. - -data_file_error_type: # TOREVIEW - description: > - Type of error for the data file object. - -data_format: # TOREVIEW - description: > - Format of the data files. - -data_type: # TOREVIEW - description: > - Specific content type of the data file. - -datetime: - description: > - A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm] - -days_to_birth: - description: > - Time interval from a person's date of birth to the date of initial pathologic diagnosis, - represented as a calculated negative number of days. - termDef: - term: Person Birth Date Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3008233 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008233&version=1.0" - -days_to_collection: - description: > - Time interval from the date of biospecimen collection to the date of initial pathologic - diagnosis, represented as a calculated number of days. - termDef: - term: Biospecimen Collection Date Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3008340 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008340&version=1.0" - -days_to_death: - description: > - Time interval from a person's date of death to the date of initial pathologic diagnosis, - represented as a calculated number of days. - termDef: - term: Death Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3165475 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3165475&version=1.0" - -days_to_hiv_diagnosis: - description: > - Time interval from the date of the initial pathologic diagnosis to the date of human - immunodeficiency diagnosis, represented as a calculated number of days. - termDef: - term: Human Immunodeficiency Virus Diagnosis Subtract Initial Pathologic Diagnosis Time Duration Day Calculation Value - source: caDSR - cde_id: 4618491 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4618491&version=1.0" - -days_to_last_follow_up: - description: > - Time interval from the date of last follow up to the date of initial pathologic diagnosis, - represented as a calculated number of days. - termDef: - term: Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3008273 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" - -days_to_last_known_disease_status: - description: > - Time interval from the date of last follow up to the date of initial pathologic diagnosis, - represented as a calculated number of days. - termDef: - term: Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3008273 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" - -days_to_new_event: - description: > - Time interval from the date of new tumor event including progression, recurrence and new - primary malignacies to the date of initial pathologic diagnosis, represented as a calculated - number of days. - termDef: - term: New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3392464 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" - -days_to_recurrence: - description: > - Time interval from the date of new tumor event including progression, recurrence and new primary - malignancies to the date of initial pathologic diagnosis, represented as a calculated number of - days. - termDef: - term: New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3392464 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" - -days_to_sample_procurement: - description: > - The number of days from the date the patient was diagnosed to the date of the procedure that - produced the sample. - -days_to_treatment: - description: > - Number of days from date of initial pathologic diagnosis that treatment began. - termDef: - term: Days to Treatment Start - source: null - cde_id: null - cde_version: null - term_url: null - -days_to_treatment_end: - description: > - Time interval from the date of the initial pathologic diagnosis to the date of treatment end, - represented as a calculated number of days. - termDef: - term: Treatment End Subtract First Pathologic Diagnosis Day Calculation Value - source: caDSR - cde_id: 5102431 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102431&version=1.0" - -days_to_treatment_start: - description: > - Time interval from the date of the initial pathologic diagnosis to the start of treatment, - represented as a calculated number of days. - termDef: - term: Treatment Start Subtract First Pathologic Diagnosis Time Day Calculation Value - source: caDSR - cde_id: 5102411 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102411&version=1.0" - -diagnosis_pathologically_confirmed: - description: > - The histologic description of tissue or cells confirmed by a pathology review of frozen or - formalin fixed slide(s) completed after the diagnostic pathology review of the tumor sample used - to extract analyte(s). - termDef: - term: Post-Diagnostic Pathology Review Confirmation - source: null - cde_id: null - cde_version: null - term_url: null - -dlco_ref_predictive_percent: - description: > - The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide - detected in a patient's lungs. - termDef: - term: Lung Carbon Monoxide Diffusing Capability Test Assessment Predictive Value Percentage Value - source: caDSR - cde_id: 2180255 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2180255&version=1.0" - -encoding: - description: > - Version of ASCII encoding of quality values found in the file. - termDef: - term: Encoding - source: FastQC - cde_id: null - cde_version: null - term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" - -estrogen_receptor_percent_positive_ihc: - description: > - Classification to represent ER Positive results expressed as a percentage value. - termDef: - term: ER Level Cell Percentage Category - source: caDSR - cde_id: 3128341 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128341&version=1.0" - -estrogen_receptor_result_ihc: - description: > - Text term to represent the overall result of Estrogen Receptor (ER) testing. - termDef: - term: Breast Carcinoma Estrogen Receptor Status - source: caDSR - cde_id: 2957359 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957359&version=2.0" - -ethnicity: - description: > - An individual's self-described social and cultural grouping, specifically whether an individual - describes themselves as Hispanic or Latino. The provided values are based on the categories - defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. - termDef: - term: Ethnic Group Category Text - source: caDSR - cde_id: 2192217 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192217&version=2.0" - -experiment_name: # TOREVIEW - description: > - Submitter-defined name for the experiment. - -experimental_strategy: # TOREVIEW - description: > - The sequencing strategy used to generate the data file. - -fastq_name: # TOREVIEW - description: > - Names of FASTQs. - -fev1_ref_post_bronch_percent: - description: > - The percentage comparison to a normal value reference range of the volume of air that a - patient can forcibly exhale from the lungs in one second post-bronchodilator. - termDef: - term: Post Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value - source: caDSR - cde_id: 3302948 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302948&version=1.0" - -fev1_ref_pre_bronch_percent: - description: > - The percentage comparison to a normal value reference range of the volume of air that a - patient can forcibly exhale from the lungs in one second pre-bronchodilator. - termDef: - term: Pre Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value - source: caDSR - cde_id: 3302947 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302947&version=1.0" - -fev1_fvc_post_bronch_percent: - description: > - Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided - by the Forced Vital Capacity (FVC) post-bronchodilator. - termDef: - term: Post Bronchodilator FEV1/FVC Percent Value - source: caDSR - cde_id: 3302956 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302956&version=1.0" - -fev1_fvc_pre_bronch_percent: - description: > - Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided - by the Forced Vital Capacity (FVC) pre-bronchodilator. - termDef: - term: Pre Bronchodilator FEV1/FVC Percent Value - source: caDSR - cde_id: 3302955 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302955&version=1.0" - -figo_stage: - description: > - The extent of a cervical or endometrial cancer within the body, especially whether the - disease has spread from the original site to other parts of the body, as described by the - International Federation of Gynecology and Obstetrics (FIGO) stages. - termDef: - term: Gynecologic Tumor Grouping Cervical Endometrial FIGO 2009 Stage - source: caDSR - cde_id: 3225684 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225684&version=1.0" - -file_name: # TOREVIEW - description: > - The name (or part of a name) of a file (of any type). - -file_size: # TOREVIEW - description: > - The size of the data file (object) in bytes. - -file_state: # TOREVIEW - description: > - The current state of the data file object. - -flow_cell_barcode: # TOREVIEW - description: > - Flow Cell Barcode. - -freezing_method: - description: > - Text term that represents the method used for freezing the sample. - termDef: - term: Tissue Sample Freezing Method Type - source: caDSR - cde_id: 5432607 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432607&version=1.0" - -gender: - description: > - Text designations that identify gender. Gender is described as the assemblage of properties that - distinguish people on the basis of their societal roles. [Explanatory Comment 1: Identification - of gender is based upon self-report and may come from a form, questionnaire, interview, etc.] - termDef: - term: Person Gender Text Type - source: caDSR - cde_id: 2200604 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2200604&version=3.0" - -height: - description: > - The height of the patient in centimeters. - termDef: - term: Patient Height Measurement - source: caDSR - cde_id: 649 - cde_version: 4.1 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=649&version=4.1" - -her2_erbb2_percent_positive_ihc: - description: > - Classification to represent the number of positive HER2/ERBB2 cells in a specimen or sample. - termDef: - term: HER2 ERBB Positive Finding Cell Percentage Category - source: caDSR - cde_id: 3086980 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3086980&version=1.0" - -her2_erbb2_result_fish: - description: > - the type of outcome for HER2 as determined by an in situ hybridization (ISH) assay. - termDef: - term: Laboratory Procedure HER2/neu in situ Hybridization Outcome Type - source: caDSR - cde_id: 2854089 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2854089&version=1.0" - -her2_erbb2_result_ihc: - description: > - Text term to signify the result of the medical procedure that involves testing a sample of - blood or tissue for HER2 by histochemical localization of immunoreactive substances using - labeled antibodies as reagents. - termDef: - term: Laboratory Procedure HER2/neu Immunohistochemistry Receptor Status - source: caDSR - cde_id: 2957563 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957563&version=2.0" - -hiv_positive: - description: > - Text term to signify whether a physician has diagnosed HIV infection in a patient. - termDef: - term: Physician Diagnosed HIV Infection Personal Medical History Yes No Not Applicable Indicator - source: caDSR - cde_id: 4030799 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4030799&version=1.0" - -hpv_positive_type: - description: > - Text classification to represent the strain or type of human papillomavirus identified in an - individual. - termDef: - term: Human Papillomavirus Type - source: caDSR - cde_id: 2922649 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2922649&version=1.0" - -hpv_status: - description: > - The findings of the oncogenic HPV. - termDef: - term: Oncogenic Human Papillomavirus Result Type - source: caDSR - cde_id: 2230033 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2230033&version=1.0" - -includes_spike_ins: # TOREVIEW - description: > - Spike-in included? - -initial_weight: - description: > - Numeric value that represents the initial weight of the sample, measured in milligrams. - termDef: - term: Tissue Sample Initial Weight Milligram Value - source: caDSR - cde_id: 5432605 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432605&version=1.0" - -instrument_model: - description: > - Numeric value that represents the sample dimension that is greater than the shortest - dimension and less than the longest dimension, measured in millimeters. - termDef: - term: Tissue Sample Intermediate Dimension Millimeter Measurement - source: caDSR - cde_id: 5432604 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432604&version=1.0" - -intermediate_dimension: # TOREVIEW - description: > - Intermediate dimension of the sample, in millimeters. - -is_ffpe: - description: > - Indicator to signify whether or not the tissue sample was fixed in formalin and embedded in - paraffin (FFPE). - termDef: - term: Specimen Processing Formalin Fixed Paraffin Embedded Tissue Indicator - source: caDSR - cde_id: 4170557 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4170557&version=1.0" - -is_paired_end: # TOREVIEW - description: > - Are the reads paired end? - -last_known_disease_status: - description: > - Text term that describes the last known state or condition of an individual's neoplasm. - termDef: - term: Person Last Known Neoplasm Status - source: caDSR - cde_id: 5424231 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2759550&version=1.0" - -laterality: - description: > - For tumors in paired organs, designates the side on which the cancer originates. - termDef: - term: Primary Tumor Laterality - source: caDSR - cde_id: 827 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=827&version=3.0" - -ldh_level_at_diagnosis: - description: > - The 2 decimal place numeric laboratory value measured, assigned or computed related to the - assessment of lactate dehydrogenase in a specimen. - termDef: - term: Laboratory Procedure Lactate Dehydrogenase Result Integer::2 Decimal Place Value - source: caDSR - cde_id: 2798766 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2798766&version=1.0" - -ldh_normal_range_upper: - description: > - The top value of the range of statistical characteristics that are supposed to represent - accepted standard, non-pathological pattern for lactate dehydrogenase (units not specified). - termDef: - term: Laboratory Procedure Lactate Dehydrogenase Result Upper Limit of Normal Value - source: caDSR - cde_id: 2597015 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2597015&version=1.0" - -library_strategy: # TOREVIEW - description: > - Library strategy. - -library_selection: # TOREVIEW - description: > - Library Selection Method - -library_name: # TOREVIEW - description: > - Name of the library. - -library_preparation_kit_name: # TOREVIEW - description: > - Name of Library Preparation Kit - -library_preparation_kit_vendor: # TOREVIEW - description: > - Vendor of Library Preparation Kit - -library_preparation_kit_catalog_number: # TOREVIEW - description: > - Catalog of Library Preparation Kit - -library_preparation_kit_version: # TOREVIEW - description: > - Version of Library Preparation Kit - -library_strand: # TOREVIEW - description: > - Library stranded-ness. - -longest_dimension: - description: > - Numeric value that represents the longest dimension of the sample, measured in millimeters. - termDef: - term: Tissue Sample Longest Dimension Millimeter Measurement - source: caDSR - cde_id: 5432602 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432602&version=1.0" - -lymph_nodes_positive: - description: > - The number of lymph nodes involved with disease as determined by pathologic examination. - termDef: - term: Lymph Node(s) Positive Number - source: caDSR - cde_id: 89 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=89&version=3.0" - -lymphatic_invasion_present: - description: > - A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating - lymphatic involvement - termDef: - term: Lymphatic/Small vessel Invasion Ind - source: caDSR - cde_id: 64171 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64171&version=3.0" - -method_of_diagnosis: - description: > - The method used to initially the patient's diagnosis. - termDef: - term: Method of Diagnosis - source: null - cde_id: null - cde_version: null - term_url: null - -method_of_sample_procurement: - description: > - The method used to procure the sample used to extract analyte(s). - termDef: - term: Method of Sample Procurement - source: null - cde_id: null - cde_version: null - term_url: null - -md5sum: # TOREVIEW - description: > - The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital - fingerprint. - -microsatellite_instability_abnormal: - description: > - The yes/no indicator to signify the status of a tumor for microsatellite instability. - termDef: - term: Microsatellite Instability Occurrence Indicator - source: caDSR - cde_id: 3123142 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3123142&version=1.0" - -morphology: - description: > - The third edition of the International Classification of Diseases for Oncology, published in - 2000 used principally in tumor and cancer registries for coding the site (topography) and the - histology (morphology) of neoplasms. The study of the structure of the cells and their - arrangement to constitute tissues and, finally, the association among these to form organs. In - pathology, the microscopic process of identifying normal and abnormal morphologic - characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A - system of numbered categories for representation of data. - termDef: - term: International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code - source: caDSR - cde_id: 3226275 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226275&version=1.0" - -new_event_anatomic_site: - description: > - Text term to specify the anatomic location of the return of tumor after treatment. - termDef: - term: New Neoplasm Event Occurrence Anatomic Site - source: caDSR - cde_id: 3108271 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3108271&version=2.0" - -new_event_type: - description: > - Text term to identify a new tumor event. - termDef: - term: New Neoplasm Event Type - source: caDSR - cde_id: 3119721 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3119721&version=1.0" - -normal_tumor_genotype_snp_match: - description: > - Text term that represents whether or not the genotype of the normal tumor matches or if the data - is not available. - termDef: - term: Normal Tumor Genotype Match Indicator - source: caDSR - cde_id: 4588156 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4588156&version=1.0" - -number_proliferating_cells: - description: > - Numeric value that represents the count of proliferating cells determined during pathologic - review of the sample slide(s). - termDef: - term: Pathology Review Slide Proliferating Cell Count - source: caDSR - cde_id: 5432636 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432636&version=1.0" - -oct_embedded: - description: > - Indicator of whether or not the sample was embedded in Optimal Cutting Temperature (OCT) compound. - termDef: - term: Tissue Sample Optimal Cutting Temperature Compound Embedding Indicator - source: caDSR - cde_id: 5432538 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432538&version=1.0" - -pack_years_smoked: - description: > - Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes - smoked per day x number of years smoked divided by 20. - termDef: - term: Person Cigarette Smoking History Pack Year Value - source: caDSR - cde_id: 2955385 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" - -percent_eosinophil_infiltration: - description: > - Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or - specimen. - termDef: - term: Specimen Eosinophilia Percentage Value - source: caDSR - cde_id: 2897700 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897700&version=2.0" - -percent_gc_content: - description: > - The overall %GC of all bases in all sequences. - termDef: - term: "%GC" - source: FastQC - cde_id: null - cde_version: null - term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" - -percent_granulocyte_infiltration: - description: > - Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or - specimen. - termDef: - term: Specimen Granulocyte Infiltration Percentage Value - source: caDSR - cde_id: 2897705 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897705&version=2.0" - -percent_inflam_infiltration: - description: > - Numeric value to represent local response to cellular injury, marked by capillary dilatation, - edema and leukocyte infiltration; clinically, inflammation is manifest by reddness, heat, pain, - swelling and loss of function, with the need to heal damaged tissue. - termDef: - term: Specimen Inflammation Change Percentage Value - source: caDSR - cde_id: 2897695 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897695&version=1.0" - -percent_lymphocyte_infiltration: - description: > - Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue - normal sample or specimen. - termDef: - term: Specimen Lymphocyte Infiltration Percentage Value - source: caDSR - cde_id: 2897710 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897710&version=2.0" - -percent_monocyte_infiltration: - description: > - Numeric value to represent the percentage of monocyte infiltration in a sample or specimen. - termDef: - term: Specimen Monocyte Infiltration Percentage Value - source: caDSR - cde_id: 5455535 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5455535&version=1.0" - -percent_necrosis: - description: > - Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen. - termDef: - term: Malignant Neoplasm Necrosis Percentage Value - source: caDSR - cde_id: 2841237 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841237&version=1.0" - -percent_neutrophil_infiltration: - description: > - Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or - specimen. - termDef: - term: Malignant Neoplasm Neutrophil Infiltration Percentage Cell Value - source: caDSR - cde_id: 2841267 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841267&version=1.0" - -percent_normal_cells: - description: > - Numeric value to represent the percentage of normal cell content in a malignant tumor sample or - specimen. - termDef: - term: Malignant Neoplasm Normal Cell Percentage Value - source: caDSR - cde_id: 2841233 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841233&version=1.0" - -percent_stromal_cells: - description: > - Numeric value to represent the percentage of reactive cells that are present in a malignant - tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc. - termDef: - term: Malignant Neoplasm Stromal Cell Percentage Value - source: caDSR - cde_id: 2841241 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841241&version=1.0" - -percent_tumor_cells: - description: > - Numeric value that represents the percentage of infiltration by granulocytes in a sample. - termDef: - term: Specimen Tumor Cell Percentage Value - source: caDSR - cde_id: 5432686 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432686&version=1.0" - -percent_tumor_nuclei: - description: > - Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen. - termDef: - term: Malignant Neoplasm Neoplasm Nucleus Percentage Cell Value - source: caDSR - cde_id: 2841225 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841225&version=1.0" - -perineural_invasion_present: - description: > - a yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is - present. - termDef: - term: Tumor Perineural Invasion Ind - source: caDSR - cde_id: 64181 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64181&version=3.0" - -platform: # TOREVIEW - description: > - Name of the platform used to obtain data. - -portion_number: - description: > - Numeric value that represents the sequential number assigned to a portion of the sample. - termDef: - term: Biospecimen Portion Sequence Number - source: caDSR - cde_id: 5432711 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432711&version=1.0" - -portion_weight: - description: > - Numeric value that represents the sample portion weight, measured in milligrams. - termDef: - term: Biospecimen Portion Weight Milligram Value - source: caDSR - cde_id: 5432593 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432593&version=1.0" - -preservation_method: - description: > - Text term that represents the method used to preserve the sample. - termDef: - term: Tissue Sample Preservation Method Type - source: caDSR - cde_id: 5432521 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432521&version=1.0" - -primary_diagnosis: - description: > - Text term for the structural pattern of cancer cells used to define a microscopic diagnosis. - termDef: - term: Neoplasm Histologic Type Name - source: caDSR - cde_id: 3081934 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3081934&version=3.0" - -prior_malignancy: - description: > - Text term to describe the patient's history of prior cancer diagnosis and the spatial location - of any previous cancer occurrence. - termDef: - term: Prior Cancer Diagnosis Occurrence Description Text - source: caDSR - cde_id: 3382736 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3382736&version=2.0" - -prior_treatment: - description: > - A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents - received before the body specimen was collected. - termDef: - term: Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator - source: caDSR - cde_id: 4231463 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" - -progesterone_receptor_percent_positive_ihc: - description: > - Classification to represent Progesterone Receptor Positive results expressed as a percentage - value. - termDef: - term: Progesterone Receptor Level Cell Percentage Category - source: caDSR - cde_id: 3128342 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128342&version=1.0" - -progesterone_receptor_result_ihc: - description: > - Text term to represent the overall result of Progresterone Receptor (PR) testing. - termDef: - term: Breast Carcinoma Progesterone Receptor Status - source: caDSR - cde_id: 2957357 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957357&version=2.0" - -progression_or_recurrence: - description: > - Yes/No/Unknown indicator to identify whether a patient has had a new tumor event - after initial treatment. - termDef: - term: New Neoplasm Event Post Initial Therapy Indicator - source: caDSR - cde_id: 3121376 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121376&version=1.0" - -project_id: # TOREVIEW - description: > - Unique ID for any specific defined piece of work that is undertaken or attempted to - meet a single requirement. - -qc_metric_state: - description: > - State classification given by FASTQC for the metric. Metric specific details about the states - are available on their website. - termDef: - term: QC Metric State - source: FastQC - cde_id: null - cde_version: null - term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/" - -race: - description: > - An arbitrary classification of a taxonomic group that is a division of a species. It usually - arises as a consequence of geographical isolation within a species and is characterized by - shared heredity, physical attributes and behavior, and in the case of humans, by common history, - nationality, or geographic distribution. The provided values are based on the categories defined - by the U.S. Office of Management and Business and used by the U.S. Census Bureau. - termDef: - term: Race Category Text - source: caDSR - cde_id: 2192199 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192199&version=1.0" - -read_length: # TOREVIEW - description: > - The length of the reads. - -read_group_name: # TOREVIEW - description: > - The name of the read group. - -relationship_age_at_diagnosis: - description: > - The age (in years) when the patient's relative was first diagnosed. - termDef: - term: Relative Diagnosis Age Value - source: caDSR - cde_id: 5300571 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5300571&version=1.0" - -relationship_type: - description: > - The subgroup that describes the state of connectedness between members of the unit of society - organized around kinship ties. - termDef: - term: Family Member Relationship Type - source: caDSR - cde_id: 2690165 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2690165&version=2.0" - -relative_with_cancer_history: - description: > - Indicator to signify whether or not an individual's biological relative has been diagnosed with - another type of cancer. - termDef: - term: Other Cancer Biological Relative History Indicator - source: caDSR - cde_id: 3901752 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3901752&version=1.0" - -residual_disease: - description: > - Text terms to describe the status of a tissue margin following surgical resection. - termDef: - term: Surgical Margin Resection Status - source: caDSR - cde_id: 2608702 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2608702&version=1.0" - -RIN: - description: > - A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the - RNA sample including the presence or absence of degradation products. - termDef: - term: Biospecimen RNA Integrity Number Value - source: caDSR - cde_id: 5278775 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5278775&version=1.0" - -sample_type: - description: > - Text term to describe the source of a biospecimen used for a laboratory test. - termDef: - term: Specimen Type Collection Biospecimen Type - source: caDSR - cde_id: 3111302 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3111302&version=2.0" - -sample_type_id: # TOREVIEW - description: > - The accompanying sample type id for the sample type. - -section_location: # TOREVIEW - description: > - Tissue source of the slide. - -sequencing_center: # TOREVIEW - description: > - Name of the center that provided the sequence files. - -shortest_dimension: - description: > - Numeric value that represents the shortest dimension of the sample, measured in millimeters. - termDef: - term: Tissue Sample Short Dimension Millimeter Measurement - source: caDSR - cde_id: 5432603 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432603&version=1.0" - -site_of_resection_or_biopsy: - description: > - The third edition of the International Classification of Diseases for Oncology, published in - 2000, used principally in tumor and cancer registries for coding the site (topography) and the - histology (morphology) of neoplasms. The description of an anatomical region or of a body part. - Named locations of, or within, the body. A system of numbered categories for representation of - data. - termDef: - term: International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code - source: caDSR - cde_id: 3226281 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226281&version=1.0" - -size_selection_range: # TOREVIEW - description: > - Range of size selection. - -smoking_history: - description: > - Category describing current smoking status and smoking history as self-reported by a patient. - termDef: - term: Smoking History - source: caDSR - cde_id: 2181650 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" - -smoking_intensity: - description: > - Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes - smoked per day x number of years smoked divided by 20 - termDef: - term: Person Cigarette Smoking History Pack Year Value - source: caDSR - cde_id: 2955385 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" - -source_center: # TOREVIEW - description: > - Name of the center that provided the item. - -spectrophotometer_method: - description: > - Name of the method used to determine the concentration of purified nucleic acid within a - solution. - termDef: - term: Purification Nucleic Acid Solution Concentration Determination Method Type - source: caDSR - cde_id: 3008378 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008378&version=1.0" - -spike_ins_fasta: # TOREVIEW - description: > - Name of the FASTA file that contains the spike-in sequences. - -spike_ins_concentration: # TOREVIEW - description: > - Spike in concentration. - -state: # TOREVIEW - description: > - The current state of the object. - -target_capture_kit_name: # TOREVIEW - description: > - Name of Target Capture Kit. - -target_capture_kit_vendor: # TOREVIEW - description: > - Vendor of Target Capture Kit. - -target_capture_kit_catalog_number: # TOREVIEW - description: > - Catalog of Target Capture Kit. - -target_capture_kit_version: # TOREVIEW - description: > - Version of Target Capture Kit. - -target_capture_kit_target_region: # TOREVIEW - description: > - Target Capture Kit BED file. - -therapeutic_agents: - description: > - Text identification of the individual agent(s) used as part of a prior treatment regimen. - termDef: - term: Prior Therapy Regimen Text - source: caDSR - cde_id: 2975232 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2975232&version=1.0" - -time_between_clamping_and_freezing: - description: > - Numeric representation of the elapsed time between the surgical clamping of blood supply and - freezing of the sample, measured in minutes. - termDef: - term: Tissue Sample Clamping and Freezing Elapsed Minute Time - source: caDSR - cde_id: 5432611 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432611&version=1.0" - -time_between_excision_and_freezing: - description: > - Numeric representation of the elapsed time between the excision and freezing of the sample, - measured in minutes. - termDef: - term: Tissue Sample Excision and Freezing Elapsed Minute Time - source: caDSR - cde_id: 5432612 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432612&version=1.0" - -tissue_or_organ_of_origin: - description: > - Text term that describes the anatomic site of the tumor or disease. - termDef: - term: Tumor Disease Anatomic Site - source: caDSR - cde_id: 3427536 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3427536&version=3.0" - -tissue_type: - description: > - Text term that represents a description of the kind of tissue collected with respect to disease - status or proximity to tumor tissue. - termDef: - term: Tissue Sample Description Type - source: caDSR - cde_id: 5432687 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432687&version=1.0" - -to_trim_adapter_sequence: # TOREVIEW - description: > - Does the user suggest adapter trimming? - -tobacco_smoking_onset_year: - description: > - The year in which the participant began smoking. - termDef: - term: Started Smoking Year - source: caDSR - cde_id: 2228604 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228604&version=1.0" - -tobacco_smoking_quit_year: - description: > - The year in which the participant quit smoking. - termDef: - term: Stopped Smoking Year - source: caDSR - cde_id: 2228610 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228610&version=1.0" - -tobacco_smoking_status: - description: > - Category describing current smoking status and smoking history as self-reported by a - patient. - termDef: - term: Patient Smoking History Category - source: caDSR - cde_id: 2181650 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" - -total_sequences: - description: > - A count of the total number of sequences processed. - termDef: - term: Total Sequences - source: FastQC - cde_id: null - cde_version: null - term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" - -treatment_anatomic_site: - description: > - The anatomic site or field targeted by a treatment regimen or single agent therapy. - termDef: - term: Treatment Anatomic Site - source: null - cde_id: null - cde_version: null - term_url: null - -treatment_intent_type: - description: > - Text term to identify the reason for the administration of a treatment regimen. [Manually-curated] - termDef: - term: Treatment Regimen Intent Type - source: caDSR - cde_id: 2793511 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2793511&version=1.0" - -treatment_or_therapy: - description: > - A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents - received before the body specimen was collected. - termDef: - term: Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator - source: caDSR - cde_id: 4231463 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" - -treatment_outcome: - description: > - Text term that describes the patient¿s final outcome after the treatment was administered. - termDef: - term: Treatment Outcome Type - source: caDSR - cde_id: 5102383 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102383&version=1.0" - -treatment_type: - description: > - Text term that describes the kind of treatment administered. - termDef: - term: Treatment Method Type - source: caDSR - cde_id: 5102381 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102381&version=1.0" - -tumor_grade: - description: > - Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation - and aggressiveness. - termDef: - term: Neoplasm Histologic Grade - source: caDSR - cde_id: 2785839 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2785839&version=2.0" - -tumor_code: # TOREVIEW - description: > - Diagnostic tumor code of the tissue sample source. - -tumor_code_id: # TOREVIEW - description: > - BCR-defined id code for the tumor sample. - -tumor_descriptor: - description: > - Text that describes the kind of disease present in the tumor specimen as related to a specific - timepoint. - termDef: - term: Tumor Tissue Disease Description Type - source: caDSR - cde_id: 3288124 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" - -tumor_stage: - description: > - The extent of a cancer in the body. Staging is usually based on the size of the tumor, whether - lymph nodes contain cancer, and whether the cancer has spread from the original site to other - parts of the body. The accepted values for tumor_stage depend on the tumor site, type, and - accepted staging system. These items should accompany the tumor_stage value as associated - metadata. - termDef: - term: Tumor Stage - source: NCIt - cde_id: C16899 - cde_version: null - term_url: "https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI%20Thesaurus&code=C16899" - -UUID: - description: > - A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to - be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be - different. Its relatively small size lends itself well to sorting, ordering, and hashing of all - sorts, storing in databases, simple allocation, and ease of programming in general. - termDef: - term: Universally Unique Identifier - source: NCIt - cde_id: C54100 - cde_version: null - term_url: "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" - -vascular_invasion_present: - description: > - The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or - presence in a tumor specimen. - termDef: - term: Tumor Vascular Invasion Ind-3 - source: caDSR - cde_id: 64358 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64358&version=3.0" - -vital_status: - description: > - The survival state of the person registered on the protocol. - termDef: - term: Patient Vital Status - source: caDSR - cde_id: 5 - cde_version: 5.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5&version=5.0" - -weight: - description: > - The weight of the patient measured in kilograms. - termDef: - term: Patient Weight Measurement - source: caDSR - cde_id: 651 - cde_version: 4.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=651&version=4.0" - -well_number: - description: > - Numeric value that represents the the well location within a plate for the analyte or - aliquot from the sample. - termDef: - term: Biospecimen Analyte or Aliquot Plate Well Number - source: caDSR - cde_id: 5432613 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432613&version=1.0" - -workflow_type: - description: > - Generic name for the workflow used to analyze a data set. - -year_of_birth: - description: > - Numeric value to represent the calendar year in which an individual was born. - termDef: - term: Year Birth Date Number - source: caDSR - cde_id: 2896954 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896954&version=1.0" - -year_of_diagnosis: - description: > - Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer. - termDef: - term: Year of initial pathologic diagnosis - source: caDSR - cde_id: 2896960 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896960&version=1.0" - -year_of_death: - description: > - Numeric value to represent the year of the death of an individual. - termDef: - term: Year Death Number - source: caDSR - cde_id: 2897030 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897030&version=1.0" - -years_smoked: - description: > - Numeric value (or unknown) to represent the number of years a person has been smoking. - termDef: - term: Person Smoking Duration Year Count - source: caDSR - cde_id: 3137957 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" diff --git a/test/resources/schemas/aliquot.yaml b/test/resources/schemas/aliquot.yaml index 078cb17..0522f8b 100644 --- a/test/resources/schemas/aliquot.yaml +++ b/test/resources/schemas/aliquot.yaml @@ -1,103 +1,74 @@ -$schema: "http://json-schema.org/draft-04/schema#" - -id: "aliquot" +$schema: https://json-schema.org/draft/2020-12/schema +$id: aliquot title: Aliquot type: object -category: biospecimen -program: '*' -project: '*' -description: > - Pertaining to a portion of the whole; any one of two or more samples of something, of the same - volume or weight. -additionalProperties: false -submittable: true -validators: [] - -systemProperties: - - id - - project_id - - state - - created_datetime - - updated_datetime +description: 'Pertaining to a portion of the whole; any one of two or more samples + of something, of the same volume or weight. + ' required: - - submitter_id - - type - - samples - -uniqueKeys: - - [id] - - [project_id, submitter_id] - +- submitter_id +- project_id +- id links: - - name: samples +- rel: sample + href: sample/{id} + templateRequired: + - id + targetSchema: + $ref: sample.yaml + templatePointers: + id: /sample/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + backref: aliquots +- rel: projects + href: project/{id} + templateRequired: + - id + targetSchema: + $ref: project.yaml + templatePointers: + id: /projects/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many backref: aliquots - label: derived_from - multiplicity: many_to_many - target_type: sample - required: true - -constraints: null - -# Aliquot properties properties: - type: - type: string id: - $ref: "_definitions.yaml#/UUID" - systemAlias: node_id - state: - $ref: "_definitions.yaml#/state" - submitter_id: - type: - - string - - "null" - description: > - The legacy barcode used before prior to the use - UUIDs. For TCGA this is bcraliquotbarcode. - aliquot_quantity: - term: - $ref: "_terms.yaml#/aliquot_quantity" - type: number - aliquot_volume: - term: - $ref: "_terms.yaml#/aliquot_volume" - type: number - amount: - term: - $ref: "_terms.yaml#/amount" - type: number - analyte_type: - term: - $ref: "_terms.yaml#/analyte_type" type: string - analyte_type_id: - term: - $ref: "_terms.yaml#/analyte_type_id" - enum: - - D - - E - - G - - H - - R - - S - - T - - W - - X - - Y - concentration: - term: - $ref: "_terms.yaml#/concentration" - type: number + cellline_attributes: + type: + - 'null' + - object + gdc_attributes: + type: + - 'null' + - object project_id: - $ref: "_definitions.yaml#/project_id" - source_center: - term: - $ref: "_terms.yaml#/source_center" + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: type: string - samples: - $ref: "_definitions.yaml#/to_one" created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: _definitions.yaml#/datetime updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: _definitions.yaml#/datetime + sample: + type: + - array + items: + $ref: reference.yaml + projects: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/allele.yaml b/test/resources/schemas/allele.yaml new file mode 100644 index 0000000..5ce00f7 --- /dev/null +++ b/test/resources/schemas/allele.yaml @@ -0,0 +1,119 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: allele +title: Allele +type: object +required: +- id +- chromosome +- start +- genome +- reference_bases +- alternate_bases +links: +- rel: gene + href: gene/{id} + templateRequired: + - id + targetSchema: + $ref: gene.yaml + templatePointers: + id: /gene/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +- rel: effects + href: effect/{id} + templateRequired: + - id + targetSchema: + $ref: allele_effect.yaml + templatePointers: + id: /effects/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +- rel: transcript + href: transcript/{id} + templateRequired: + - id + targetSchema: + $ref: transcript.yaml + templatePointers: + id: /transcript/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +- rel: protein + href: protein/{id} + templateRequired: + - id + targetSchema: + $ref: protein.yaml + templatePointers: + id: /protein/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +properties: + id: + type: string + reference_bases: + type: string + alternate_bases: + type: string + genome: + $ref: _definitions.yaml#/genome + chromosome: + $ref: _definitions.yaml#/chromosome + start: + type: integer + end: + type: integer + strand: + $ref: _definitions.yaml#/strand + dbsnp_rs: + type: string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + gene: + type: + - array + items: + $ref: reference.yaml + effects: + type: + - array + items: + $ref: reference.yaml + transcript: + type: + - array + items: + $ref: reference.yaml + protein: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/allele_effect.yaml b/test/resources/schemas/allele_effect.yaml new file mode 100644 index 0000000..8e6fc50 --- /dev/null +++ b/test/resources/schemas/allele_effect.yaml @@ -0,0 +1,72 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: allele_effect +title: AlleleEffect +type: object +links: +- rel: ensembl_gene + href: ensemblgene/{id} + templateRequired: + - id + targetSchema: + $ref: gene.yaml + templatePointers: + id: /ensembl_gene/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +- rel: ensembl_transcript + href: ensembltranscript/{id} + templateRequired: + - id + targetSchema: + $ref: transcript.yaml + templatePointers: + id: /ensembl_transcript/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +properties: + id: + type: string + annotation: + type: string + annotation_impact: + type: string + aa_position: + type: integer + aa_length: + type: integer + cds_position: + type: integer + cds_length: + type: integer + cdna_position: + type: integer + cdna_length: + type: integer + hgnc_id: + type: string + hgvsc: + type: string + hgvsp: + type: string + hugo_symbol: + type: string + biotype: + type: string + ensembl_gene: + type: + - string + items: + $ref: reference.yaml + ensembl_transcript: + type: + - string + items: + $ref: reference.yaml diff --git a/test/resources/schemas/case.yaml b/test/resources/schemas/case.yaml index 3db55f5..211c67a 100644 --- a/test/resources/schemas/case.yaml +++ b/test/resources/schemas/case.yaml @@ -1,71 +1,122 @@ -$schema: "http://json-schema.org/draft-04/schema#" - -id: "case" +$schema: https://json-schema.org/draft/2020-12/schema +$id: case title: Case type: object -namespace: http://gdc.nci.nih.gov -category: administrative -program: '*' -project: '*' -description: > - The collection of all data related to a specific subject in the - context of a specific experiment. -additionalProperties: false -submittable: true -validators: null - -systemProperties: - - id - - project_id - - created_datetime - - updated_datetime - - state +description: 'The collection of all data related to a specific subject in the context + of a specific experiment. + ' +required: +- submitter_id +- project_id +- case_id links: - - name: experiments +- rel: compounds + href: compound/{id} + templateRequired: + - id + targetSchema: + $ref: compound.yaml + templatePointers: + id: /compounds/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: cases +- rel: projects + href: project/{id} + templateRequired: + - id + targetSchema: + $ref: project.yaml + templatePointers: + id: /projects/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: cases +- rel: phenotypes + href: phenotype/{id} + templateRequired: + - id + targetSchema: + $ref: phenotype.yaml + templatePointers: + id: /phenotypes/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: cases +- rel: same_as + href: case/{id} + templateRequired: + - id + targetSchema: + $ref: case.yaml + templatePointers: + id: /same_as/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many backref: cases - label: member_of - target_type: experiment - multiplicity: many_to_one - required: true - -required: - - submitter_id - - type - - experiments - -uniqueKeys: - - [id] - - [project_id, submitter_id] - -# Case properties properties: - type: + case_id: type: string - id: - $ref: "_definitions.yaml#/UUID" - systemAlias: node_id - state: - $ref: "_definitions.yaml#/state" + cellline_attributes: + type: + - 'null' + - object + gdc_attributes: + type: + - 'null' + - object + gtex_attributes: + type: + - 'null' + - object + sex: + type: string + project_id: + $ref: _definitions.yaml#/project_id submitter_id: type: - - string - - "null" - consent_codes: - type: array - items: - type: string - primary_site: - description: "Primary site for the case." + - string + - 'null' + id: type: string - disease_type: - description: "Name of the disease for the case." + comment: + type: string + type: type: string - experiments: - $ref: "_definitions.yaml#/to_one" - project_id: - $ref: "_definitions.yaml#/project_id" created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: _definitions.yaml#/datetime updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: _definitions.yaml#/datetime + compounds: + type: + - array + items: + $ref: reference.yaml + projects: + type: + - array + items: + $ref: reference.yaml + phenotypes: + type: + - array + items: + $ref: reference.yaml + same_as: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/command.yaml b/test/resources/schemas/command.yaml new file mode 100644 index 0000000..3db7846 --- /dev/null +++ b/test/resources/schemas/command.yaml @@ -0,0 +1,55 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: command +title: Command +type: object +description: 'A DVC command that was run + + ' +required: +- submitter_id +- project_id +- md5 +- cmd +- filename +links: +- rel: writes + href: file/{id} + templateRequired: + - id + targetSchema: + $ref: file.yaml + templatePointers: + id: /writes/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: command +properties: + md5: + type: string + cmd: + type: string + filename: + type: string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + id: + $ref: _definitions.yaml#/UUID + systemAlias: node_id + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + writes: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/compound.yaml b/test/resources/schemas/compound.yaml new file mode 100644 index 0000000..ca2df11 --- /dev/null +++ b/test/resources/schemas/compound.yaml @@ -0,0 +1,96 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: compound +title: Compound +type: object +description: Definitions for Compound +required: +- id +- submitter_id +- project_id +links: +- rel: similar_compounds + href: compound/{id} + templateRequired: + - id + targetSchema: + $ref: compound.yaml + templatePointers: + id: /similar_compounds/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: compounds +properties: + id: + type: string + pubchem_id: + type: + - 'null' + - string + chebi_id: + type: + - 'null' + - string + chembl_id: + type: + - 'null' + - string + drugbank_id: + type: + - 'null' + - string + synonym: + type: array + items: + type: string + inchi: + type: + - 'null' + - string + inchi_key: + type: + - 'null' + - string + usan_stem_definition: + type: + - 'null' + - string + taxonomy: + type: + - 'null' + - object + approved_countries: + type: + - 'null' + - array + source_url: + type: + - 'null' + - string + id_source: + type: + - 'null' + - string + morgan_fingerprint_2: + type: + - 'null' + - array + similar_compounds: + type: + - array + items: + $ref: reference.yaml + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime diff --git a/test/resources/schemas/copy_number_alteration.yaml b/test/resources/schemas/copy_number_alteration.yaml new file mode 100644 index 0000000..568f046 --- /dev/null +++ b/test/resources/schemas/copy_number_alteration.yaml @@ -0,0 +1,56 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: copy_number_alteration +title: CopyNumberAlteration +type: object +description: 'Gene level copy number estimates for an aliquot + + ' +required: +- submitter_id +- project_id +- values +- method +links: +- rel: aliquot + href: aliquot/{id} + templateRequired: + - id + targetSchema: + $ref: aliquot.yaml + templatePointers: + id: /aliquot/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + backref: copy_number_alterations +properties: + method: + type: string + values: + type: object + propertyNames: + pattern: ^ENSG[0-9]+ + additionalProperties: + type: number + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + id: + $ref: _definitions.yaml#/UUID + systemAlias: node_id + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + aliquot: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/drug_response.yaml b/test/resources/schemas/drug_response.yaml new file mode 100644 index 0000000..9a9f4a6 --- /dev/null +++ b/test/resources/schemas/drug_response.yaml @@ -0,0 +1,149 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: drug_response +title: DrugResponse +type: object +description: 'Drug response curve fit parameters. + + ' +required: +- id +- submitter_id +- project_id +links: +- rel: compounds + href: compound/{id} + templateRequired: + - id + targetSchema: + $ref: compound.yaml + templatePointers: + id: /compounds/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: drug_responses +- rel: aliquot + href: aliquot/{id} + templateRequired: + - id + targetSchema: + $ref: aliquot.yaml + templatePointers: + id: /aliquot/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + backref: drug_response +properties: + id: + type: string + dose_um: + description: 'The drug doses (micromolar) for which responses were measured. + + ' + type: + - 'null' + - array + response: + description: 'The measured drug response for a given drug dose. + + ' + type: + - 'null' + - array + hs: + description: 'The Hill Slope + + ' + type: + - 'null' + - number + einf: + description: 'The maximum theoretical inhibition + + ' + type: + - 'null' + - number + ec50: + description: 'The dose at which 50% of the maximum response is observed + + ' + type: + - 'null' + - number + ic50: + description: 'The dose that achieves 50% inhibition of cell viability + + ' + type: + - 'null' + - number + aac: + description: 'Area above curve + + ' + type: + - 'null' + - number + auc: + description: 'Area under curve + + ' + type: + - 'null' + - number + dss1: + description: 'Drug sensitivity score 1; an AUC measurement with the baseline noise + subtracted. https://www.ncbi.nlm.nih.gov/pubmed/24898935 + + ' + type: + - 'null' + - number + dss2: + description: 'Drug sensitivity score 2; DSS1 further normalized by the logarithm + of the top asymptote Rmax. https://www.ncbi.nlm.nih.gov/pubmed/24898935 + + ' + type: + - 'null' + - number + dss3: + description: 'Drug sensitivity score 3; DSS1 further normalized by the dose range + over which the response exceeds the activity threshold Amin. https://www.ncbi.nlm.nih.gov/pubmed/24898935 + + ' + type: + - 'null' + - number + source_drug_name: + type: string + source_cell_name: + type: string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + compounds: + type: + - array + items: + $ref: reference.yaml + aliquot: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/exon.yaml b/test/resources/schemas/exon.yaml new file mode 100644 index 0000000..141f125 --- /dev/null +++ b/test/resources/schemas/exon.yaml @@ -0,0 +1,63 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: exon +title: Exon +type: object +description: 'An exon. + + ' +required: +- submitter_id +- project_id +- chromosome +- strand +- start +- genome +- end +- exon_id +links: +- rel: transcripts + href: transcript/{id} + templateRequired: + - id + targetSchema: + $ref: transcript.yaml + templatePointers: + id: /transcripts/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: exons +properties: + id: + type: string + exon_id: + type: string + genome: + $ref: _definitions.yaml#/genome + chromosome: + $ref: _definitions.yaml#/chromosome + start: + type: integer + end: + type: integer + strand: + $ref: _definitions.yaml#/strand + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + transcripts: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/file.yaml b/test/resources/schemas/file.yaml new file mode 100644 index 0000000..ff183a6 --- /dev/null +++ b/test/resources/schemas/file.yaml @@ -0,0 +1,56 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: file +title: File +type: object +description: 'A file + + ' +required: +- submitter_id +- project_id +- md5 +- filename +links: +- rel: aliquots + href: aliquot/{id} + templateRequired: + - id + targetSchema: + $ref: aliquot.yaml + templatePointers: + id: /aliquots/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +properties: + id: + $ref: _definitions.yaml#/UUID + systemAlias: node_id + md5: + type: string + path: + type: string + cmd: + type: string + filename: + type: string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + aliquots: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/gene.yaml b/test/resources/schemas/gene.yaml new file mode 100644 index 0000000..8085225 --- /dev/null +++ b/test/resources/schemas/gene.yaml @@ -0,0 +1,47 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: gene +title: Gene +type: object +description: 'A gene. + + ' +required: +- submitter_id +- project_id +- description +- chromosome +- strand +- start +- genome +- end +- symbol +links: [] +properties: + id: + type: string + description: + type: string + symbol: + type: string + genome: + $ref: _definitions.yaml#/genome + chromosome: + $ref: _definitions.yaml#/chromosome + start: + type: integer + end: + type: integer + strand: + $ref: _definitions.yaml#/strand + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime diff --git a/test/resources/schemas/gene_expression.yaml b/test/resources/schemas/gene_expression.yaml new file mode 100644 index 0000000..13300b4 --- /dev/null +++ b/test/resources/schemas/gene_expression.yaml @@ -0,0 +1,59 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: gene_expression +title: GeneExpression +type: object +description: 'Gene level expression values for an aliquot + + ' +required: +- submitter_id +- project_id +- values +- method +- metric +links: +- rel: aliquot + href: aliquot/{id} + templateRequired: + - id + targetSchema: + $ref: aliquot.yaml + templatePointers: + id: /aliquot/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + backref: gene_expressions +properties: + id: + type: string + systemAlias: node_id + method: + type: string + metric: + $ref: _definitions.yaml#/expression_metric + values: + type: object + propertyNames: + pattern: ^ENSG[0-9]+ + additionalProperties: + type: number + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + aliquot: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/gene_ontology_term.yaml b/test/resources/schemas/gene_ontology_term.yaml new file mode 100644 index 0000000..bafa66a --- /dev/null +++ b/test/resources/schemas/gene_ontology_term.yaml @@ -0,0 +1,86 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: gene_ontology_term +title: GeneOntologyTerm +type: object +description: 'The Gene Ontology project provides an ontology of defined terms representing gene + product properties. + + ' +required: +- submitter_id +- synonym +- project_id +- name +- xref +- go_id +- definition +- namespace +links: +- rel: genes + href: gene/{id} + templateRequired: + - id + targetSchema: + $ref: gene.yaml + templatePointers: + id: /genes/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: gene_ontology_terms +- rel: child_terms + href: gene_ontology_term/{id} + templateRequired: + - id + targetSchema: + $ref: gene_ontology_term.yaml + templatePointers: + id: /child_terms/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: gene_ontology_terms +properties: + go_id: + type: string + name: + type: string + namespace: + type: string + definition: + type: string + synonym: + type: array + xref: + type: array + items: + type: string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + id: + type: string + systemAlias: node_id + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + genes: + type: + - array + items: + $ref: reference.yaml + child_terms: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/gene_phenotype_association.yaml b/test/resources/schemas/gene_phenotype_association.yaml new file mode 100644 index 0000000..ec961d0 --- /dev/null +++ b/test/resources/schemas/gene_phenotype_association.yaml @@ -0,0 +1,166 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: gene_phenotype_association +title: GenePhenotypeAssociation +type: object +description: 'Associations of genomic features, drugs and diseases + + ' +required: +- submitter_id +- description +- source +- project_id +links: +- rel: compounds + href: compound/{id} + templateRequired: + - id + targetSchema: + $ref: compound.yaml + templatePointers: + id: /compounds/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: gene_phenotype_associations +- rel: alleles + href: allele/{id} + templateRequired: + - id + targetSchema: + $ref: allele.yaml + templatePointers: + id: /alleles/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: gene_phenotype_associations +- rel: genes + href: gene/{id} + templateRequired: + - id + targetSchema: + $ref: gene.yaml + templatePointers: + id: /genes/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: gene_phenotype_associations +- rel: genomic_features + href: genomic_feature/{id} + templateRequired: + - id + targetSchema: + $ref: genomic_feature.yaml + templatePointers: + id: /genomic_features/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: gene_phenotype_associations +- rel: publications + href: publication/{id} + templateRequired: + - id + targetSchema: + $ref: publication.yaml + templatePointers: + id: /publications/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: gene_phenotype_associations +- rel: phenotypes + href: phenotype/{id} + templateRequired: + - id + targetSchema: + $ref: phenotype.yaml + templatePointers: + id: /phenotypes/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: gene_phenotype_associations +properties: + id: + type: string + description: + type: string + evidence_label: + type: + - 'null' + - string + oncogenic: + type: + - 'null' + - string + response_type: + type: + - 'null' + - string + source: + type: string + source_document: + type: + - 'null' + - string + source_url: + type: + - 'null' + - string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + compounds: + type: + - array + items: + $ref: reference.yaml + alleles: + type: + - array + items: + $ref: reference.yaml + genes: + type: + - array + items: + $ref: reference.yaml + genomic_features: + type: + - array + items: + $ref: reference.yaml + publications: + type: + - array + items: + $ref: reference.yaml + phenotypes: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/gene_set.yaml b/test/resources/schemas/gene_set.yaml new file mode 100644 index 0000000..a3895a0 --- /dev/null +++ b/test/resources/schemas/gene_set.yaml @@ -0,0 +1,93 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: gene_set +title: GeneSet +type: object +description: 'A set of biologically related genes + + ' +required: +- id +- submitter_id +- project_id +links: +- rel: genes + href: gene/{id} + templateRequired: + - id + targetSchema: + $ref: gene.yaml + templatePointers: + id: /genes/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: gene_sets +- rel: publications + href: publication/{id} + templateRequired: + - id + targetSchema: + $ref: publication.yaml + templatePointers: + id: /publications/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: gene_sets +properties: + id: + type: string + standard_name: + type: string + systematic_name: + type: string + historical_names: + type: string + geoid: + type: string + exact_source: + type: string + geneset_listing_url: + type: string + external_details_url: + type: string + chip: + type: string + category_code: + type: string + sub_category_code: + type: string + contributor: + type: string + contributor_org: + type: string + description_brief: + type: string + description_full: + type: string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + genes: + type: + - array + items: + $ref: reference.yaml + publications: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/genomic_feature.yaml b/test/resources/schemas/genomic_feature.yaml new file mode 100644 index 0000000..bb65fb9 --- /dev/null +++ b/test/resources/schemas/genomic_feature.yaml @@ -0,0 +1,77 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: genomic_feature +title: GenomicFeature +type: object +description: 'An abstract genomic feature + + ' +required: +- submitter_id +- project_id +- name +links: +- rel: genes + href: gene/{id} + templateRequired: + - id + targetSchema: + $ref: gene.yaml + templatePointers: + id: /genes/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: genomic_features +properties: + annotations: + type: + - 'null' + - array + effect: + type: + - 'null' + - string + genome: + oneOf: + - type: 'null' + - $ref: _definitions.yaml#/genome + chromosome: + oneOf: + - type: 'null' + - $ref: _definitions.yaml#/chromosome + end: + type: + - 'null' + - integer + start: + type: + - 'null' + - integer + strand: + oneOf: + - type: 'null' + - $ref: _definitions.yaml#/strand + name: + type: string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + id: + $ref: _definitions.yaml#/UUID + systemAlias: node_id + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + genes: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/interaction.yaml b/test/resources/schemas/interaction.yaml new file mode 100644 index 0000000..3d00297 --- /dev/null +++ b/test/resources/schemas/interaction.yaml @@ -0,0 +1,89 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: interaction +title: Interaction +type: object +description: 'A biological interaction. This node represent an interaction between + two or more entities (e.g. protein-protein, gene-drug, catalysis, or synthesis). + + ' +required: +- submitter_id +- project_id +- source +- type +links: +- rel: interaction_output + href: gene/{id} + templateRequired: + - id + targetSchema: + $ref: gene.yaml + templatePointers: + id: /interaction_output/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: interactions +- rel: publications + href: publication/{id} + templateRequired: + - id + targetSchema: + $ref: publication.yaml + templatePointers: + id: /publications/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: interactions +- rel: interaction_input + href: interactioninpu/{id} + templateRequired: + - id + targetSchema: + $ref: protein.yaml + templatePointers: + id: /interaction_input/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +properties: + source: + type: string + type: + type: string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + id: + type: string + systemAlias: node_id + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + interaction_output: + type: + - array + items: + $ref: reference.yaml + publications: + type: + - array + items: + $ref: reference.yaml + interaction_input: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/methylation.yaml b/test/resources/schemas/methylation.yaml new file mode 100644 index 0000000..273ef48 --- /dev/null +++ b/test/resources/schemas/methylation.yaml @@ -0,0 +1,58 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: methylation +title: Methylation +type: object +description: 'Methylatyion values for an aliquot + + ' +required: +- submitter_id +- project_id +- values +- method +links: +- rel: aliquot + href: aliquot/{id} + templateRequired: + - id + targetSchema: + $ref: aliquot.yaml + templatePointers: + id: /aliquot/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + backref: methylations +properties: + method: + type: string + metric: + type: string + values: + type: object + additionalProperties: + type: + - number + - 'null' + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + id: + $ref: _definitions.yaml#/UUID + systemAlias: node_id + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + aliquot: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/methylation_probe.yaml b/test/resources/schemas/methylation_probe.yaml new file mode 100644 index 0000000..971f33f --- /dev/null +++ b/test/resources/schemas/methylation_probe.yaml @@ -0,0 +1,59 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: methylation_probe +title: MethylationProbe +type: object +description: 'Definition for a methylation probe + + ' +required: +- submitter_id +- project_id +- probe_id +- chromosome +- position +links: +- rel: gene + href: gene/{id} + templateRequired: + - id + targetSchema: + $ref: gene.yaml + templatePointers: + id: /gene/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + backref: methylation_probes +properties: + probe_id: + type: string + chromosome: + $ref: _definitions.yaml#/chromosome + position: + type: integer + target: + type: + - string + - 'null' + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + id: + $ref: _definitions.yaml#/UUID + systemAlias: node_id + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + gene: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/pathway.yaml b/test/resources/schemas/pathway.yaml new file mode 100644 index 0000000..be5b99c --- /dev/null +++ b/test/resources/schemas/pathway.yaml @@ -0,0 +1,106 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: pathway +title: Pathway +type: object +description: 'A biological pathway + + ' +required: +- submitter_id +- project_id +- name +links: +- rel: genes + href: gene/{id} + templateRequired: + - id + targetSchema: + $ref: gene.yaml + templatePointers: + id: /genes/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: pathways +- rel: interactions + href: interaction/{id} + templateRequired: + - id + targetSchema: + $ref: interaction.yaml + templatePointers: + id: /interactions/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: pathways +- rel: sub_pathways + href: pathway/{id} + templateRequired: + - id + targetSchema: + $ref: pathway.yaml + templatePointers: + id: /sub_pathways/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: pathways +- rel: publications + href: publication/{id} + templateRequired: + - id + targetSchema: + $ref: publication.yaml + templatePointers: + id: /publications/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +properties: + id: + type: string + systemAlias: node_id + name: + type: string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + genes: + type: + - array + items: + $ref: reference.yaml + interactions: + type: + - array + items: + $ref: reference.yaml + sub_pathways: + type: + - array + items: + $ref: reference.yaml + publications: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/phenotype.yaml b/test/resources/schemas/phenotype.yaml new file mode 100644 index 0000000..c0870cc --- /dev/null +++ b/test/resources/schemas/phenotype.yaml @@ -0,0 +1,58 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: phenotype +title: Phenotype +type: object +description: 'An observable characteristics of a case or sample resulting from the interaction + of its genotype with the environment (i.e. a disease). + + ' +required: +- submitter_id +- term_id +- term +- project_id +links: +- rel: child_terms + href: phenotype/{id} + templateRequired: + - id + targetSchema: + $ref: phenotype.yaml + templatePointers: + id: /child_terms/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: phenotypes +properties: + id: + type: string + term: + type: string + term_id: + type: string + name: + type: + - 'null' + - string + description: + type: string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + child_terms: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/program.yaml b/test/resources/schemas/program.yaml new file mode 100644 index 0000000..a80b9a3 --- /dev/null +++ b/test/resources/schemas/program.yaml @@ -0,0 +1,31 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: program +title: Program +type: object +description: 'A broad framework of goals to be achieved. (i.e. TCGA or FM-AD) + + ' +required: +- submitter_id +- program_id +links: [] +properties: + program_id: + type: string + gdc_attributes: + type: + - 'null' + - object + submitter_id: + type: + - string + - 'null' + id: + $ref: _definitions.yaml#/UUID + systemAlias: node_id + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime diff --git a/test/resources/schemas/project.yaml b/test/resources/schemas/project.yaml new file mode 100644 index 0000000..edc3acc --- /dev/null +++ b/test/resources/schemas/project.yaml @@ -0,0 +1,51 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: project +title: Project +type: object +description: 'Any specifically defined piece of work that is undertaken or attempted + to meet a single requirement. + + ' +required: +- id +- submitter_id +- project_id +links: +- rel: programs + href: program/{id} + templateRequired: + - id + targetSchema: + $ref: program.yaml + templatePointers: + id: /programs/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: projects +properties: + id: + type: string + project_id: + $ref: _definitions.yaml#/project_id + gdc_attributes: + type: + - 'null' + - object + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + programs: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/protein.yaml b/test/resources/schemas/protein.yaml new file mode 100644 index 0000000..9d0c27d --- /dev/null +++ b/test/resources/schemas/protein.yaml @@ -0,0 +1,71 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: protein +title: Protein +type: object +description: 'A protein. + + ' +required: +- id +- submitter_id +- project_id +links: +- rel: gene + href: gene/{id} + templateRequired: + - id + targetSchema: + $ref: gene.yaml + templatePointers: + id: /gene/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +- rel: transcript + href: transcript/{id} + templateRequired: + - id + targetSchema: + $ref: transcript.yaml + templatePointers: + id: /transcript/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +properties: + id: + type: string + sequence: + type: string + submitter_id: + type: + - string + - 'null' + project_id: + $ref: _definitions.yaml#/project_id + length: + type: number + mass: + type: number + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + gene: + type: + - array + items: + $ref: reference.yaml + transcript: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/protein_compound_association.yaml b/test/resources/schemas/protein_compound_association.yaml new file mode 100644 index 0000000..59ebc09 --- /dev/null +++ b/test/resources/schemas/protein_compound_association.yaml @@ -0,0 +1,129 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: protein_compound_association +title: ProteinCompoundAssociation +type: object +description: Definitions for protein-compound Associations +required: +- id +- submitter_id +- project_id +links: +- rel: proteins + href: protein/{id} + templateRequired: + - id + targetSchema: + $ref: protein.yaml + templatePointers: + id: /proteins/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: protein_compound_associations +- rel: genes + href: gene/{id} + templateRequired: + - id + targetSchema: + $ref: gene.yaml + templatePointers: + id: /genes/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: protein_compound_associations +- rel: compound + href: compound/{id} + templateRequired: + - id + targetSchema: + $ref: compound.yaml + templatePointers: + id: /compound/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + backref: protein_compound_associations +- rel: publications + href: publication/{id} + templateRequired: + - id + targetSchema: + $ref: publication.yaml + templatePointers: + id: /publications/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: protein_compound_associations +- rel: protein_structures + href: protein_structure/{id} + templateRequired: + - id + targetSchema: + $ref: protein_structure.yaml + templatePointers: + id: /protein_structures/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: protein_compound_associations +properties: + id: + type: string + association_type: + type: string + description: protein-compound association keyword, example inhibitor + project_id: + $ref: _definitions.yaml#/project_id + source: + type: string + submitter_id: + type: + - string + - 'null' + ki_nm: + type: + - number + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + proteins: + type: + - array + items: + $ref: reference.yaml + genes: + type: + - array + items: + $ref: reference.yaml + compound: + type: + - array + items: + $ref: reference.yaml + publications: + type: + - array + items: + $ref: reference.yaml + protein_structures: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/protein_structure.yaml b/test/resources/schemas/protein_structure.yaml new file mode 100644 index 0000000..7d3af0a --- /dev/null +++ b/test/resources/schemas/protein_structure.yaml @@ -0,0 +1,60 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: protein_structure +title: ProteinStructure +type: object +description: 'A protein structure. + + ' +required: +- id +- submitter_id +- project_id +links: +- rel: protein + href: protein/{id} + templateRequired: + - id + targetSchema: + $ref: protein.yaml + templatePointers: + id: /protein/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + backref: protein_structures +properties: + id: + type: string + resolution: + type: + - number + - 'null' + description: + type: string + short_description: + type: string + source: + type: string + submission_date: + type: string + experiment_type: + type: string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + protein: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/publication.yaml b/test/resources/schemas/publication.yaml new file mode 100644 index 0000000..dccb112 --- /dev/null +++ b/test/resources/schemas/publication.yaml @@ -0,0 +1,54 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: publication +title: Publication +type: object +description: 'A publication. + + ' +required: +- url +- submitter_id +- project_id +links: [] +properties: + id: + type: string + systemAlias: node_id + url: + type: string + abstract: + type: + - 'null' + - string + author: + type: + - 'null' + - array + citation: + type: + - 'null' + - array + date: + type: + - 'null' + - string + text: + type: + - 'null' + - string + title: + type: + - 'null' + - string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime diff --git a/test/resources/schemas/reference.yaml b/test/resources/schemas/reference.yaml new file mode 100644 index 0000000..f3da4bc --- /dev/null +++ b/test/resources/schemas/reference.yaml @@ -0,0 +1,14 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: reference +id: reference +title: reference +type: object +description: | + A reference to another entity in the graph. + The id of the entity is required. +required: +- id +properties: + id: + type: + - string diff --git a/test/resources/schemas/sample.yaml b/test/resources/schemas/sample.yaml index 7680e5c..b94f3b6 100644 --- a/test/resources/schemas/sample.yaml +++ b/test/resources/schemas/sample.yaml @@ -1,686 +1,101 @@ -$schema: "http://json-schema.org/draft-04/schema#" - -id: "sample" +$schema: https://json-schema.org/draft/2020-12/schema +$id: sample title: Sample type: object -namespace: http://gdc.nci.nih.gov -category: biospecimen -program: '*' -project: '*' -description: > - Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment - or research purposes, including a sample obtained from a living organism or taken from the - biological object after halting of all its life functions. Biospecimen can contain one or more - components including but not limited to cellular molecules, cells, tissues, organs, body fluids, - embryos, and body excretory products. -additionalProperties: false -submittable: true -validators: null - -systemProperties: - - id - - project_id - - state - - created_datetime - - updated_datetime +description: 'Any material sample taken from a biological entity for testing, diagnostic, + propagation, treatment or research purposes, including a sample obtained from a + living organism or taken from the biological object after halting of all its life + functions. Biospecimen can contain one or more components including but not limited + to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory + products. + ' required: - - submitter_id - - type - - cases - -uniqueKeys: - - [id] - - [project_id, submitter_id] - +- id +- submitter_id +- project_id links: - - name: cases +- rel: case + href: case/{id} + templateRequired: + - id + targetSchema: + $ref: case.yaml + templatePointers: + id: /case/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one backref: samples - label: derived_from - target_type: case - multiplicity: many_to_one #not sure - required: true - - name: diagnoses +- rel: projects + href: project/{id} + templateRequired: + - id + targetSchema: + $ref: project.yaml + templatePointers: + id: /projects/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: samples +- rel: phenotypes + href: phenotype/{id} + templateRequired: + - id + targetSchema: + $ref: phenotype.yaml + templatePointers: + id: /phenotypes/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many backref: samples - label: related_to - target_type: diagnosis - multiplicity: many_to_one - required: false - -# Sample properties: keep TCGA-specific fields properties: - type: - type: string id: - $ref: "_definitions.yaml#/UUID" - systemAlias: node_id - state: - $ref: "_definitions.yaml#/state" - submitter_id: - type: - - string - - "null" - description: > - The legacy barcode used before prior to the use UUIDs, varies by project. - For TCGA this is bcrsamplebarcode. - biospecimen_anatomic_site: - term: - $ref: "_terms.yaml#/biospecimen_anatomic_site" - enum: - - Abdomen - - Abdominal Wall - - Acetabulum - - Adenoid - - Adipose - - Adrenal - - Alveolar Ridge - - Amniotic Fluid - - Ampulla Of Vater - - Anal Sphincter - - Ankle - - Anorectum - - Antecubital Fossa - - Antrum - - Anus - - Aorta - - Aortic Body - - Appendix - - Aqueous Fluid - - Arm - - Artery - - Ascending Colon - - Ascending Colon Hepatic Flexure - - Auditory Canal - - Autonomic Nervous System - - Axilla - - Back - - Bile Duct - - Bladder - - Blood - - Blood Vessel - - Bone - - Bone Marrow - - Bowel - - Brain - - Brain Stem - - Breast - - Broad Ligament - - Bronchiole - - Bronchus - - Brow - - Buccal Cavity - - Buccal Mucosa - - Buttock - - Calf - - Capillary - - Cardia - - Carina - - Carotid Artery - - Carotid Body - - Cartilage - - Cecum - - Cell-Line - - Central Nervous System - - Cerebellum - - Cerebral Cortex - - Cerebrospinal Fluid - - Cerebrum - - Cervical Spine - - Cervix - - Chest - - Chest Wall - - Chin - - Clavicle - - Clitoris - - Colon - - Colon - Mucosa Only - - Common Duct - - Conjunctiva - - Connective Tissue - - Dermal - - Descending Colon - - Diaphragm - - Duodenum - - Ear - - Ear Canal - - Ear, Pinna (External) - - Effusion - - Elbow - - Endocrine Gland - - Epididymis - - Epidural Space - - Esophagogastric Junction - - Esophagus - - Esophagus - Mucosa Only - - Eye - - Fallopian Tube - - Femoral Artery - - Femoral Vein - - Femur - - Fibroblasts - - Fibula - - Finger - - Floor Of Mouth - - Fluid - - Foot - - Forearm - - Forehead - - Foreskin - - Frontal Cortex - - Frontal Lobe - - Fundus Of Stomach - - Gallbladder - - Ganglia - - Gastroesophageal Junction - - Gastrointestinal Tract - - Groin - - Gum - - Hand - - Hard Palate - - Head & Neck - - Head - Face Or Neck, Nos - - Heart - - Hepatic - - Hepatic Duct - - Hepatic Vein - - Hip - - Hippocampus - - Humerus - - Hypopharynx - - Ileum - - Ilium - - Index Finger - - Ischium - - Islet Cells - - Jaw - - Jejunum - - Joint - - Kidney - - Knee - - Lacrimal Gland - - Large Bowel - - Laryngopharynx - - Larynx - - Leg - - Leptomeninges - - Ligament - - Lip - - Liver - - Lumbar Spine - - Lung - - Lymph Node - - Lymph Node(s) Axilla - - Lymph Node(s) Cervical - - Lymph Node(s) Distant - - Lymph Node(s) Epitrochlear - - Lymph Node(s) Femoral - - Lymph Node(s) Hilar - - Lymph Node(s) Iliac-Common - - Lymph Node(s) Iliac-External - - Lymph Node(s) Inguinal - - Lymph Node(s) Internal Mammary - - Lymph Node(s) Mammary - - Lymph Node(s) Mesenteric - - Lymph Node(s) Occipital - - Lymph Node(s) Paraaortic - - Lymph Node(s) Parotid - - Lymph Node(s) Pelvic - - Lymph Node(s) Popliteal - - Lymph Node(s) Regional - - Lymph Node(s) Retroperitoneal - - Lymph Node(s) Scalene - - Lymph Node(s) Splenic - - Lymph Node(s) Subclavicular - - Lymph Node(s) Submandibular - - Lymph Node(s) Supraclavicular - - Lymph Nodes(s) Mediastinal - - Mandible - - Maxilla - - Mediastinal Soft Tissue - - Mediastinum - - Mesentery - - Mesothelium - - Middle Finger - - Mitochondria - - Muscle - - Nails - - Nasal Cavity - - Nasal Soft Tissue - - Nasopharynx - - Neck - - Nerve - - Nerve(s) Cranial - - Occipital Cortex - - Ocular Orbits - - Omentum - - Oral Cavity - - Oral Cavity - Mucosa Only - - Oropharynx - - Other - - Ovary - - Palate - - Pancreas - - Paraspinal Ganglion - - Parathyroid - - Parotid Gland - - Patella - - Pelvis - - Penis - - Pericardium - - Periorbital Soft Tissue - - Peritoneal Cavity - - Peritoneum - - Pharynx - - Pineal - - Pineal Gland - - Pituitary Gland - - Placenta - - Pleura - - Popliteal Fossa - - Prostate - - Pylorus - - Rectosigmoid Junction - - Rectum - - Retina - - Retro-Orbital Region - - Retroperitoneum - - Rib - - Ring Finger - - Round Ligament - - Sacrum - - Salivary Gland - - Scalp - - Scapula - - Sciatic Nerve - - Scrotum - - Seminal Vesicle - - Shoulder - - Sigmoid Colon - - Sinus - - Sinus(es), Maxillary - - Skeletal Muscle - - Skin - - Skull - - Small Bowel - - Small Bowel - Mucosa Only - - Small Finger - - Soft Tissue - - Spinal Column - - Spinal Cord - - Spleen - - Splenic Flexure - - Sternum - - Stomach - - Stomach - Mucosa Only - - Subcutaneous Tissue - - Synovium - - Temporal Cortex - - Tendon - - Testis - - Thigh - - Thoracic Spine - - Thorax - - Throat - - Thumb - - Thymus - - Thyroid - - Tibia - - Tongue - - Tonsil - - Tonsil (Pharyngeal) - - Trachea / Major Bronchi - - Transverse Colon - - Trunk - - Umbilical Cord - - Ureter - - Urethra - - Urinary Tract - - Uterus - - Uvula - - Vagina - - Vas Deferens - - Vein - - Venous - - Vertebra - - Vulva - - White Blood Cells - - Wrist - - Unknown - - Not Reported - - Not Allowed To Collect - composition: - term: - $ref: "_terms.yaml#/composition" - enum: - - Buccal Cells - - Buffy Coat - - Bone Marrow Components - - Bone Marrow Components NOS - - Control Analyte - - Cell - - Circulating Tumor Cell (CTC) - - Derived Cell Line - - EBV Immortalized - - Fibroblasts from Bone Marrow Normal - - Granulocytes - - Human Original Cells - - Lymphocytes - - Mononuclear Cells from Bone Marrow Normal - - Peripheral Blood Components NOS - - Peripheral Blood Nucleated Cells - - Pleural Effusion - - Plasma - - Peripheral Whole Blood - - Serum - - Saliva - - Sputum - - Solid Tissue - - Whole Bone Marrow - - Unknown - - Not Reported - - Not Allowed To Collect - current_weight: - term: - $ref: "_terms.yaml#/current_weight" - type: number - days_to_collection: - term: - $ref: "_terms.yaml#/days_to_collection" - type: integer - days_to_sample_procurement: - term: - $ref: "_terms.yaml#/days_to_sample_procurement" - type: integer - diagnosis_pathologically_confirmed: - term: - ref: "_terms.yaml#/diagnosis_pathologically_confirmed" - enum: - - "Yes" - - "No" - - Unknown - freezing_method: - term: - $ref: "_terms.yaml#/freezing_method" - type: string - initial_weight: - term: - $ref: "_terms.yaml#/initial_weight" - type: number - intermediate_dimension: - terms: - $ref: "_terms.yaml#/intermediate_dimension" type: string - is_ffpe: - term: - $ref: "_terms.yaml#/is_ffpe" - type: boolean - longest_dimension: - terms: - $ref: "_terms.yaml#/longest_dimension" - type: string - method_of_sample_procurement: - term: - $ref: "_terms.yaml#/method_of_sample_procurement" - enum: - - Abdomino-perineal Resection of Rectum - - Anterior Resection of Rectum - - Aspirate - - Biopsy - - Blood Draw - - Bone Marrow Aspirate - - Core Biopsy - - Cystectomy - - Endo Rectal Tumor Resection - - Endoscopic Biopsy - - Endoscopic Mucosal Resection (EMR) - - Enucleation - - Excisional Biopsy - - Fine Needle Aspiration - - Full Hysterectomy - - Gross Total Resection - - Hand Assisted Laparoscopic Radical Nephrectomy - - Hysterectomy NOS - - Incisional Biopsy - - Indeterminant - - Laparoscopic Biopsy - - Laparoscopic Partial Nephrectomy - - Laparoscopic Radical Nephrectomy - - Laparoscopic Radical Prostatectomy with Robotics - - Laparoscopic Radical Prostatectomy without Robotics - - Left Hemicolectomy - - Lobectomy - - Local Resection (Exoresection; wall resection) - - Lumpectomy - - Modified Radical Mastectomy - - Needle Biopsy - - Open Craniotomy - - Open Partial Nephrectomy - - Open Radical Nephrectomy - - Open Radical Prostatectomy - - Orchiectomy - - Other - - Other Surgical Resection - - Pan-Procto Colectomy - - Pneumonectomy - - Right Hemicolectomy - - Sigmoid Colectomy - - Simple Mastectomy - - Subtotal Resection - - Surgical Resection - - Thoracoscopic Biopsy - - Total Colectomy - - Total Mastectomy - - Transplant - - Transurethral resection (TURBT) - - Transverse Colectomy - - Tumor Resection - - Wedge Resection - - Unknown - - Not Reported - - Not Allowed To Collect - oct_embedded: - term: - $ref: "_terms.yaml#/oct_embedded" - type: string - preservation_method: - term: - $ref: "_terms.yaml#/preservation_method" - enum: - - Cryopreserved - - FFPE - - Fresh - - OCT - - Snap Frozen - - Frozen - - Unknown - - Not Reported - - Not Allowed To Collect - sample_type: - description: "Characterization of the sample as either clinical or contrived." - enum: - - Additional Metastatic - - Additional - New Primary - - Blood Derived Cancer - Bone Marrow, Post-treatment - - Blood Derived Cancer - Peripheral Blood, Post-treatment - - Blood Derived Normal - - Bone Marrow Normal - - Buccal Cell Normal - - Cell Line Derived Xenograft Tissue - - Cell Lines - - cfDNA - - Circulating Tumor Cell (CTC) - - Control Analyte - - Clinical - - Contrived - - ctDNA - - DNA - - EBV Immortalized Normal - - FFPE Recurrent - - FFPE Scrolls - - Fibroblasts from Bone Marrow Normal - - GenomePlex (Rubicon) Amplified DNA - - Granulocytes - - Human Tumor Original Cells - - Metastatic - - Mononuclear Cells from Bone Marrow Normal - - Primary Blood Derived Cancer - Peripheral Blood - - Recurrent Blood Derived Cancer - Peripheral Blood - - Pleural Effusion - - Primary Blood Derived Cancer - Bone Marrow - - Primary Tumor - - Primary Xenograft Tissue - - Post neo-adjuvant therapy - - Recurrent Blood Derived Cancer - Bone Marrow - - Recurrent Tumor - - Repli-G (Qiagen) DNA - - Repli-G X (Qiagen) DNA - - RNA - - Slides - - Solid Tissue Normal - - Total RNA - - Xenograft Tissue - - Unknown - - Not Reported - - Not Allowed To Collect - sample_type_id: - term: - $ref: "_terms.yaml#/sample_type_id" - enum: - - '01' - - '02' - - '03' - - '04' - - '05' - - '06' - - '07' - - '08' - - '09' - - '10' - - '11' - - '12' - - '13' - - '14' - - '15' - - '16' - - '20' - - '40' - - '41' - - '42' - - '50' - - '60' - - '61' - - '99' - sample_volume: - description: "The volume of the sample in mL." - type: number - shortest_dimension: - term: - $ref: "_terms.yaml#/shortest_dimension" - type: string - time_between_clamping_and_freezing: - term: - $ref: "_terms.yaml#/time_between_clamping_and_freezing" - type: string - time_between_excision_and_freezing: - term: - $ref: "_terms.yaml#/time_between_excision_and_freezing" - type: string - tissue_type: - term: - $ref: "_terms.yaml#/tissue_type" - enum: - - Tumor - - Normal - - Abnormal - - Peritumoral - - Contrived - - Unknown - - Not Reported - - Not Allowed To Collect - tumor_code: - term: - $ref: "_terms.yaml#/tumor_code" - enum: - - Non cancerous tissue - - Diffuse Large B-Cell Lymphoma (DLBCL) - - Lung Cancer (all types) - - Lung Adenocarcinoma - - Non-small Cell Lung Carcinoma (NSCLC) - - Colon Cancer (all types) - - Breast Cancer (all types) - - Cervical Cancer (all types) - - Anal Cancer (all types) - - Acute lymphoblastic leukemia (ALL) - - Acute myeloid leukemia (AML) - - Induction Failure AML (AML-IF) - - Neuroblastoma (NBL) - - Osteosarcoma (OS) - - Ewing sarcoma - - Wilms tumor (WT) - - Clear cell sarcoma of the kidney (CCSK) - - Rhabdoid tumor (kidney) (RT) - - CNS, ependymoma - - CNS, glioblastoma (GBM) - - CNS, rhabdoid tumor - - CNS, low grade glioma (LGG) - - CNS, medulloblastoma - - CNS, other - - NHL, anaplastic large cell lymphoma - - NHL, Burkitt lymphoma (BL) - - Rhabdomyosarcoma - - Soft tissue sarcoma, non-rhabdomyosarcoma - - Castration-Resistant Prostate Cancer (CRPC) - - Prostate Cancer - - Hepatocellular Carcinoma (HCC) - tumor_code_id: - term: - $ref: "_terms.yaml#/tumor_code_id" - enum: - - "00" - - "01" - - "02" - - "03" - - "04" - - "10" - - "20" - - "21" - - "30" - - "40" - - "41" - - "50" - - "51" - - "52" - - "60" - - "61" - - "62" - - "63" - - "64" - - "65" - - "70" - - "71" - - "80" - - "81" - tumor_descriptor: - term: - $ref: "_terms.yaml#/tumor_descriptor" - enum: - - Metastatic - - Not Applicable - - Primary - - Recurrence - - Xenograft - - NOS - - Unknown - - Not Reported - - Not Allowed To Collect - description: "A description of the tumor from which the sample was derived." # TOREVIEW - cases: - $ref: "_definitions.yaml#/to_one" - diagnoses: - $ref: "_definitions.yaml#/to_one" + cellline_attributes: + type: + - 'null' + - object + gdc_attributes: + type: + - 'null' + - object + gtex_attributes: + type: + - 'null' + - object project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: type: string created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: _definitions.yaml#/datetime updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: _definitions.yaml#/datetime + case: + type: + - array + items: + $ref: reference.yaml + projects: + type: + - array + items: + $ref: reference.yaml + phenotypes: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/somatic_callset.yaml b/test/resources/schemas/somatic_callset.yaml new file mode 100644 index 0000000..ef04733 --- /dev/null +++ b/test/resources/schemas/somatic_callset.yaml @@ -0,0 +1,71 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: somatic_callset +title: SomaticCallset +type: object +description: 'A collection of somatic variants. + + ' +required: +- submitter_id +- tumor_aliquot_id +- project_id +links: +- rel: alleles + href: allele/{id} + templateRequired: + - id + targetSchema: + $ref: allele.yaml + templatePointers: + id: /alleles/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: somatic_callsets +- rel: aliquots + href: aliquot/{id} + templateRequired: + - id + targetSchema: + $ref: aliquot.yaml + templatePointers: + id: /aliquots/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_many + backref: somatic_callsets +properties: + id: + type: string + tumor_aliquot_id: + type: string + normal_aliquot_id: + type: + - 'null' + - string + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + alleles: + type: + - array + items: + $ref: reference.yaml + aliquots: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/somatic_variant.yaml b/test/resources/schemas/somatic_variant.yaml new file mode 100644 index 0000000..09ec187 --- /dev/null +++ b/test/resources/schemas/somatic_variant.yaml @@ -0,0 +1,78 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: somatic_variant +title: SomaticVariant +type: object +description: 'A collection of somatic variants. + + ' +links: +- rel: somatic_callset + href: somaticcallset/{id} + templateRequired: + - id + targetSchema: + $ref: somatic_callset.yaml + templatePointers: + id: /somatic_callset/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +- rel: allele + href: allele/{id} + templateRequired: + - id + targetSchema: + $ref: allele.yaml + templatePointers: + id: /allele/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + association: true +properties: + id: + type: string + systemAlias: node_id + ref: + type: string + alt: + type: string + t_depth: + type: integer + t_ref_count: + type: integer + t_alt_count: + type: integer + n_depth: + type: integer + n_ref_count: + type: integer + n_alt_count: + type: integer + filter: + type: string + methods: + type: array + items: + type: string + ensembl_protein: + type: string + ensembl_transcript: + type: string + ensembl_gene: + type: string + somatic_callset: + type: + - string + items: + $ref: reference.yaml + allele: + type: + - string + items: + $ref: reference.yaml diff --git a/test/resources/schemas/transcript.yaml b/test/resources/schemas/transcript.yaml new file mode 100644 index 0000000..ee0159f --- /dev/null +++ b/test/resources/schemas/transcript.yaml @@ -0,0 +1,67 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: transcript +title: Transcript +type: object +description: 'A transcript. + + ' +required: +- submitter_id +- project_id +- biotype +- chromosome +- strand +- start +- genome +- end +- transcript_id +links: +- rel: gene + href: gene/{id} + templateRequired: + - id + targetSchema: + $ref: gene.yaml + templatePointers: + id: /gene/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + backref: transcripts +properties: + transcript_id: + type: string + biotype: + type: string + genome: + $ref: _definitions.yaml#/genome + chromosome: + $ref: _definitions.yaml#/chromosome + start: + type: integer + end: + type: integer + strand: + $ref: _definitions.yaml#/strand + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + id: + type: string + systemAlias: node_id + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + gene: + type: + - array + items: + $ref: reference.yaml diff --git a/test/resources/schemas/transcript_expression.yaml b/test/resources/schemas/transcript_expression.yaml new file mode 100644 index 0000000..b09ee24 --- /dev/null +++ b/test/resources/schemas/transcript_expression.yaml @@ -0,0 +1,59 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: transcript_expression +title: TranscriptExpression +type: object +description: 'Transcript level expression values for an aliquot + + ' +required: +- submitter_id +- project_id +- values +- method +- metric +links: +- rel: aliquot + href: aliquot/{id} + templateRequired: + - id + targetSchema: + $ref: aliquot.yaml + templatePointers: + id: /aliquot/-/id + targetHints: + directionality: + - outbound + multiplicity: + - has_one + backref: transcript_expressions +properties: + method: + type: string + metric: + $ref: _definitions.yaml#/expression_metric + values: + type: object + propertyNames: + pattern: ^ENST[0-9]+ + additionalProperties: + type: number + project_id: + $ref: _definitions.yaml#/project_id + submitter_id: + type: + - string + - 'null' + id: + type: string + systemAlias: node_id + type: + type: string + created_datetime: + $ref: _definitions.yaml#/datetime + updated_datetime: + $ref: _definitions.yaml#/datetime + aliquot: + type: + - array + items: + $ref: reference.yaml