I'm following the Getting started tutorial of Sawtooth Seth (https://sawtooth.hyperledger.org/docs/seth/releases/latest/getting_started.html), but I'm not able to set up an account on the network. The network is running properly in another shell. (I've removed the -aes128 flag for simplicity)
lorenzo#MacBook-Air-di-Lorenzo ~ $ cd gitHubRepo/sawtooth-seth/
lorenzo#MacBook-Air-di-Lorenzo ~/gitHubRepo/sawtooth-seth $ docker exec -it seth-cli bash
root#a6caea38a1a8:/project/sawtooth-seth# openssl ecparam -genkey -name secp256k1 | openssl ec -out key-file.pem
read EC key
writing EC key
root#a6caea38a1a8:/project/sawtooth-seth# seth account import key-file.pem myalias
error: Found argument 'myalias' which wasn't expected, or isn't valid in this context
USAGE:
seth account import <key-file> --pass-file <pass-file>
For more information try --help
root#a6caea38a1a8:/project/sawtooth-seth# seth account import key-file.pem --pass-file myalias
Error: No such file or directory (os error 2)
root#a6caea38a1a8:/project/sawtooth-seth# ls
bin cli common contracts key-file.pem protos tests
You ran the seth command in the seth-cli Docker container.
You need to run it in the seth-cli-go container until PR https://github.com/hyperledger/sawtooth-seth/pull/72 is merged.
EDIT: This was merged 2018-11-13.
A good resource for questions like this is also the seth chat channel at
https://chat.hyperledger.org/channel/sawtooth-seth
Related
I am trying to change my openconnect usage from command line to configfile.
I need to use a smartcard (StarSign CUT S, from Giesecke & Devrient GmbH) in order to access my VPN.
My current command line works fine and I can connect to the VPN:
$ openconnect \
--authgroup=<my_gateway> \
--protocol=gp \
--servercert <...> \
--disable-ipv6 \
--cafile <file.pem> \
<my_server_url> \
-c "pkcs11:model=XXXXXXXXXXXXXXXX;manufacturer=A.E.T.%20Europe%20B.V.;serial=XXXXXXXXXXXXXXXX;token=XXXXXXXXX;id=<...>;object=<...>;type=cert"
But when I try this configfile:
(All arguments are exactly the same!)
# vpn.config
authgroup = <my_gateway>
protocol = gp
servercert = <...>
disable-ipv6
cafile = <file.pem>
server = <my_server_url>
certificate = "pkcs11:model=XXXXXXXXXXXXXXXX;manufacturer=A.E.T.%20Europe%20B.V.;serial=XXXXXXXXXXXXXXXX;token=XXXXXXXXX;id=<...>;object=<...>;type=cert"
I get this error:
$ openconnect --config=vpn.config
Failed to open key/certificate file <...>: File name too long
Loading certificate failed. Aborting.
Failed to open HTTPS connection to <...>
Failed to complete authentication
Any idea on how to make it work? Or is it a bug in openconnect?
Thanks.
PS 1:
$ openconnect --version
OpenConnect version v9.01
Using GnuTLS 3.7.7. Features present: PKCS#11, HOTP software token, TOTP software token, System keys, DTLS, ESP
Supported protocols: anyconnect (default), nc, gp, pulse, f5, fortinet, array
Default vpnc-script (override with --script): /etc/vpnc/vpnc-script
PS 2: All commands executed as root.
Remove the double quotes from the configuration file:
# vpn.config
...
certificate = pkcs11:model=XXXXXXXXXXXXXXXX;manufacturer=A.E.T.%20Europe%20B.V.;serial=XXXXXXXXXXXXXXXX;token=XXXXXXXXX;id=<...>;object=<...>;type=cert
I have a pipeline which uses a global singularity image and rule-based conda wrappers.
However, some of the tools don't have wrappers (i.e. htslib's bgzip and tabix).
Now I need to learn how to run jobs in containers.
In the official documentation link it says:
"Allowed image urls entail everything supported by singularity (e.g., shub:// and docker://)."
Now I've tried the following image from singularity hub but I get an error:
minimal reproducible example:
config.yaml
# Files
REF_GENOME: "c_elegans.PRJNA13758.WS265.genomic.fa"
GENOME_ANNOTATION: "c_elegans.PRJNA13758.WS265.annotations.gff3"
Snakefile
# Directories------------------------------------------------------------------
configfile: "config.yaml"
# Setting the names of all directories
dir_list = ["REF_DIR", "LOG_DIR", "BENCHMARK_DIR", "QC_DIR", "TRIM_DIR", "ALIGN_DIR", "MARKDUP_DIR", "CALLING_DIR", "ANNOT_DIR"]
dir_names = ["refs", "logs", "benchmarks", "qc", "trimming", "alignment", "mark_duplicates", "variant_calling", "annotation"]
dirs_dict = dict(zip(dir_list, dir_names))
GENOME_INDEX=config["REF_GENOME"]+".fai"
VEP_ANNOT=config["GENOME_ANNOTATION"]+".gz"
VEP_ANNOT_INDEX=config["GENOME_ANNOTATION"]+".gz.tbi"
# Singularity with conda wrappers
singularity: "docker://continuumio/miniconda3:4.5.11"
# Rules -----------------------------------------------------------------------
rule all:
input:
expand('{REF_DIR}/{GENOME_ANNOTATION}{ext}', REF_DIR=dirs_dict["REF_DIR"], GENOME_ANNOTATION=config["GENOME_ANNOTATION"], ext=['', '.gz', '.gz.tbi']),
expand('{REF_DIR}/{REF_GENOME}{ext}', REF_DIR=dirs_dict["REF_DIR"], REF_GENOME=config["REF_GENOME"], ext=['','.fai']),
rule download_references:
params:
ref_genome=config["REF_GENOME"],
genome_annotation=config["GENOME_ANNOTATION"],
ref_dir=dirs_dict["REF_DIR"]
output:
os.path.join(dirs_dict["REF_DIR"],config["REF_GENOME"]),
os.path.join(dirs_dict["REF_DIR"],config["GENOME_ANNOTATION"]),
os.path.join(dirs_dict["REF_DIR"],VEP_ANNOT),
os.path.join(dirs_dict["REF_DIR"],VEP_ANNOT_INDEX)
resources:
mem=80000,
time=45
log:
os.path.join(dirs_dict["LOG_DIR"],"references","download.log")
singularity:
"shub://biocontainers/tabix"
shell: """
cd {params.ref_dir}
wget ftp://ftp.wormbase.org/pub/wormbase/releases/WS265/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS265.genomic.fa.gz
bgzip -d {params.ref_genome}.gz
wget ftp://ftp.wormbase.org/pub/wormbase/releases/WS265/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS265.annotations.gff3.gz
bgzip -d {params.genome_annotation}.gz
grep -v "#" {params.genome_annotation} | sort -k1,1 -k4,4n -k5,5n -t$'\t' | bgzip -c > {params.genome_annotation}.gz
tabix -p gff {params.genome_annotation}.gz
"""
rule index_reference:
input:
os.path.join(dirs_dict["REF_DIR"],config["REF_GENOME"])
output:
os.path.join(dirs_dict["REF_DIR"],GENOME_INDEX)
resources:
mem=2000,
time=30,
log:
os.path.join(dirs_dict["LOG_DIR"],"references", "faidx_index.log")
wrapper:
"0.64.0/bio/samtools/faidx"
Error
Building DAG of jobs...
Pulling singularity image shub://biocontainers/tabix.
WorkflowError:
Failed to pull singularity image from shub://biocontainers/tabix:
ESC[31mFATAL: ESC[0m While pulling shub image: failed to get manifest for: shub://biocontainers/tabix: the requested manifest was not found in singularity hub
File "/home/moldach/anaconda3/envs/snakemake/lib/python3.7/site-packages/snakemake/deployment/singularity.py", line 88, in pull
~
It appears this is a problem with the container?
(snakemake) [moldach#arc CONTAINER_TROUBLESHOOT]$ singularity pull shub://biocontainers/tabix
FATAL: While pulling shub image: failed to get manifest for: shub://biocontainers/tabix: the requested manifest was not found in singularity hub
In fact, I experience this problem with other biocontainers containers.
For example, I also need to use a container to do bowtie2 indexing and this is the error I get from the biocontainers/bowtie2 versus another developers container of the same tool comics/bowtie2:
^C(snakemake) [moldach#arc CONTAINER_TROUBLESHOOT]$ singularity pull docker://biocontainers/bowtie2
FATAL: While making image from oci registry: failed to get checksum for docker://biocontainers/bowtie2: Error reading manifest latest in docker.io/biocontainers/bowtie2: manifest unknown: manifest unknown
(snakemake) [moldach#arc CONTAINER_TROUBLESHOOT]$ singularity pull docker://comics/bowtie2
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
Getting image source signatures
Copying blob a02a4930cb5d done
Does anyone know why?
Biocontainers does not allow latest as tag for their containers, and therefore you will need to specify the tag to be used.
From their doc:
The BioContainers community had decided to remove the latest tag. Then, the following command docker pull biocontainers/crux will fail. Read more about this decision in Getting started with Docker
When no tag is specified, it defaults to latest tag, which of course is not allowed here. See here for bowtie2's tags. Usage like this will work:
singularity pull docker://biocontainers/bowtie2:v2.4.1_cv1
Using another container solves the issue; however, the fact I'm getting errors from biocontainers is troubling given that these are both very common and used as examples in the literature so I will award the top-answer to whomever can solve that specific issue.
As it were, the use of stackleader/bgzip-utility solve the issue of actually running this rule in a container.
container:
"docker://stackleader/bgzip-utility"
Once again, for those coming to this post, it's probably best to test any container first before running snakemake, e.g. singularity pull docker://stackleader/bgzip-utility.
I am new to Fabric 2.0 and recently installed all samples and I was able to run test-network without an issue with 2 orgs. Then I followed the directory on addOrg3 to add 3rd organization and join the channel I created earlier.
Now the fun part came in when I wanted to add 4th organization. What I did was, I copied the addOrg3 folder and renamed almost everything in each file to represent 4th organization. I even assigned new PORT for this organization. However I am seeing the following error.
I've also added the following in Scripts/envVar.sh
export PEER0_ORG4_CA=${PWD}/organizations/peerOrganizations/org4.example.com/peers/peer0.org4.example.com/tls/ca.crt
And added the following in envVarCLI.sh
elif [ $ORG -eq 4 ]; then
CORE_PEER_LOCALMSPID="Org4MSP"
CORE_PEER_TLS_ROOTCERT_FILE=$PEER0_ORG4_CA
CORE_PEER_ADDRESS=peer0.org4.example.com:12051
CORE_PEER_MSPCONFIGPATH=/opt/gopath/src/github.com/hyperledger/fabric/peer/organizations/peerOrganizations/org4.example.com/users/Admin#.../msp
I have also added step1Org4.sh and step2Org4.sh basically following by following addOrg3's structure.
What steps do you follow to add additional organizations ? Please help.
"No such container: Org4cli"
Sorry for the formatting since I wasn't able to put in to coding style but here is the output from running the command "./addOrg4.sh up"
**Add Org4 to channel 'mychannel' with '10' seconds and CLI delay of '3' seconds and using database 'leveldb'
Desktop/blockchain/BSI/fabric-samples/test-network/addOrg4/../../bin/cryptogen
##########################################################
##### Generate certificates using cryptogen tool #########
##########################################################
##########################################################
############ Create Org4 Identities ######################
##########################################################
+ cryptogen generate --config=org4-crypto.yaml --output=../organizations
org4.example.com
+ res=0
+ set +x
Generate CCP files for Org4
Desktop/blockchain/BSI/fabric-samples/test-network/addOrg4/../../bin/configtxgen
##########################################################
####### Generating Org4 organization definition #########
##########################################################
+ configtxgen -printOrg Org4MSP
2020-05-29 13:33:04.609 EDT [common.tools.configtxgen] main -> INFO 001 Loading configuration
2020-05-29 13:33:04.617 EDT [common.tools.configtxgen.localconfig] LoadTopLevel -> INFO 002 Loaded configuration: /Desktop/blockchain/BSI/fabric-samples/test-network/addOrg4/configtx.yaml
+ res=0
+ set +x
###############################################################
####### Generate and submit config tx to add Org4 #############
###############################################################
Error: No such container: Org4cli
ERROR !!!! Unable to create config tx **
In your addOrg4.sh have condition check like this:
CONTAINER_IDS=$(docker ps -a | awk '($2 ~ /fabric-tools/) {print $1}')
if [ -z "$CONTAINER_IDS" -o "$CONTAINER_IDS" == " " ]; then
echo "Bringing up network"
Org4Up
fi
If you already run addOrg3.sh up, CONTAINER_IDS alway have value (Example: 51b4ad60d812). It is ContainerID of Org3cli. So function Org4Up will never call. Simple way is just comment code like this:
# CONTAINER_IDS=$(docker ps -a | awk '($2 ~ /fabric-tools/) {print $1}')
# if [ -z "$CONTAINER_IDS" -o "$CONTAINER_IDS" == " " ]; then
echo "Bringing up network"
Org4Up
# fi
It will bring up Org4cli you missing.
First check the container is up or not and if it is up then I think the CLI where the command is executed is not bootstrapped with the Org4 details.
I have added the 4th Organization from the three Org Hyperledger Fabric Network .Firstly, you have to create the Org4-artifacts (Crypto.yaml and Org4 docker file including the Org4Cli) and then try to follow the manual (step by step) process to add the new Organization from the official documentation.
https://hyperledger-fabric.readthedocs.io/en/release-2.0/channel_update_tutorial.html
Omit the process of editing scripts (step1 Org3.sh ...) because the workflow for adding the 4th or a new Org is slightly changed.So,you will spend a lot of time in just modifying the scripts.
I will write an article to add a new Org (4th) on medium,will paste the link here too.
This is my first post on Stackoverflow. Please bear with me...
I am new to basically everything around hyperledger-fabric.
While trying to follow the "Writing Your First Application Tutorial" i am unable to generate the genesis block.
I am running:
windows 10
Docker version 18.03.0-ce, build 0520e24302
docker-compose version 1.20.1, build 5d8c71b2
npm 6.1.2
node.js v12.1
python 2.7
I used the curl commands given in the instructions.
When i run
./startFabric.sh javascript
at first everything is going ok. I am getting some warnings but starting the Channel seems to work fine.
In the next few lines however i am getting an error.
Generate CCP files for Org1 and Org2
/c/Users/Jonathan/Hyperledger_Fabric/fabric-samples/bin/configtxgen
Generating Orderer Genesis block
CONSENSUS_TYPE=solo
+ '[' solo == solo ']'
+ configtxgen -profile TwoOrgsOrdererGenesis -channelID byfn-sys-channel -outputBlock ./channel-artifacts/genesis.block
2019-11-25 10:35:01.676 CET [common.tools.configtxgen] main -> INFO 001 Loading configuration
2019-11-25 10:35:01.677 CET [common.tools.configtxgen.localconfig] Load -> PANI 002 Error reading configuration: Unsupported Config Type ""
2019-11-25 10:35:01.679 CET [common.tools.configtxgen] func1 -> PANI 003 Error reading configuration: Unsupported Config Type ""
panic: Error reading configuration: Unsupported Config Type "" [recovered]
panic: Error reading configuration: Unsupported Config Type ""
It seems that the configuration is missing/not the right "type".
I googled my error and came up with people having similar/the same issue but i havent been able to solve my issue by following the advice they were given (hence why i am here).
Similar posts i found:
https://jira.hyperledger.org/browse/FAB-3467
Error cryptogen tool in Hyperledger Fabric
The people responding to the posts above generally seem to think its an issue regarding the path to the config file which apparently can be fixed with
FABRIC_CFG_PATH=$PWD
But that hasnt worked for me.
Full Console Output:
https://pastebin.com/CHxjZ1Uq
Look at the warning at the start: you are missing some prerequisites.
First, use the generate script to generate the crypto-config and artifacts folder.
Once you got your certificates you can start fabric.
You should have a generte.sh script or something like that.
Essentially it runs the certificate generation for your network using cryptogen.
The code is something like this:
which cryptogen
if [ "$?" -ne 0 ]; then
echo "cryptogen tool not found. exiting"
exit 1
fi
if [ -d "crypto-config" ]; then
rm -Rf crypto-config
fi
set -x
cryptogen generate --config=./crypto-config.yaml
Once you generated the certificates, you can now generate the genesis block with something like:
which configtxgen
if [ -d "config" ]; then
rm -Rf config
fi
mkdir config
configtxgen -profile OneOrgOrdererGenesis -outputBlock ./config/genesis.block
configtxgen -profile OneOrgChannel -outputCreateChannelTx ./config/channel.tx -channelID $CHANNEL_NAME
configtxgen -profile OneOrgChannel -outputAnchorPeersUpdate ./config/${MSP_NAME}anchors.tx -channelID $CHANNEL_NAME -asOrg $MSP_NAME
Obviously replacing with your names and variables.
I am playing with hyperledger-fabric v.1.0 - actually a newbie. How can I check the chain height ? Is there a command or something that I can use to "ask" about the blockchain height? Thanks in advance.
Well, you have a few options of how you can do it:
You can leverage peer cli command line tool to obtain latest available block by running
peer channel fetch newest -o ordererIP:7050 -c mychannel last.block
Next you can leverage configtxlator to decode content of the block as following:
curl -X POST --data-binary #last.block http://localhost:7059/protolator/decode/common.Block
(note you need to start configtxlator first)
Alternative path assumes you are going to use one of available SDK's to invoke QSCC (Query System ChainCode) with GetChainInfo command. This will return you back following structure:
type BlockchainInfo struct {
Height uint64 `protobuf:"varint,1,opt,name=height" json:"height,omitempty"`
CurrentBlockHash []byte `protobuf:"bytes,2,opt,name=currentBlockHash,proto3" json:"currentBlockHash,omitempty"`
PreviousBlockHash []byte `protobuf:"bytes,3,opt,name=previousBlockHash,proto3" json:"previousBlockHash,omitempty"`
}
Which has information about current ledger height.
Another alternative.
Using the cli peer command line (for example docker exec -it cli bash) you can do:
peer channel getinfo -c mychannel
It seems that I found something - maybe cumbersome, but better than nothing:
Command:
docker logs -f peer0.org1.example.com 2>&1 | grep blockNo
Check for the "latest" line in the output, something like:
2017-07-18 19:40:39.586 UTC [historyleveldb] Commit -> DEBU b75b Channel [mychannel]: Updates committed to history database for blockNo [34]
So, if I am not wrong, in this case the block height is: 34
Thanks
you can use blockchain-explorer (UI tool)
https://github.com/hyperledger/blockchain-explorer
You should also be able to use the fabric CORE API (JSON/REST).
See the docs for the Blockchain GET/chain operation at;
https://github.com/hyperledger-archives/fabric/blob/master/docs/API/CoreAPI.md#rest-api