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Hadoop streaming map/reduce jobs written in python using the mrjob library.
## Development and Testing
System dependencies on Linux (ubuntu/debian):
sudo apt install -y python3-dev python3-pip python3-wheel libjpeg-dev build-essential
pip3 install --user pipenv
On macOS (using Homebrew):
brew install libjpeg pipenv
You probably need `~/.local/bin` on your `$PATH`.
Fetch all python dependencies with:
pipenv install --dev
Run the tests with:
pipenv run pytest
Check test coverage with:
pytest --cov --cov-report html
# open ./htmlcov/index.html in a browser
## Troubleshooting
If you get pipenv errors like:
AttributeError: '_NamespacePath' object has no attribute 'sort'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /1/tmp/pip-install-h7lb6tqz/proto-google-cloud-datastore-v1/
☤ ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 0/8 — 00:00:03
bnewbold@bnewbold-dev$
bnewbold@bnewbold-dev$ pipenv install --deploy --dev
Installing dependencies from Pipfile.lock (e82980)…
An error occurred while installing proto-google-cloud-logging-v2==0.91.3! Will try again.
An error occurred while installing gapic-google-cloud-error-reporting-v1beta1==0.15.3! Will try again.
An error occurred while installing gapic-google-cloud-datastore-v1==0.15.3! Will try again.
An error occurred while installing proto-google-cloud-datastore-v1==0.90.4! Will try again.
Then something has gone horribly wrong with your pip/pipenv/python setup. Don't
have a good workaround yet.
## Running Python Jobs on Hadoop
The `../please` script automates these steps; you should use that instead.
When running python streaming jobs on the actual hadoop cluster, we need to
bundle along our python dependencies in a virtual env tarball. Building this
tarball can be done like:
export PIPENV_VENV_IN_PROJECT=1
pipenv install --deploy
tar -czf venv-current.tar.gz -C .venv .
### Extraction Task
An example actually connecting to HBase from a local machine, with thrift
running on a devbox and GROBID running on a dedicated machine:
./extraction_cdx_grobid.py \
--hbase-table wbgrp-journal-extract-0-qa \
--hbase-host wbgrp-svc263.us.archive.org \
--grobid-uri http://wbgrp-svc096.us.archive.org:8070 \
tests/files/example.cdx
Running from the cluster (once a ./venv-current.tar.gz tarball exists):
./extraction_cdx_grobid.py \
--hbase-table wbgrp-journal-extract-0-qa \
--hbase-host wbgrp-svc263.us.archive.org \
--grobid-uri http://wbgrp-svc096.us.archive.org:8070 \
-r hadoop \
-c mrjob.conf \
--archive venv-current.tar.gz#venv \
hdfs:///user/bnewbold/journal_crawl_cdx/citeseerx_crawl_2017.cdx
### Backfill Task
An example actually connecting to HBase from a local machine, with thrift
running on a devbox:
./backfill_hbase_from_cdx.py \
--hbase-table wbgrp-journal-extract-0-qa \
--hbase-host wbgrp-svc263.us.archive.org \
tests/files/example.cdx
Running from the cluster (once a ./venv-current.tar.gz tarball exists):
./backfill_hbase_from_cdx.py \
--hbase-host wbgrp-svc263.us.archive.org \
--hbase-table wbgrp-journal-extract-0-qa \
-r hadoop \
-c mrjob.conf \
--archive venv-current.tar.gz#venv \
hdfs:///user/bnewbold/journal_crawl_cdx/citeseerx_crawl_2017.cdx
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