theisuru-patch-13

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Workflow

The following workflow defines all tasks necessary to upload, preprocess, share, and map a new data dictionary.

Upload cohort data
Open Google Sheet
Run automated mapping for new data dictionary
Share Google Sheet with submitter
Prepare data dictionary for build
Run automated validation
Build data dictionary
View results
Add data dictionary to Version Control
Prepare git commit (click on Commit in Version menu)
Push changes to GitHub (click on Push in Version menu), and make pull request.
Delete Google sheet (Caution, cannot be undone)

IHCC Data Admin Tasks

Console

Action create-docker-image-and-container started at 2022-11-30T22:10:13.546Z (2022-11-30T22:10:13.546Z)

Success

$ docker build --tag ihcc-cohorts-data-harmonization-theisuru-patch-13:latest . > /home/centos/DROID/projects/IHCC-cohorts-data-harmonization/temp/theisuru-patch-13/console.txt 2>&1 && docker create --interactive --tty --name IHCC-cohorts-data-harmonization-theisuru-patch-13 --volume /home/centos/DROID/projects/IHCC-cohorts-data-harmonization/workspace/theisuru-patch-13/:/workspace/ --volume /home/centos/DROID/projects/IHCC-cohorts-data-harmonization/temp/theisuru-patch-13/:/tmp/droid/ ihcc-cohorts-data-harmonization-theisuru-patch-13 sh >> /home/centos/DROID/projects/IHCC-cohorts-data-harmonization/temp/theisuru-patch-13/console.txt 2>&1 && docker start IHCC-cohorts-data-harmonization-theisuru-patch-13 >> /home/centos/DROID/projects/IHCC-cohorts-data-harmonization/temp/theisuru-patch-13/console.txt 2>&1

Sending build context to Docker daemon  26.97MB

Step 1/4 : FROM obolibrary/odkfull
 ---> 742aa3c8a1a2
Step 2/4 : COPY requirements.txt /tools/ihcc-requirements.txt
 ---> 11e5ba4b1136
Step 3/4 : RUN pip install -r /tools/ihcc-requirements.txt
 ---> Running in f103b5e583c0
Requirement already satisfied: jinja2 in /usr/local/lib/python3.8/dist-packages (from -r /tools/ihcc-requirements.txt (line 1)) (3.0.1)
Requirement already satisfied: pandas in /usr/local/lib/python3.8/dist-packages (from -r /tools/ihcc-requirements.txt (line 2)) (1.2.4)
Requirement already satisfied: rdflib in /usr/local/lib/python3.8/dist-packages (from -r /tools/ihcc-requirements.txt (line 3)) (5.0.0)
Collecting xlsx2csv
  Downloading xlsx2csv-0.8.0-py3-none-any.whl (13 kB)
Requirement already satisfied: requests in /usr/lib/python3/dist-packages (from -r /tools/ihcc-requirements.txt (line 5)) (2.22.0)
Requirement already satisfied: pyyaml in /usr/local/lib/python3.8/dist-packages (from -r /tools/ihcc-requirements.txt (line 6)) (5.4.1)
Collecting scikit-learn
  Downloading scikit_learn-1.1.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (31.2 MB)
Requirement already satisfied: numpy in /usr/local/lib/python3.8/dist-packages (from -r /tools/ihcc-requirements.txt (line 8)) (1.20.3)
Requirement already satisfied: jsonschema in /usr/local/lib/python3.8/dist-packages (from -r /tools/ihcc-requirements.txt (line 9)) (3.2.0)
Collecting openpyxl
  Downloading openpyxl-3.0.10-py2.py3-none-any.whl (242 kB)
Collecting ontodev-cogs==0.3.3
  Downloading ontodev_cogs-0.3.3-py3-none-any.whl (47 kB)
Collecting ontodev-gizmos==0.3.1
  Downloading ontodev_gizmos-0.3.1-py3-none-any.whl (42 kB)
Collecting urlp
  Downloading urlp-0.0.3-py2.py3-none-any.whl (3.3 kB)
Requirement already satisfied: gspread-formatting in /usr/local/lib/python3.8/dist-packages (from ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (1.0.0)
Requirement already satisfied: daff in /usr/local/lib/python3.8/dist-packages (from ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (1.3.46)
Requirement already satisfied: termcolor in /usr/local/lib/python3.8/dist-packages (from ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (1.1.0)
Requirement already satisfied: gspread in /usr/local/lib/python3.8/dist-packages (from ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (3.7.0)
Requirement already satisfied: tabulate in /usr/local/lib/python3.8/dist-packages (from ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (0.8.9)
Requirement already satisfied: google-api-python-client in /usr/local/lib/python3.8/dist-packages (from ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (2.8.0)
Requirement already satisfied: google in /usr/local/lib/python3.8/dist-packages (from ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (3.0.0)
Requirement already satisfied: rdflib-jsonld in /usr/local/lib/python3.8/dist-packages (from ontodev-gizmos==0.3.1->-r /tools/ihcc-requirements.txt (line 12)) (0.5.0)
Collecting SQLAlchemy
  Downloading SQLAlchemy-1.4.44-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.6 MB)
Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.8/dist-packages (from jinja2->-r /tools/ihcc-requirements.txt (line 1)) (2.0.1)
Requirement already satisfied: pytz>=2017.3 in /usr/local/lib/python3.8/dist-packages (from pandas->-r /tools/ihcc-requirements.txt (line 2)) (2021.1)
Requirement already satisfied: python-dateutil>=2.7.3 in /usr/local/lib/python3.8/dist-packages (from pandas->-r /tools/ihcc-requirements.txt (line 2)) (2.8.1)
Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.7.3->pandas->-r /tools/ihcc-requirements.txt (line 2)) (1.14.0)
Requirement already satisfied: isodate in /usr/local/lib/python3.8/dist-packages (from rdflib->-r /tools/ihcc-requirements.txt (line 3)) (0.6.0)
Requirement already satisfied: pyparsing in /usr/local/lib/python3.8/dist-packages (from rdflib->-r /tools/ihcc-requirements.txt (line 3)) (2.4.7)
Collecting threadpoolctl>=2.0.0
  Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Collecting joblib>=1.0.0
  Downloading joblib-1.2.0-py3-none-any.whl (297 kB)
Requirement already satisfied: scipy>=1.3.2 in /usr/local/lib/python3.8/dist-packages (from scikit-learn->-r /tools/ihcc-requirements.txt (line 7)) (1.6.3)
Requirement already satisfied: attrs>=17.4.0 in /usr/local/lib/python3.8/dist-packages (from jsonschema->-r /tools/ihcc-requirements.txt (line 9)) (21.2.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /usr/local/lib/python3.8/dist-packages (from jsonschema->-r /tools/ihcc-requirements.txt (line 9)) (0.17.3)
Requirement already satisfied: setuptools in /usr/local/lib/python3.8/dist-packages (from jsonschema->-r /tools/ihcc-requirements.txt (line 9)) (57.0.0)
Collecting et-xmlfile
  Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)
Collecting tldextract
  Downloading tldextract-3.4.0-py3-none-any.whl (93 kB)
Requirement already satisfied: beautifulsoup4 in /usr/local/lib/python3.8/dist-packages (from google->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (4.9.3)
Requirement already satisfied: soupsieve>1.2 in /usr/local/lib/python3.8/dist-packages (from beautifulsoup4->google->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (2.2.1)
Requirement already satisfied: httplib2<1dev,>=0.15.0 in /usr/local/lib/python3.8/dist-packages (from google-api-python-client->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (0.19.1)
Requirement already satisfied: google-auth<2dev,>=1.16.0 in /usr/local/lib/python3.8/dist-packages (from google-api-python-client->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (1.31.0)
Requirement already satisfied: uritemplate<4dev,>=3.0.0 in /usr/local/lib/python3.8/dist-packages (from google-api-python-client->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (3.0.1)
Requirement already satisfied: google-api-core<2dev,>=1.21.0 in /usr/local/lib/python3.8/dist-packages (from google-api-python-client->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (1.30.0)
Requirement already satisfied: google-auth-httplib2>=0.1.0 in /usr/local/lib/python3.8/dist-packages (from google-api-python-client->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (0.1.0)
Requirement already satisfied: googleapis-common-protos<2.0dev,>=1.6.0 in /usr/local/lib/python3.8/dist-packages (from google-api-core<2dev,>=1.21.0->google-api-python-client->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (1.53.0)
Requirement already satisfied: packaging>=14.3 in /usr/local/lib/python3.8/dist-packages (from google-api-core<2dev,>=1.21.0->google-api-python-client->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (20.9)
Requirement already satisfied: protobuf>=3.12.0 in /usr/local/lib/python3.8/dist-packages (from google-api-core<2dev,>=1.21.0->google-api-python-client->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (3.17.3)
Requirement already satisfied: pyasn1-modules>=0.2.1 in /usr/local/lib/python3.8/dist-packages (from google-auth<2dev,>=1.16.0->google-api-python-client->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (0.2.8)
Requirement already satisfied: cachetools<5.0,>=2.0.0 in /usr/local/lib/python3.8/dist-packages (from google-auth<2dev,>=1.16.0->google-api-python-client->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (4.2.2)
Requirement already satisfied: rsa<5,>=3.1.4 in /usr/local/lib/python3.8/dist-packages (from google-auth<2dev,>=1.16.0->google-api-python-client->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (4.7.2)
Requirement already satisfied: pyasn1<0.5.0,>=0.4.6 in /usr/local/lib/python3.8/dist-packages (from pyasn1-modules>=0.2.1->google-auth<2dev,>=1.16.0->google-api-python-client->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (0.4.8)
Requirement already satisfied: google-auth-oauthlib>=0.4.1 in /usr/local/lib/python3.8/dist-packages (from gspread->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (0.4.4)
Requirement already satisfied: requests-oauthlib>=0.7.0 in /usr/local/lib/python3.8/dist-packages (from google-auth-oauthlib>=0.4.1->gspread->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (1.3.0)
Requirement already satisfied: oauthlib>=3.0.0 in /usr/local/lib/python3.8/dist-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib>=0.4.1->gspread->ontodev-cogs==0.3.3->-r /tools/ihcc-requirements.txt (line 11)) (3.1.1)
Collecting greenlet!=0.4.17
  Downloading greenlet-2.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (544 kB)
Collecting requests-file>=1.4
  Downloading requests_file-1.5.1-py2.py3-none-any.whl (3.7 kB)
Collecting filelock>=3.0.8
  Downloading filelock-3.8.0-py3-none-any.whl (10 kB)
Requirement already satisfied: idna in /usr/lib/python3/dist-packages (from tldextract->urlp->-r /tools/ihcc-requirements.txt (line 13)) (2.8)
Installing collected packages: requests-file, greenlet, filelock, tldextract, threadpoolctl, SQLAlchemy, joblib, et-xmlfile, xlsx2csv, urlp, scikit-learn, openpyxl, ontodev-gizmos, ontodev-cogs
  Attempting uninstall: ontodev-cogs
    Found existing installation: ontodev-cogs 0.3.1
    Uninstalling ontodev-cogs-0.3.1:
      Successfully uninstalled ontodev-cogs-0.3.1
Successfully installed SQLAlchemy-1.4.44 et-xmlfile-1.1.0 filelock-3.8.0 greenlet-2.0.1 joblib-1.2.0 ontodev-cogs-0.3.3 ontodev-gizmos-0.3.1 openpyxl-3.0.10 requests-file-1.5.1 scikit-learn-1.1.3 threadpoolctl-3.1.0 tldextract-3.4.0 urlp-0.0.3 xlsx2csv-0.8.0
WARNING: Running pip as root will break packages and permissions. You should install packages reliably by using venv: https://pip.pypa.io/warnings/venv
WARNING: You are using pip version 21.1.2; however, version 22.3.1 is available.
You should consider upgrading via the '/usr/bin/python3 -m pip install --upgrade pip' command.
Removing intermediate container f103b5e583c0
 ---> 2ec27f7e50f1
Step 4/4 : RUN apt-get install aha dos2unix sqlite3
 ---> Running in 72a09720d370
Reading package lists...
Building dependency tree...
Reading state information...
aha is already the newest version (0.5-1).
dos2unix is already the newest version (7.4.0-2).
sqlite3 is already the newest version (3.31.1-4ubuntu0.2).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Removing intermediate container 72a09720d370
 ---> 46f0167211bc
Successfully built 46f0167211bc
Successfully tagged ihcc-cohorts-data-harmonization-theisuru-patch-13:latest
760bd9b1f581cdb8c7dec05b2c0d38bdae313a16e27a1ff473ca754cc0a66eb9
IHCC-cohorts-data-harmonization-theisuru-patch-13

Success