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RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
MIT License
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`setup-kg2-build.sh` Fails to Install `pip` #327

Closed ecwood closed 11 months ago

ecwood commented 11 months ago

While working on #312, aws configure was not triggered by setup-kg2-build.sh.

ubuntu@ip-172-31-62-73:~/RTX-KG2$ bash -x setup-kg2-build.sh 
+ set -o nounset -o pipefail -o errexit
+ [[ '' == \-\-\h\e\l\p ]]
+ [[ '' == \-\h ]]
+ build_flag=
++ dirname setup-kg2-build.sh
+ config_dir=.
+ [[ '' == \c\i ]]
+ source ./master-config.shinc
++ '[' -z ']'
++ test_suffix=
++ BUILD_DIR=/home/ubuntu/kg2-build
++ VENV_DIR=/home/ubuntu/kg2-venv
++ CODE_DIR=/home/ubuntu/kg2-code
++ umls_dir=/home/ubuntu/kg2-build/umls
++ umls_dest_dir=/home/ubuntu/kg2-build/umls/META
++ s3_region=us-west-2
++ s3_bucket=rtx-kg2
++ s3_bucket_public=rtx-kg2-public
++ s3_bucket_versioned=rtx-kg2-versioned
++ s3_cp_cmd='aws s3 cp --no-progress --region us-west-2'
++ mysql_conf=/home/ubuntu/kg2-build/mysql-config.conf
++ curl_get='curl -s -L -f'
++ curies_to_categories_file=/home/ubuntu/kg2-code/curies-to-categories.yaml
++ curies_to_urls_file=/home/ubuntu/kg2-code/curies-to-urls-map.yaml
++ predicate_mapping_file=/home/ubuntu/kg2-code/predicate-remap.yaml
++ infores_mapping_file=/home/ubuntu/kg2-code/kg2-provided-by-curie-to-infores-curie.yaml
++ ont_load_inventory_file=/home/ubuntu/kg2-code/ont-load-inventory.yaml
++ umls2rdf_config_master=/home/ubuntu/kg2-code/umls2rdf-umls.conf
++ rtx_config_file=RTXConfiguration-config.json
++ biolink_model_version=3.5.1
+ [[ '' != \t\e\s\t ]]
+ test_str=
+ mysql_user=ubuntu
+ mysql_password=1337
+ [[ '' != \c\i ]]
+ psql_user=ubuntu
+ mkdir -p /home/ubuntu/kg2-build
+ setup_log_file=/home/ubuntu/kg2-build/setup-kg2-build.log
+ touch /home/ubuntu/kg2-build/setup-kg2-build.log
+ [[ '' == \c\i ]]
ecwood commented 11 months ago

This was the actual line that failed:

++ curl -s https://bootstrap.pypa.io/get-pip.py -o /tmp/get-pip.py
ecwood commented 11 months ago

Here's the error:

ubuntu@ip-172-31-62-73:~/kg2-code$ curl https://bootstrap.pypa.io/get-pip.py
curl: (60) SSL: no alternative certificate subject name matches target host name 'bootstrap.pypa.io'
More details here: https://curl.se/docs/sslcerts.html

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
ecwood commented 11 months ago

This appears to be a known issue: https://github.com/pypa/get-pip/issues/178

ecwood commented 11 months ago

Now, the script fails here:

curl -s -L -f -H 'Accept: application/zip' https://github.com/RTXteam/robot/releases/download/v1.3.0/robot.jar
ecwood commented 11 months ago

Honestly, I think the problem is curl on this instance, which seems to be marking every webpage as not having a certificate:

ubuntu@ip-172-31-62-73:~/RTX-KG2$ curl -L -f https://raw.githubusercontent.com/biolink/biolink-model/master/semmed-exclude-list.yaml
curl: (60) SSL: no alternative certificate subject name matches target host name 'raw.githubusercontent.com'
More details here: https://curl.se/docs/sslcerts.html

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
ecwood commented 11 months ago

This is surprising because kg2erica.rtx.ai and buildkg2.rtx.ai (where the problem is) both have the same version of curl:

kg2erica.rtx.ai:

ubuntu@ip-172-31-59-112:~$ curl --version
curl 7.81.0 (x86_64-pc-linux-gnu) libcurl/7.81.0 OpenSSL/3.0.2 zlib/1.2.11 brotli/1.0.9 zstd/1.4.8 libidn2/2.3.2 libpsl/0.21.0 (+libidn2/2.3.2) libssh/0.9.6/openssl/zlib nghttp2/1.43.0 librtmp/2.3 OpenLDAP/2.5.14
Release-Date: 2022-01-05
Protocols: dict file ftp ftps gopher gophers http https imap imaps ldap ldaps mqtt pop3 pop3s rtmp rtsp scp sftp smb smbs smtp smtps telnet tftp 
Features: alt-svc AsynchDNS brotli GSS-API HSTS HTTP2 HTTPS-proxy IDN IPv6 Kerberos Largefile libz NTLM NTLM_WB PSL SPNEGO SSL TLS-SRP UnixSockets zstd

buildkg2.rtx.ai:

ubuntu@ip-172-31-62-73:~/RTX-KG2$ curl --version
curl 7.81.0 (x86_64-pc-linux-gnu) libcurl/7.81.0 OpenSSL/3.0.2 zlib/1.2.11 brotli/1.0.9 zstd/1.4.8 libidn2/2.3.2 libpsl/0.21.0 (+libidn2/2.3.2) libssh/0.9.6/openssl/zlib nghttp2/1.43.0 librtmp/2.3 OpenLDAP/2.5.14
Release-Date: 2022-01-05
Protocols: dict file ftp ftps gopher gophers http https imap imaps ldap ldaps mqtt pop3 pop3s rtmp rtsp scp sftp smb smbs smtp smtps telnet tftp 
Features: alt-svc AsynchDNS brotli GSS-API HSTS HTTP2 HTTPS-proxy IDN IPv6 Kerberos Largefile libz NTLM NTLM_WB PSL SPNEGO SSL TLS-SRP UnixSockets zstd
ecwood commented 11 months ago

This completed successfully in the KG2.8.4pre build so I am going to close out this issue.