chore: Update dependencies including go-ipfs (#1112)

Relevant issue(s)
Resolves #451

Description
This PR updates most of our direct dependencies including IPFS packages that impacted the CID creation

datastore/blockstore.go

@@ -13,13 +13,13 @@ package datastore
 import (
 	"context"
 
-	blocks "github.com/ipfs/go-block-format"
 	"github.com/ipfs/go-cid"
 	ds "github.com/ipfs/go-datastore"
 	dsq "github.com/ipfs/go-datastore/query"
 	blockstore "github.com/ipfs/go-ipfs-blockstore"
 	dshelp "github.com/ipfs/go-ipfs-ds-help"
 	ipld "github.com/ipfs/go-ipld-format"
+	"github.com/ipfs/go-libipfs/blocks"
 
 	"github.com/sourcenetwork/defradb/errors"
 )

db/collection_delete.go

@@ -14,11 +14,11 @@ import (
 	"context"
 	"fmt"
 
-	block "github.com/ipfs/go-block-format"
 	cid "github.com/ipfs/go-cid"
 	ds "github.com/ipfs/go-datastore"
 	query "github.com/ipfs/go-datastore/query"
 	ipld "github.com/ipfs/go-ipld-format"
+	"github.com/ipfs/go-libipfs/blocks"
 	dag "github.com/ipfs/go-merkledag"
 
 	"github.com/sourcenetwork/defradb/client"
@@ -368,7 +368,7 @@ func (d dagDeleter) run(ctx context.Context, targetCid cid.Cid) error {
 func (d dagDeleter) delete(
 	ctx context.Context,
 	targetCid cid.Cid,
-	targetBlock block.Block) error {
+	targetBlock blocks.Block) error {
 	targetNode, err := dag.DecodeProtobuf(targetBlock.RawData())
 	if err != nil {
 		return err

docs/data_format_changes/i451-codec-package-update

@@ -0,0 +1,3 @@
+# Updating the `github.com/ugorji/go/codec` package changes CIDs
+
+Updating of github.com/ugorji/go/codec going from `1.1.7` to `1.2.9` change the way the encoder behaves with the same input. This causes the input to the CID generation function to be different and thus the resulting CID is different.

go.mod

@@ -4,63 +4,62 @@ go 1.19
 
 require (
 	github.com/bxcodec/faker v2.0.1+incompatible
-	github.com/dgraph-io/badger/v3 v3.2103.4
+	github.com/dgraph-io/badger/v3 v3.2103.5
 	github.com/fxamacker/cbor/v2 v2.4.0
-	github.com/go-chi/chi/v5 v5.0.7
+	github.com/go-chi/chi/v5 v5.0.8
 	github.com/go-chi/cors v1.2.1
-	github.com/go-errors/errors v1.0.1
+	github.com/go-errors/errors v1.4.2
 	github.com/gogo/protobuf v1.3.2
 	github.com/graphql-go/graphql v0.8.0
 	github.com/iancoleman/strcase v0.2.0
-	github.com/ipfs/go-bitswap v0.10.2
-	github.com/ipfs/go-block-format v0.0.3
-	github.com/ipfs/go-blockservice v0.4.0
+	github.com/ipfs/go-blockservice v0.5.0
 	github.com/ipfs/go-cid v0.3.2
 	github.com/ipfs/go-datastore v0.6.0
 	github.com/ipfs/go-ipfs-blockstore v1.2.0
 	github.com/ipfs/go-ipfs-ds-help v1.1.0
 	github.com/ipfs/go-ipfs-exchange-interface v0.2.0
 	github.com/ipfs/go-ipld-format v0.4.0
-	github.com/ipfs/go-ipns v0.2.0
+	github.com/ipfs/go-ipns v0.3.0
+	github.com/ipfs/go-libipfs v0.5.0
 	github.com/ipfs/go-log v1.0.5
 	github.com/ipfs/go-log/v2 v2.5.1
-	github.com/ipfs/go-merkledag v0.8.0
+	github.com/ipfs/go-merkledag v0.9.0
 	github.com/jbenet/goprocess v0.1.4
-	github.com/libp2p/go-libp2p v0.23.2
-	github.com/libp2p/go-libp2p-gostream v0.3.1
-	github.com/libp2p/go-libp2p-kad-dht v0.18.0
-	github.com/libp2p/go-libp2p-pubsub v0.8.1
+	github.com/libp2p/go-libp2p v0.25.1
+	github.com/libp2p/go-libp2p-gostream v0.5.0
+	github.com/libp2p/go-libp2p-kad-dht v0.21.0
+	github.com/libp2p/go-libp2p-pubsub v0.9.0
 	github.com/libp2p/go-libp2p-record v0.2.0
 	github.com/mitchellh/mapstructure v1.5.0
-	github.com/multiformats/go-multiaddr v0.7.0
+	github.com/multiformats/go-multiaddr v0.8.0
 	github.com/multiformats/go-multibase v0.1.1
 	github.com/multiformats/go-multihash v0.2.1
-	github.com/multiformats/go-varint v0.0.6
+	github.com/multiformats/go-varint v0.0.7
 	github.com/pkg/errors v0.9.1
 	github.com/satori/go.uuid v1.2.0
 	github.com/sourcenetwork/immutable v0.2.1
 	github.com/spf13/cobra v1.6.1
-	github.com/spf13/viper v1.11.0
+	github.com/spf13/viper v1.15.0
 	github.com/stretchr/testify v1.8.1
 	github.com/textileio/go-libp2p-pubsub-rpc v0.0.9
-	github.com/tidwall/btree v1.5.0
-	github.com/ugorji/go/codec v1.1.7
-	github.com/valyala/fastjson v1.6.3
+	github.com/tidwall/btree v1.6.0
+	github.com/ugorji/go/codec v1.2.9
+	github.com/valyala/fastjson v1.6.4
 	go.opentelemetry.io/otel/metric v0.34.0
 	go.opentelemetry.io/otel/sdk/metric v0.34.0
-	go.uber.org/zap v1.23.0
-	golang.org/x/crypto v0.0.0-20221005025214-4161e89ecf1b
-	google.golang.org/grpc v1.46.2
+	go.uber.org/zap v1.24.0
+	golang.org/x/crypto v0.6.0
+	google.golang.org/grpc v1.53.0
 )
 
 require (
 	github.com/alecthomas/units v0.0.0-20211218093645-b94a6e3cc137 // indirect
 	github.com/benbjohnson/clock v1.3.0 // indirect
 	github.com/beorn7/perks v1.0.1 // indirect
 	github.com/cespare/xxhash v1.1.0 // indirect
-	github.com/cespare/xxhash/v2 v2.1.2 // indirect
+	github.com/cespare/xxhash/v2 v2.2.0 // indirect
 	github.com/containerd/cgroups v1.0.4 // indirect
-	github.com/coreos/go-systemd/v22 v22.4.0 // indirect
+	github.com/coreos/go-systemd/v22 v22.5.0 // indirect
 	github.com/cpuguy83/go-md2man/v2 v2.0.2 // indirect
 	github.com/cskr/pubsub v1.0.2 // indirect
 	github.com/davecgh/go-spew v1.1.1 // indirect
@@ -70,9 +69,10 @@ require (
 	github.com/docker/go-units v0.5.0 // indirect
 	github.com/dustin/go-humanize v1.0.0 // indirect
 	github.com/elastic/gosigar v0.14.2 // indirect
+	github.com/emirpasic/gods v1.18.1 // indirect
 	github.com/flynn/noise v1.0.0 // indirect
 	github.com/francoispqt/gojay v1.2.13 // indirect
-	github.com/fsnotify/fsnotify v1.5.4 // indirect
+	github.com/fsnotify/fsnotify v1.6.0 // indirect
 	github.com/go-logr/logr v1.2.3 // indirect
 	github.com/go-logr/stdr v1.2.2 // indirect
 	github.com/go-task/slim-sprig v0.0.0-20210107165309-348f09dbbbc0 // indirect
@@ -84,17 +84,19 @@ require (
 	github.com/golang/snappy v0.0.4 // indirect
 	github.com/google/flatbuffers v2.0.6+incompatible // indirect
 	github.com/google/gopacket v1.1.19 // indirect
+	github.com/google/pprof v0.0.0-20221203041831-ce31453925ec // indirect
 	github.com/google/uuid v1.3.0 // indirect
-	github.com/gorilla/websocket v1.5.0 // indirect
 	github.com/hashicorp/errwrap v1.1.0 // indirect
 	github.com/hashicorp/go-multierror v1.1.1 // indirect
 	github.com/hashicorp/golang-lru v0.5.5-0.20210104140557-80c98217689d // indirect
+	github.com/hashicorp/golang-lru/v2 v2.0.1 // indirect
 	github.com/hashicorp/hcl v1.0.0 // indirect
 	github.com/hsanjuan/ipfs-lite v1.4.1 // indirect
 	github.com/huin/goupnp v1.0.3 // indirect
 	github.com/inconshreveable/mousetrap v1.0.1 // indirect
 	github.com/ipfs/bbloom v0.0.4 // indirect
-	github.com/ipfs/go-fetcher v1.6.1 // indirect
+	github.com/ipfs/go-bitswap v0.12.0 // indirect
+	github.com/ipfs/go-block-format v0.1.1 // indirect
 	github.com/ipfs/go-ipfs-config v0.19.0 // indirect
 	github.com/ipfs/go-ipfs-delay v0.0.1 // indirect
 	github.com/ipfs/go-ipfs-files v0.1.1 // indirect
@@ -103,97 +105,95 @@ require (
 	github.com/ipfs/go-ipld-cbor v0.0.6 // indirect
 	github.com/ipfs/go-ipld-legacy v0.1.1 // indirect
 	github.com/ipfs/go-metrics-interface v0.0.1 // indirect
-	github.com/ipfs/go-peertaskqueue v0.7.1 // indirect
-	github.com/ipfs/go-verifcid v0.0.1 // indirect
-	github.com/ipld/go-codec-dagpb v1.4.0 // indirect
-	github.com/ipld/go-ipld-prime v0.16.0 // indirect
+	github.com/ipfs/go-peertaskqueue v0.8.0 // indirect
+	github.com/ipfs/go-verifcid v0.0.2 // indirect
+	github.com/ipld/go-codec-dagpb v1.5.0 // indirect
+	github.com/ipld/go-ipld-prime v0.19.0 // indirect
 	github.com/jackpal/go-nat-pmp v1.0.2 // indirect
 	github.com/jbenet/go-temp-err-catcher v0.1.0 // indirect
-	github.com/klauspost/compress v1.15.10 // indirect
-	github.com/klauspost/cpuid/v2 v2.1.1 // indirect
+	github.com/klauspost/compress v1.15.12 // indirect
+	github.com/klauspost/cpuid/v2 v2.2.1 // indirect
 	github.com/koron/go-ssdp v0.0.3 // indirect
 	github.com/libp2p/go-buffer-pool v0.1.0 // indirect
 	github.com/libp2p/go-cidranger v1.1.0 // indirect
 	github.com/libp2p/go-flow-metrics v0.1.0 // indirect
 	github.com/libp2p/go-libp2p-asn-util v0.2.0 // indirect
 	github.com/libp2p/go-libp2p-connmgr v0.4.0 // indirect
 	github.com/libp2p/go-libp2p-core v0.20.0 // indirect
-	github.com/libp2p/go-libp2p-kbucket v0.4.7 // indirect
-	github.com/libp2p/go-libp2p-routing-helpers v0.2.3 // indirect
-	github.com/libp2p/go-msgio v0.2.0 // indirect
+	github.com/libp2p/go-libp2p-kbucket v0.5.0 // indirect
+	github.com/libp2p/go-libp2p-routing-helpers v0.4.0 // indirect
+	github.com/libp2p/go-msgio v0.3.0 // indirect
 	github.com/libp2p/go-nat v0.1.0 // indirect
-	github.com/libp2p/go-netroute v0.2.0 // indirect
-	github.com/libp2p/go-openssl v0.1.0 // indirect
+	github.com/libp2p/go-netroute v0.2.1 // indirect
 	github.com/libp2p/go-reuseport v0.2.0 // indirect
 	github.com/libp2p/go-yamux/v4 v4.0.0 // indirect
-	github.com/lucas-clemente/quic-go v0.29.1 // indirect
-	github.com/magiconair/properties v1.8.6 // indirect
-	github.com/marten-seemann/qtls-go1-18 v0.1.2 // indirect
-	github.com/marten-seemann/qtls-go1-19 v0.1.0 // indirect
+	github.com/magiconair/properties v1.8.7 // indirect
 	github.com/marten-seemann/tcp v0.0.0-20210406111302-dfbc87cc63fd // indirect
-	github.com/mattn/go-isatty v0.0.16 // indirect
-	github.com/mattn/go-pointer v0.0.1 // indirect
-	github.com/matttproud/golang_protobuf_extensions v1.0.1 // indirect
+	github.com/mattn/go-isatty v0.0.17 // indirect
+	github.com/matttproud/golang_protobuf_extensions v1.0.4 // indirect
 	github.com/miekg/dns v1.1.50 // indirect
 	github.com/mikioh/tcpinfo v0.0.0-20190314235526-30a79bb1804b // indirect
 	github.com/mikioh/tcpopt v0.0.0-20190314235656-172688c1accc // indirect
 	github.com/minio/sha256-simd v1.0.0 // indirect
 	github.com/mr-tron/base58 v1.2.0 // indirect
 	github.com/multiformats/go-base32 v0.1.0 // indirect
-	github.com/multiformats/go-base36 v0.1.0 // indirect
+	github.com/multiformats/go-base36 v0.2.0 // indirect
 	github.com/multiformats/go-multiaddr-dns v0.3.1 // indirect
 	github.com/multiformats/go-multiaddr-fmt v0.1.0 // indirect
-	github.com/multiformats/go-multicodec v0.6.0 // indirect
-	github.com/multiformats/go-multistream v0.3.3 // indirect
-	github.com/nxadm/tail v1.4.8 // indirect
-	github.com/onsi/ginkgo v1.16.5 // indirect
+	github.com/multiformats/go-multicodec v0.7.0 // indirect
+	github.com/multiformats/go-multistream v0.4.1 // indirect
+	github.com/onsi/ginkgo/v2 v2.5.1 // indirect
 	github.com/opencontainers/runtime-spec v1.0.2 // indirect
 	github.com/opentracing/opentracing-go v1.2.0 // indirect
 	github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58 // indirect
-	github.com/pelletier/go-toml v1.9.5 // indirect
-	github.com/pelletier/go-toml/v2 v2.0.1 // indirect
+	github.com/pelletier/go-toml/v2 v2.0.6 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
 	github.com/polydawn/refmt v0.0.0-20201211092308-30ac6d18308e // indirect
-	github.com/prometheus/client_golang v1.13.0 // indirect
-	github.com/prometheus/client_model v0.2.0 // indirect
+	github.com/prometheus/client_golang v1.14.0 // indirect
+	github.com/prometheus/client_model v0.3.0 // indirect
 	github.com/prometheus/common v0.37.0 // indirect
 	github.com/prometheus/procfs v0.8.0 // indirect
+	github.com/quic-go/qpack v0.4.0 // indirect
+	github.com/quic-go/qtls-go1-18 v0.2.0 // indirect
+	github.com/quic-go/qtls-go1-19 v0.2.0 // indirect
+	github.com/quic-go/qtls-go1-20 v0.1.0 // indirect
+	github.com/quic-go/quic-go v0.32.0 // indirect
+	github.com/quic-go/webtransport-go v0.5.1 // indirect
 	github.com/raulk/go-watchdog v1.3.0 // indirect
 	github.com/russross/blackfriday/v2 v2.1.0 // indirect
-	github.com/spacemonkeygo/spacelog v0.0.0-20180420211403-2296661a0572 // indirect
 	github.com/spaolacci/murmur3 v1.1.0 // indirect
-	github.com/spf13/afero v1.8.2 // indirect
+	github.com/spf13/afero v1.9.3 // indirect
 	github.com/spf13/cast v1.5.0 // indirect
 	github.com/spf13/jwalterweatherman v1.1.0 // indirect
 	github.com/spf13/pflag v1.0.5 // indirect
 	github.com/stretchr/objx v0.5.0 // indirect
-	github.com/subosito/gotenv v1.2.0 // indirect
+	github.com/subosito/gotenv v1.4.2 // indirect
 	github.com/textileio/go-log/v2 v2.1.3-gke-2 // indirect
-	github.com/whyrusleeping/cbor-gen v0.0.0-20220514204315-f29c37e9c44c // indirect
+	github.com/whyrusleeping/cbor-gen v0.0.0-20221220214510-0333c149dec0 // indirect
 	github.com/whyrusleeping/go-keyspace v0.0.0-20160322163242-5b898ac5add1 // indirect
-	github.com/whyrusleeping/timecache v0.0.0-20160911033111-cfcb2f1abfee // indirect
 	github.com/x448/float16 v0.8.4 // indirect
-	go.opencensus.io v0.23.0 // indirect
-	go.opentelemetry.io/otel v1.11.2 // indirect
-	go.opentelemetry.io/otel/sdk v1.11.2 // indirect
-	go.opentelemetry.io/otel/trace v1.11.2 // indirect
+	go.opencensus.io v0.24.0 // indirect
+	go.opentelemetry.io/otel v1.13.0 // indirect
+	go.opentelemetry.io/otel/sdk v1.13.0 // indirect
+	go.opentelemetry.io/otel/trace v1.13.0 // indirect
 	go.uber.org/atomic v1.10.0 // indirect
+	go.uber.org/dig v1.15.0 // indirect
+	go.uber.org/fx v1.18.2 // indirect
 	go.uber.org/multierr v1.8.0 // indirect
-	golang.org/x/exp v0.0.0-20220916125017-b168a2c6b86b // indirect
-	golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4 // indirect
-	golang.org/x/net v0.0.0-20220920183852-bf014ff85ad5 // indirect
-	golang.org/x/sync v0.0.0-20220722155255-886fb9371eb4 // indirect
-	golang.org/x/sys v0.0.0-20221010170243-090e33056c14 // indirect
-	golang.org/x/text v0.3.7 // indirect
-	golang.org/x/tools v0.1.12 // indirect
-	golang.org/x/xerrors v0.0.0-20220411194840-2f41105eb62f // indirect
-	google.golang.org/genproto v0.0.0-20220505152158-f39f71e6c8f3 // indirect
+	golang.org/x/exp v0.0.0-20221205204356-47842c84f3db // indirect
+	golang.org/x/mod v0.7.0 // indirect
+	golang.org/x/net v0.6.0 // indirect
+	golang.org/x/sync v0.1.0 // indirect
+	golang.org/x/sys v0.5.0 // indirect
+	golang.org/x/text v0.7.0 // indirect
+	golang.org/x/tools v0.3.0 // indirect
+	golang.org/x/xerrors v0.0.0-20220907171357-04be3eba64a2 // indirect
+	google.golang.org/genproto v0.0.0-20230110181048-76db0878b65f // indirect
 	google.golang.org/protobuf v1.28.1 // indirect
-	gopkg.in/ini.v1 v1.66.4 // indirect
-	gopkg.in/tomb.v1 v1.0.0-20141024135613-dd632973f1e7 // indirect
-	gopkg.in/yaml.v2 v2.4.0 // indirect
+	gopkg.in/ini.v1 v1.67.0 // indirect
 	gopkg.in/yaml.v3 v3.0.1 // indirect
 	lukechampine.com/blake3 v1.1.7 // indirect
+	nhooyr.io/websocket v1.8.7 // indirect
 )
 
 // SourceNetwork fork og graphql-go