Opened 19 months ago
Last modified 4 months ago
#2330 new enhancement
opendatacube jupyter notebooks
| Reported by: | darkblueb | Owned by: | |
|---|---|---|---|
| Priority: | major | Milestone: | OSGeoLive15.0 |
| Component: | OSGeoLive | Keywords: | jupyter, opendatacube |
| Cc: | osgeolive@… |
Description
Change history (13)
comment:1 by , 18 months ago
| Milestone: | OSGeoLive14.0 → OSGeoLive15.0 |
|---|
comment:3 by , 5 months ago
Is it possible to make a dot-deb package of py3 module -LINK-
lark_parser-0.12.0-py2.py3-none-any.whl
ref
comment:4 by , 4 months ago
attempting a setup with datacube installed
http://ppa.launchpad.net/osgeolive/nightly/ubuntu/pool/main/d/datacube/
when I make a call on the command line to datacube tool, I get
rasterio.errors.CRSError: The EPSG code is unknown. PROJ: proj_create_from_database: Cannot find proj.db
inline in ipython3, I can import individually rasterio, datacube, pyproj with no errors
I manually set the bash shell environment variable
$ DATACUBE_CONFIG_PATH=~/.config/datacube/datacube.conf datacube product add landsat-clip.yaml
PROJ Debug
https://proj.org/usage/environmentvars.html#envvar-PROJ_LIB
those files are in /usr/share/proj/
the error looks a lot like this https://rasterio.readthedocs.io/en/latest/faq.html#why-can-t-rasterio-find-proj-db-rasterio-versions-1-2-0
what is odd is that rio and inline rasterio work fine
more details here:
comment:5 by , 4 months ago
lark-parser 0.12.0 is an older version of lark 1.1.1 that is available upstream on Ubuntu.
OpenDataCube needs to update to the latest version at some point, until then I have prepared a deb package of the old version.
comment:6 by , 4 months ago
| Cc: | added |
|---|---|
| Priority: | normal → major |
comment:7 by , 4 months ago
ol15 build 167s
user@osgeolive:~$ ./do_setup_datacube.sh CREATE EXTENSION CREATE EXTENSION 2022-08-04 04:52:11,495 8363 datacube INFO Running datacube command: /usr/bin/datacube -v system init Initialising database... 2022-08-04 04:52:11,991 8363 datacube.drivers.postgres._core INFO Ensuring user roles. 2022-08-04 04:52:11,997 8363 datacube.drivers.postgres._core INFO Creating schema. 2022-08-04 04:52:11,998 8363 datacube.drivers.postgres._core INFO Creating tables. 2022-08-04 04:52:12,028 8363 datacube.drivers.postgres._core INFO Creating triggers. 2022-08-04 04:52:12,032 8363 datacube.drivers.postgres._core INFO Creating added column. 2022-08-04 04:52:12,033 8363 datacube.drivers.postgres._core INFO Adding role grants. 2022-08-04 04:52:12,035 8363 datacube.index.postgres.index INFO Adding default metadata types. Created. Checking indexes/views. 2022-08-04 04:52:12,217 8363 datacube.drivers.postgres._api INFO Checking dynamic views/indexes. (rebuild views=True, indexes=False) Done. Adding "clip_landsat" (this might take a while) DONE
user@osgeolive:~$ cat do_setup_datacube.sh
#!/bin/sh
set -e
createdb datacube
psql datacube -c 'create extension postgis'
psql datacube -c 'create extension hstore'
# reset
# rm -rf .config/datacube
# psql -c 'drop database datacube'
##-------------------------------------------------
USER=user
DCONF=/home/${USER}/.config/datacube
mkdir -p ${DCONF}
export DATACUBE_CONFIG_PATH=${DCONF}/datacube.conf
#----------------------------------------------
cat << EOF > ${DCONF}/datacube.conf
[datacube]
db_database: datacube
# A blank host will use a local socket. Specify a hostname (such as localhost) to use TCP.
db_hostname:
# Credentials are optional: you might have other Postgres authentication configured.
# The default username otherwise is the current user id.
db_username: user
db_password: user
EOF
##---------------------------------------------
cat << EOF > ${DCONF}/landsat-clip.yml
name: clip_landsat
description: example ortho imagery
metadata_type: eo3
license: CC-BY-4.0
metadata:
product:
name: clip_landsat
storage:
crs: EPSG:32619
resolution:
longitude: 28.497418829384827
latitude: -28.503958771796388
measurements:
- name: imagery
dtype: uint8
nodata: -32768.0
units: "metre"
EOF
##-------------------------------------------------
datacube -v system init
datacube product add ${DCONF}/landsat-clip.yml
comment:8 by , 4 months ago
Excellent progress Brian!
Can you please draft an install_opendatacube.sh with the above and make a pull request in the labs folder?
comment:9 by , 4 months ago
ol15 build 179
user@osgeolive:~$ pip3 install --upgrade-strategy=only-if-needed --user odc-stac
Collecting odc-stac
Downloading odc_stac-0.3.1-py3-none-any.whl (53 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.1/53.1 KB 400.8 kB/s eta 0:00:00
Requirement already satisfied: rasterio in /usr/lib/python3/dist-packages (from odc-stac) (1.3.0)
Requirement already satisfied: pandas in /usr/lib/python3/dist-packages (from odc-stac) (1.3.5)
Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (from odc-stac) (1.21.5)
Requirement already satisfied: affine in /usr/lib/python3/dist-packages (from odc-stac) (2.3.0)
Collecting xarray>=0.19
Downloading xarray-2022.6.0-py3-none-any.whl (927 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 927.2/927.2 KB 393.8 kB/s eta 0:00:00
Collecting odc-geo>=0.1.3
Downloading odc_geo-0.2.1-py3-none-any.whl (102 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 102.8/102.8 KB 398.9 kB/s eta 0:00:00
Collecting pystac<2,>=1.0.0
Downloading pystac-1.6.1-py3-none-any.whl (146 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 146.0/146.0 KB 408.3 kB/s eta 0:00:00
Requirement already satisfied: toolz in /usr/lib/python3/dist-packages (from odc-stac) (0.11.2)
Requirement already satisfied: dask[array] in /usr/lib/python3/dist-packages (from odc-stac) (2022.1.0+dfsg)
Requirement already satisfied: shapely in /usr/lib/python3/dist-packages (from odc-geo>=0.1.3->odc-stac) (1.8.0)
Requirement already satisfied: pyproj in /usr/lib/python3/dist-packages (from odc-geo>=0.1.3->odc-stac) (3.3.0)
Requirement already satisfied: cachetools in /usr/lib/python3/dist-packages (from odc-geo>=0.1.3->odc-stac) (5.0.0)
Requirement already satisfied: python-dateutil>=2.7.0 in /usr/lib/python3/dist-packages (from pystac<2,>=1.0.0->odc-stac) (2.8.1)
Requirement already satisfied: packaging>=20.0 in /usr/lib/python3/dist-packages (from xarray>=0.19->odc-stac) (21.3)
Installing collected packages: xarray, pystac, odc-geo, odc-stac
Successfully installed odc-geo-0.2.1 odc-stac-0.3.1 pystac-1.6.1 xarray-2022.6.0
comment:10 by , 4 months ago
Thanks for the feedback, it won't be very hard to create packages for odc_stac and odc_geo. On my todo.
Ticket retargeted after milestone closed