Spaces:
Runtime error
Runtime error
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
|
|
| 9 |
|
| 10 |
RUN pip install --no-cache-dir --upgrade -r /code/requirements.txt
|
| 11 |
|
| 12 |
-
ADD https://docs.google.com/uc?export=download&id=17mI5W0qiGiBp_RV1jy3QR3KtN7Ah-1Ha /code/ihinst.db
|
| 13 |
-
|
| 14 |
# Download GBIF occurrences and prepare for use with datasette
|
| 15 |
RUN mkdir /data
|
| 16 |
ADD https://api.gbif.org/v1/occurrence/download/request/${GBIF_DOWNLOAD_ID}.zip /data/gbif-occs.zip
|
| 17 |
-
RUN ls -
|
| 18 |
RUN unzip /data/gbif-occs.zip -d /data
|
| 19 |
-
RUN ls -
|
| 20 |
COPY ./tab2csv.py /code/tab2csv.py
|
| 21 |
|
| 22 |
-
## Setup to parse collector names using Bionomia utils (reqs Ruby)
|
| 23 |
-
## Install ruby
|
| 24 |
-
#RUN \
|
| 25 |
-
# apt-get update && \
|
| 26 |
-
# apt-get install -y ruby
|
| 27 |
-
#RUN gem install dwc_agent
|
| 28 |
-
|
| 29 |
-
#COPY ./extractcollectorname.py /code/extractcollectorname.py
|
| 30 |
RUN python tab2csv.py --createcols /data/${GBIF_DOWNLOAD_ID}.csv /data/gbifocc.csv
|
| 31 |
-
#RUN python extractcollectorname.py /data/gbifocc-temp.csv /data/gbifocc.csv
|
| 32 |
RUN csvs-to-sqlite /data/gbifocc.csv /code/gbifocc.db
|
| 33 |
RUN ls -l /code
|
| 34 |
RUN sqlite-utils tables /code/gbifocc.db --counts
|
| 35 |
RUN sqlite-utils enable-fts /code/gbifocc.db gbifocc collectorNameAndNumber
|
| 36 |
|
| 37 |
-
#RUN sqlite-utils tables /code/ihinst.db --counts
|
| 38 |
RUN chmod 755 /code/gbifocc.db
|
| 39 |
|
| 40 |
COPY ./metadata.json /code/metadata.json
|
|
|
|
| 9 |
|
| 10 |
RUN pip install --no-cache-dir --upgrade -r /code/requirements.txt
|
| 11 |
|
|
|
|
|
|
|
| 12 |
# Download GBIF occurrences and prepare for use with datasette
|
| 13 |
RUN mkdir /data
|
| 14 |
ADD https://api.gbif.org/v1/occurrence/download/request/${GBIF_DOWNLOAD_ID}.zip /data/gbif-occs.zip
|
| 15 |
+
RUN ls -lh /data
|
| 16 |
RUN unzip /data/gbif-occs.zip -d /data
|
| 17 |
+
RUN ls -lh /data
|
| 18 |
COPY ./tab2csv.py /code/tab2csv.py
|
| 19 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 20 |
RUN python tab2csv.py --createcols /data/${GBIF_DOWNLOAD_ID}.csv /data/gbifocc.csv
|
|
|
|
| 21 |
RUN csvs-to-sqlite /data/gbifocc.csv /code/gbifocc.db
|
| 22 |
RUN ls -l /code
|
| 23 |
RUN sqlite-utils tables /code/gbifocc.db --counts
|
| 24 |
RUN sqlite-utils enable-fts /code/gbifocc.db gbifocc collectorNameAndNumber
|
| 25 |
|
|
|
|
| 26 |
RUN chmod 755 /code/gbifocc.db
|
| 27 |
|
| 28 |
COPY ./metadata.json /code/metadata.json
|