Exercising the MB-System dockerized execution (after a long while)
OS: macOS Ventura 12.3.1 – Intel
$ brew install socatUsing the (unchanged) /mbsystem.sh script in the repo, which still has MBSYSTEM_IMAGE=mbari/mbsystem:5.7.6beta37, as way to test things with one of the previous working images:
| (virtenv) carueda@gizo:/PAM_Analysis/pypam-space/processing_our_data/pypam-based-processing$ pip freeze | |
| WARNING: The directory '/u/carueda/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag. | |
| astroid==2.15.6 | |
| attrs==23.1.0 | |
| audioread==3.0.0 | |
| black==23.7.0 | |
| boto3==1.28.3 | |
| botocore==1.31.8 | |
| build==0.10.0 | |
| CacheControl==0.12.14 |
| (virtenv) carueda@gizo:/PAM_Analysis/pypam-space/processing_our_data/pypam-based-processing$ j setup | |
| pip3 install -r requirements.txt | |
| WARNING: The directory '/u/carueda/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag. | |
| Collecting boto3==1.28.3 | |
| Downloading boto3-1.28.3-py3-none-any.whl (135 kB) | |
| ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 135.7/135.7 kB 14.3 MB/s eta 0:00:00 | |
| Collecting dataclasses-json==0.5.9 | |
| Downloading dataclasses_json-0.5.9-py3-none-any.whl (26 kB) | |
| Collecting python-dateutil==2.8.2 | |
| Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) |
| $ cd/var/www/html/lrauv/nightly_builds/2023-06-26/lrauv-application/ | |
| tethysadmin@tethyshub: lrauv-application$ git fetch origin tag 2023-06-24 --no-tags | |
| tethysadmin@tethyshub: lrauv-application$ make tx-all | |
| make -C Build tx-all | |
| make[1]: Entering directory '/var/www/html/lrauv/nightly_builds/2023-06-26/lrauv-application/Build' | |
| Capturing information from LRAUV sources for TethysL | |
| tethysl parse-lrauv-info --lrauv=.. --dest=tl-lrauv-info |
| $ cargo install ecoz2 | |
| Updating crates.io index | |
| Downloaded ecoz2 v0.3.0 | |
| Downloaded 1 crate (108.4 KB) in 0.37s | |
| Installing ecoz2 v0.3.0 | |
| Downloaded cc v1.0.52 | |
| Downloaded structopt v0.3.14 | |
| Downloaded paw-attributes v1.0.2 | |
| Downloaded serde v1.0.106 | |
| Downloaded ryu v1.0.4 |
| $ ORR_VERSION=3.9.1 | |
| $ BACKEND_VERSION=3.8.3 | |
| $ ./build.sh ${ORR_VERSION} ${BACKEND_VERSION} | |
| building 3.9.1 (orrOntVersion=3.8.3) | |
| building image mmisw/orr:3.9.1 | |
| Sending build context to Docker daemon 459.9MB | |
| Step 1/10 : FROM tomcat:8.5.45-jdk8-openjdk-slim AS builder | |
| ---> fb7332c8aa90 | |
| Step 2/10 : RUN apt update && apt install -y curl gnupg2 && echo "deb https://dl.bintray.com/sbt/debian /" | tee -a /etc/apt/sources.list.d/sbt.list && curl -sL "https://keyserver.ubuntu.com/pks/lookup?op=get&search=0x2EE0EA64E40A89B84B2DF73499E82A75642AC823" | apt-key add && apt update && apt install -y sbt && sbt sbtVersion && curl -sL https://deb.nodesource.com/setup_10.x | bash - && apt install -y nodejs && npm install -g gulp |
| $ ./watchdog.sc update | |
| Getting Github info: ................................................................................................................................................................................................................................. | |
| (225 paths retrieved) | |
| 225 changed ontologies: | |
| http://sweetontology.net/human | |
| - uploading | |
| - registering new revision of iri=http://sweetontology.net/human | |
| => OK (20171105T203734) | |
| http://sweetontology.net/humanAgriculture |
| //////////////////////////////////////////////////////////// | |
| // NOTE: This script and other utilities are now hosted | |
| // at https://github.com/ESIPFed/sweet-tools/ | |
| //////////////////////////////////////////////////////////// | |
| /* | |
| This Scala script is to be run with [Ammonite](http://ammonite.io/#ScalaScripts). | |
| Adjust the initial section of this script below (TTL directory, and desired actions) |
| @base <http://sweetontology.net/reprSciUnits> . | |
| @prefix mrela: <http://sweetontology.net/relaMath/> . | |
| @prefix repr: <http://sweetontology.net/repr/> . | |
| @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . | |
| @prefix owl: <http://www.w3.org/2002/07/owl#> . | |
| @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . | |
| @prefix oper: <http://sweetontology.net/reprMathOperation/> . | |
| @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . | |
| @prefix units: <http://sweetontology.net/reprSciUnits/> . | |
| @prefix screla: <http://sweetontology.net/relaSci/> . |
| [root@d4a49a475dd9 stoqs]# ./manage.py makemigrations stoqs --settings=config.settings.ci --noinput | |
| /usr/lib/python3.6/site-packages/environ/environ.py:416: UserWarning: Engine not recognized from url: {'NAME': '', 'USER': '', 'PASSWORD': '', 'HOST': '', 'PORT': ''} | |
| warnings.warn("Engine not recognized from url: {0}".format(config)) | |
| Migrations for 'stoqs': | |
| stoqs/migrations/0001_initial.py | |
| - Create model Activity | |
| - Create model ActivityParameter | |
| - Create model ActivityParameterHistogram | |
| - Create model ActivityResource | |
| - Create model ActivityType |