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Nicky Nicolson
commited on
Commit
•
c3dab06
1
Parent(s):
e4bd801
Removed unused sections
Browse files- Dockerfile +2 -14
Dockerfile
CHANGED
@@ -9,32 +9,20 @@ COPY ./requirements.txt /code/requirements.txt
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RUN pip install --no-cache-dir --upgrade -r /code/requirements.txt
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ADD https://docs.google.com/uc?export=download&id=17mI5W0qiGiBp_RV1jy3QR3KtN7Ah-1Ha /code/ihinst.db
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# Download GBIF occurrences and prepare for use with datasette
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RUN mkdir /data
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ADD https://api.gbif.org/v1/occurrence/download/request/${GBIF_DOWNLOAD_ID}.zip /data/gbif-occs.zip
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RUN ls -
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RUN unzip /data/gbif-occs.zip -d /data
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RUN ls -
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COPY ./tab2csv.py /code/tab2csv.py
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## Setup to parse collector names using Bionomia utils (reqs Ruby)
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## Install ruby
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#RUN \
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# apt-get update && \
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# apt-get install -y ruby
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#RUN gem install dwc_agent
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#COPY ./extractcollectorname.py /code/extractcollectorname.py
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RUN python tab2csv.py --createcols /data/${GBIF_DOWNLOAD_ID}.csv /data/gbifocc.csv
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#RUN python extractcollectorname.py /data/gbifocc-temp.csv /data/gbifocc.csv
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RUN csvs-to-sqlite /data/gbifocc.csv /code/gbifocc.db
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RUN ls -l /code
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RUN sqlite-utils tables /code/gbifocc.db --counts
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RUN sqlite-utils enable-fts /code/gbifocc.db gbifocc collectorNameAndNumber
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#RUN sqlite-utils tables /code/ihinst.db --counts
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RUN chmod 755 /code/gbifocc.db
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COPY ./metadata.json /code/metadata.json
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RUN pip install --no-cache-dir --upgrade -r /code/requirements.txt
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# Download GBIF occurrences and prepare for use with datasette
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RUN mkdir /data
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ADD https://api.gbif.org/v1/occurrence/download/request/${GBIF_DOWNLOAD_ID}.zip /data/gbif-occs.zip
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RUN ls -lh /data
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RUN unzip /data/gbif-occs.zip -d /data
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RUN ls -lh /data
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COPY ./tab2csv.py /code/tab2csv.py
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RUN python tab2csv.py --createcols /data/${GBIF_DOWNLOAD_ID}.csv /data/gbifocc.csv
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RUN csvs-to-sqlite /data/gbifocc.csv /code/gbifocc.db
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RUN ls -l /code
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RUN sqlite-utils tables /code/gbifocc.db --counts
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RUN sqlite-utils enable-fts /code/gbifocc.db gbifocc collectorNameAndNumber
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RUN chmod 755 /code/gbifocc.db
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COPY ./metadata.json /code/metadata.json
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