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BioGrakn Knowledge Graph
Starting BioGrakn on the command line fails with the following error:
Process exited with code '1': ''
The logs point to the following exception:
2020-02-18 11:57:33,417 [main] ERROR grakn.core.daemon.GraknDaemon - An error has occurred during boot-up. Please run 'grakn server status' or check the logs located under the 'logs' directory.
grakn.core.daemon.exception.GraknDaemonException: Process exited with code '1': ''
at grakn.core.daemon.executor.Storage.start(Storage.java:222)
at grakn.core.daemon.executor.Storage.startIfNotRunning(Storage.java:147)
at grakn.core.daemon.GraknDaemon.serverStart(GraknDaemon.java:184)
at grakn.core.daemon.GraknDaemon.run(GraknDaemon.java:136)
at grakn.core.daemon.GraknDaemon.main(GraknDaemon.java:72)
Steps to create the smallest reproducible scenario:
Just following the steps on the README file
PS E:\biograkn> + ./grakn server start
程序“grakn”无法运行: 没有应用程序与此操作的指定文件有关联。所在位置 行:1 字符: 1
所在位置 行:1 字符: 1
+ CategoryInfo : ResourceUnavailable: (:) [], ApplicationFailedException
+ FullyQualifiedErrorId : NativeCommandFailed
Steps to create the smallest reproducible scenario:
I am trying to run migrate.py in diseasenetwork/migrate
and i am getting the following error
Traceback (most recent call last):
File "migrate.py", line 41, in <module>
data['protein-name'] = i[3]
IndexError: list index out of range
So i inspected the concerned csv files and found that all of them have some git-lfs message inside it similar to the following
version https://git-lfs.github.com/spec/v1
oid sha256:dd0a985f3547fa96f5a2e85f971d04a77e656324529e4a62baf3bb967c2a09da
size 3399920
The data is not proper, or I have missed something here. hence can't get it to work.
Steps to create the smallest reproducible scenario:
diseasenetwork/migrate
migrate.py
File "migrate.py", line 41, in <module>
data['protein-name'] = i[3]
IndexError: list index out of range
Please replace every line in curly brackets { like this } with an appropriate description, and remove this line.
I am using grakn core 1.4.2 and during the schema loading step , i am getting this error
Command: `../../grakn-core-1.4.2/graql console --keyspace xyz --file ./schema.gql`
Error: `INVALID_ARGUMENT: GraqlQueryException-relation doesn't have an 'isa', a 'sub' or an 'id'. Please check server logs for the stack trace.`
I am following this video's steps, have a look
I wasnt expecting this error to pop up
The Error : INVALID_ARGUMENT: GraqlQueryException-relation doesn't have an 'isa', a 'sub' or an 'id'. Please check server logs for the stack trace
{ Please describe what actually happened. }
Model CoreNLP output to Grakn Schema
N/A
Write Schema to map CoreNLP output to grakn schema types
N/A
Not sure if this is a bug or deliberate miss. When querying "person" on the keyspace "precision_medicine" I got nothing, which failed all rule-based inferences as showed in the Youtube tutorial https://www.youtube.com/watch?v=E__0XhGHXnI
Hi,
I was just wondering if you have any instructions to compile biograkn from source
on a ubuntu machine?
Thanks,
George
Make sure the distribution is compliant to the 1.4.3 release of Grakn
circle ci runs out of memory due
Circle CI
trigger circle CI
Pass
java.lang.OutOfMemoryError: GC overhead limit exceeded
GC overhead limit exceeded
ERROR: bazel ran out of memory and crashed.
https://discuss.circleci.com/t/is-git-lfs-supported-by-circleci-2-0/11283/8
Would like to have "Getting Started" articles/videos describing step by step how to get the usecases working on user's PC
Currently It is painstakingly difficult for begineers to get started with grakn, especially with begineers who want to learn from real world problem implementations, and not on toy problems.
Would like Grakn to help out with step by step guides to set up their usecase on user's pc. maybe even making scripts to automate stuff.
The Outline of the "Getting Started" can be:
{ Not able to compile due to missing csv file in dataset }
Steps to create the smallest reproducible scenario:
{ expected to finish migration }
{ should be resolved with missing file }
{ this may come from a 3rd party, but we didn't see a link }
Make BioGrakn compliant with Grakn version 1.5.2 and respective clients
Refactor migration script to collect all inert queries and run them concurrently
When trying to migrate BioGrakn over Circle CI, it times out after 5 hours since the migration takes longer than 5 hours.
Job: https://circleci.com/gh/graknlabs/biograkn/1637
Additional information: https://discuss.circleci.com/t/maximum-build-time-for-builds/18383
Suggestion 1: Splitting the migration into multiple bazel targets and then run them across multiple circle ci jobs.
The example code is to be written in Python using the Biopython library.
.fasta
fileNeed an NLP tool for the text-mining use case
N/A
-Import Standford CoreNLP
-Implement mining of information from a body of text
N/A
Am I getting something wrong or does the unzipped file from the download section only contains "grakn-core-all-mac" instead of the BioGrakn ? Correct me if I'm wrong!
Refactor BioGrakn architecture to be more modular pertaining to the domain/usecase
Only one use case present
-biograkn
-precisionMedicine
-dataset
-schema
-migrator
-textmining
-dataset
-schema
-migrator
Remove BioGrakn DN duplicate genes
N/A
N/A
N/A
N/A
N/A
Modify circle ci config to enable RBE for test-dists-ubuntu
disabled as enabling RBE produced the following error:
This is for the usecase textmining
.I have loaded schema in keyspace, but then when i try to migrate data using migrate.java, I cant understand how to get it to work
i initially tried javac migrate.java
but it failed because repo uses bazel for building.
hence i went to the textmining
directory, and ran
bazel build //migrate/migrator-bin.jar
to which i am getting the following error:
build aborted: no such package '@antlr4_tool//jar'
Traceback:
DEBUG: Rule 'io_bazel_rules_python' indicated that a canonical reproducible form can be obtained by modifying arguments shallow_since = "1545256788 -0500"
DEBUG: Rule 'com_github_grpc_grpc' indicated that a canonical reproducible form can be obtained by modifying arguments shallow_since = "1550231355 +0300"
DEBUG: Rule 'stackb_rules_proto' indicated that a canonical reproducible form can be obtained by modifying arguments shallow_since = "1561665037 -0600"
DEBUG: Rule 'graknlabs_grakn_core' indicated that a canonical reproducible form can be obtained by modifying arguments shallow_since = "1572870526 +0000"
DEBUG: Rule 'graknlabs_benchmark' indicated that a canonical reproducible form can be obtained by modifying arguments shallow_since = "1571391871 +0100"
DEBUG: Rule 'graknlabs_graql' indicated that a canonical reproducible form can be obtained by modifying arguments shallow_since = "1572870025 +0000"
DEBUG: Rule 'rules_antlr' indicated that a canonical reproducible form can be obtained by modifying arguments commit = "397361a4d252a7186bc33add33144f4ede2a3899", shallow_since = "1559662328 +0200" and dropping ["tag"]
DEBUG: Rule 'graknlabs_client_python' indicated that a canonical reproducible form can be obtained by modifying arguments shallow_since = "1569623464 +0000"
DEBUG: Rule 'graknlabs_bazel_distribution' indicated that a canonical reproducible form can be obtained by modifying arguments shallow_since = "1572869706 +0300"
DEBUG: Rule 'com_github_google_bazel_common' indicated that a canonical reproducible form can be obtained by modifying arguments shallow_since = "1551104077 +0300"
DEBUG: Rule 'graknlabs_protocol' indicated that a canonical reproducible form can be obtained by modifying arguments shallow_since = "1572870033 +0000"
INFO: Call stack for the definition of repository 'antlr4_tool' which is a http_jar (rule definition at /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/bazel_tools/tools/build_defs/repo/http.bzl:347:12):
- /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/rules_antlr/antlr/deps.bzl:49:5
- /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/rules_antlr/antlr/deps.bzl:27:9
- /home/aditya/Projects/RD/biograkn/WORKSPACE:120:1
ERROR: An error occurred during the fetch of repository 'antlr4_tool':
java.io.IOException: Error downloading [http://central.maven.org/maven2/org/antlr/antlr4/4.7.2/antlr4-4.7.2.jar] to /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/antlr4_tool/jar/downloaded.jar: Unknown host: central.maven.org
INFO: Call stack for the definition of repository 'remotejdk11_linux' which is a http_archive (rule definition at /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/bazel_tools/tools/build_defs/repo/http.bzl:229:16):
- /DEFAULT.WORKSPACE.SUFFIX:199:1
INFO: Call stack for the definition of repository 'com_google_protobuf' which is a http_archive (rule definition at /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/bazel_tools/tools/build_defs/repo/http.bzl:229:16):
- /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/com_github_grpc_grpc/bazel/grpc_deps.bzl:125:9
- /home/aditya/Projects/RD/biograkn/WORKSPACE:83:1
INFO: Call stack for the definition of repository 'com-google-protobuf-protobuf-java' which is a jar_artifact (rule definition at /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/graknlabs_grakn_core/dependencies/maven/dependencies.bzl:40:16):
- /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/graknlabs_grakn_core/dependencies/maven/dependencies.bzl:58:5
- /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/graknlabs_grakn_core/dependencies/maven/dependencies.bzl:667:9
- /home/aditya/Projects/RD/biograkn/WORKSPACE:103:1
INFO: Call stack for the definition of repository 'org-apache-lucene-lucene-analyzers-common' which is a jar_artifact (rule definition at /home/aditya/Projects/RD/biograkn/dependencies/maven/dependencies.bzl:40:16):
- /home/aditya/Projects/RD/biograkn/dependencies/maven/dependencies.bzl:58:5
- /home/aditya/Projects/RD/biograkn/dependencies/maven/dependencies.bzl:120:9
- /home/aditya/Projects/RD/biograkn/WORKSPACE:72:1
INFO: Call stack for the definition of repository 'io-netty-netty-all' which is a jar_artifact (rule definition at /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/graknlabs_grakn_core/dependencies/maven/dependencies.bzl:40:16):
- /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/graknlabs_grakn_core/dependencies/maven/dependencies.bzl:58:5
- /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/graknlabs_grakn_core/dependencies/maven/dependencies.bzl:667:9
- /home/aditya/Projects/RD/biograkn/WORKSPACE:103:1
INFO: Call stack for the definition of repository 'edu-stanford-nlp-stanford-corenlp-java-models' which is a jar_artifact (rule definition at /home/aditya/Projects/RD/biograkn/dependencies/maven/dependencies.bzl:40:16):
- /home/aditya/Projects/RD/biograkn/dependencies/maven/dependencies.bzl:58:5
- /home/aditya/Projects/RD/biograkn/dependencies/maven/dependencies.bzl:120:9
- /home/aditya/Projects/RD/biograkn/WORKSPACE:72:1
ERROR: /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/graknlabs_graql/grammar/BUILD:24:1: every rule of type antlr4 implicitly depends upon the target '@antlr4_tool//jar:jar', but this target could not be found because of: no such package '@antlr4_tool//jar': java.io.IOException: Error downloading [http://central.maven.org/maven2/org/antlr/antlr4/4.7.2/antlr4-4.7.2.jar] to /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/antlr4_tool/jar/downloaded.jar: Unknown host: central.maven.org
Documentation for implicit attribute deps of rules of type antlr4:
The dependencies to use. Defaults to the official ANTLR 4 release, but if
you need to use a different version, you can specify the dependencies here.
DEBUG: Rule 'graknlabs_common' indicated that a canonical reproducible form can be obtained by modifying arguments shallow_since = "1572870041 +0000"
DEBUG: Rule 'graknlabs_client_java' indicated that a canonical reproducible form can be obtained by modifying arguments shallow_since = "1570795516 +0000"
ERROR: Analysis of target '//migrator:migrator-bin' failed; build aborted: no such package '@antlr4_tool//jar': java.io.IOException: Error downloading [http://central.maven.org/maven2/org/antlr/antlr4/4.7.2/antlr4-4.7.2.jar] to /home/aditya/.cache/bazel/_bazel_aditya/1271badea2afdf63b6fcb04c93a3b0e2/external/antlr4_tool/jar/downloaded.jar: Unknown host: central.maven.org
INFO: Elapsed time: 7.458s
INFO: 0 processes.
FAILED: Build did NOT complete successfully (4 packages loaded, 0 targets configured)
I wanted to know how to properly build the project
I am getting the following error when ./grakn server start
inside of the unzipped https://github.com/graknlabs/biograkn#download folder:
Unsupported Java version [12] found. Grakn needs Java 1.8 in order to run.
I currently have the newest Java version:
OpenJDK Runtime Environment (build 12.0.1+12)
OpenJDK 64-Bit Server VM (build 12.0.1+12, mixed mode, sharing)
Could you please actualise the application to work with the newest Java version?
Many thanks,
David
Reproducible steps
bazel build @graknlabs_grakn_core//:assemble-mac-zip
cd bazel-bin/external/graknlabs_grakn_core/
unzip grakn-core-all-mac.zip
cd grakn-core-all-mac
./grakn server start
bazel test --test_output=streamed //migrator:assemble-mock-test
Output:
...
10:02:41.830 [grpc-default-worker-ELG-1-2] DEBUG io.grpc.netty.NettyClientHandler - [id: 0x2e64619f, L:/127.0.0.1:54882 - R:/127.0.0.1:48555] OUTBOUND DATA: streamId=873 padding=0 endStream=true length=0 bytes=
10:02:41.831 [grpc-default-worker-ELG-1-2] DEBUG io.grpc.netty.NettyClientHandler - [id: 0x2e64619f, L:/127.0.0.1:54882 - R:/127.0.0.1:48555] INBOUND HEADERS: streamId=873 headers=GrpcHttp2ResponseHeaders[grpc-status: 0] streamDependency=0 weight=16 exclusive=false padding=0 endStream=true
java.nio.file.NoSuchFileException: precisionmedicine/dataset/mock/clinvar/gene_condition_source_id.csv
at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214)
at java.nio.file.Files.newByteChannel(Files.java:361)
at java.nio.file.Files.newByteChannel(Files.java:407)
at java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:384)
...
<Hit>
<Hit_num>100</Hit_num>
<Hit_id>gi|472390071|ref|XP_004414351.1|</Hit_id>
<Hit_def>PREDICTED: double-stranded RNA-specific editase B2 [Odobenus rosmarus divergens]</Hit_def>
<Hit_accession>XP_004414351</Hit_accession>
<Hit_len>745</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>315.079</Hsp_bit-score>
<Hsp_score>806</Hsp_score>
<Hsp_evalue>1.34662e-99</Hsp_evalue>
<Hsp_query-from>70</Hsp_query-from>
<Hsp_query-to>248</Hsp_query-to>
<Hsp_hit-from>567</Hsp_hit-from>
<Hsp_hit-to>745</Hsp_hit-to>
<Hsp_query-frame>0</Hsp_query-frame>
<Hsp_hit-frame>0</Hsp_hit-frame>
<Hsp_identity>150</Hsp_identity>
<Hsp_positive>163</Hsp_positive>
<Hsp_gaps>0</Hsp_gaps>
<Hsp_align-len>179</Hsp_align-len>
<Hsp_qseq>RWNVLGLQGALLSHFVEPVYLQSIVVGSLHHTGHLARVMSHRMEGVGQLPASYRHNRPLLSGVSDAEARQPGKSPPFSMNWVVGSADLEIINATTGRRSCGGPSRLCKHVLSARWARLYGRLSTRTPSPGDTPSMYCEAKLGAHTYQSVKQQLFKAFQKAGLGTWVRKPPEQQQFLLTL</Hsp_qseq>
<Hsp_hseq>RWNVLGLQGALLCHFIEPVYLHSIIVGSLHHTGHLSRVMSLRTEDIGQLPASYRHNQPLLSGVSLAEARQPGKSPHFSVNWVMGNADVEVIDGTTGKRSCGGSSRLCKHVFSARWARLYGKLSTRIPSHGDTPSMYFEAKRGAGTYQSVKQQLFKAFQKAGLGTWVRKPPEQDQFLLTL</Hsp_hseq>
<Hsp_midline>RWNVLGLQGALL HF+EPVYL SI+VGSLHHTGHL+RVMS R E +GQLPASYRHN+PLLSGVS AEARQPGKSP FS+NWV+G+AD+E+I+ TTG+RSCGG SRLCKHV SARWARLYG+LSTR PS GDTPSMY EAK GA TYQSVKQQLFKAFQKAGLGTWVRKPPEQ QFLLTL</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
define
name sub attribute datatype string;
identifier sub attribute datatype string;
gi sub attribute datatype string;
ref sub attribute datatype string;
sequence-identicality sub attribute datatype double;
sequence-positivity sub attribute datatype double;
sequence-gaps sub attribute datatype double;
####################################################################################
#
####################################################################################
sequence sub attribute datatype string,
plays sourced-information,
plays target-sequence,
plays matched-sequence;
protein sub entity,
has identifier,
has sequence,
has gi,
has ref,
plays owned-protein;
species sub entity,
has name,
plays species-owner;
####################################################################################
# Alignment
####################################################################################
alignment sub relationship,
relates aligning-element;
protein-protein-alignment sub alignment,
relates aligning-protein,
relates target-protein as aligning-protein,
relates matched-protein as aligning-protein;
sequence-sequence-alignment sub alignment,
relates aligned-sequence as aligning-element,
relates target-sequence as aligned-sequence,
relates matched-sequence as aligned-sequence,
has sequence-identicality,
has sequence-positivity,
has sequence-gaps;
sequence-alignment-implies-protein-alignment sub rule,
when {
(target-sequence: $ts, matching-sequence: $ms) isa sequence-sequence-alignment;
$tp isa protein, has sequence $ts;
$mp isa protein, has sequence $ms;
} then {
(target-protein: $tp, matching-protein: $mp) isa protein-protein-alignment;
};
####################################################################################
# BLAST Architecture
####################################################################################
# BLAST Itself is an instance
search-tool sub entity,
has name,
plays owner;
search-tool-programme sub entity,
has name,
plays owner,
plays property;
search-algorithm sub entity,
has name,
plays property;
database sub entity,
plays information-source,
has name;
sourcing-of-information sub relationship,
relates information-source,
relates sourced-information;
####################################################################################
# Ownership
####################################################################################
ownership sub relationship,
relates owner,
relates property;
transitive-ownership sub rule,
when {
(owner: $a, property: $b) isa ownership;
(owner: $b, property: $c) isa ownership;
} then {
(owner: $a, property: $c) isa ownership;
};
protein-ownership sub ownership,
relates species-owner as owner,
relates owned-protein as property;
Circle CI pipeline to release BioGrakn distributions for mac and linux.
Please replace every line in curly brackets { like this } with an appropriate description, and remove this line.
{ I am new to Grakn as well as Java. Can you please provide a document which helps novice like us to run the Java code for Text mining in grakn. Or Can the same be implemented in Python }
Request to provide a step by step instructions.
Migrating Core NLP output to Grakn
N/A
Implement script to map output to schema and migrate using the Java client
N/A
The elements in the BioGrakn DN Workspace screenshots look very small.
Steps to create the smallest reproducible scenario:
To see the workbase screenshots without having my nose touch the screen.
My nose touches the screen.
The screenshots need to be taken at a lower resolution.
Architect and implement the release workflows for automating the testing and release of BioGrakn on GCP
Currently, BioGrakn-nightly workflow on circle ci is triggered everyday according to the cron scheduled. Configure it to trigger only once after a commit is made on master.
Architect and implement the release workflows for automating the testing and release of BioGrakn on GitHub
Make sure the migration is compliant to the precision medicine schema
The git history contains large files which slows git operation. This diminishes developers productivity and we should move these big objects into Git LFS.
First, we'll need to identify what those objects are and in which commits they are located.
Second, remove them from the commit (maybe by using https://rtyley.github.io/bfg-repo-cleaner ?) and move them to git LFS.
Attempt to import the minimum number of datasets in order to create a proof of concept for the precision medicine use-case.
"InvalidKBException-A structural validation error has occurred. Please correct the [`1`] errors found.
Rule [entity-extraction-rule] asserts [$e] plays role [extracted-entity] that it can never play
. Please check server logs for the stack trace."
$bazel build //... OR $bazel test //...
ERROR: The Build Event Protocol upload failed: INVALID_ARGUMENT: INVALID_ARGUMENT: Request contains an invalid argument.
INFO: Partial Build Event Protocol results may be available at https://source.cloud.google.com/results/invocations/61a83ee3-9b74-4518-b896-18cee2c2ea60
INFO: Build completed successfully, 333 total actions
Exited with code 38
BioGrakn DN along with its README need will go out of sync with the 1.5 release.
Release and publish the README for BioGrakn DN compatible with Grakn Core 1.5.0
I can't find the Precision Medicine Knowledge Graph project!
Steps to create the smallest reproducible scenario:
To see instructions to run:
I only see instructions for running BioGrakn DN.
The folder ./examples/biograkn-queries/ does not exist, so there are no pictures displayed in the README page here.
It should be fixed asap, because the outgoing paper refers to this repository.
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