Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Switch *_postgres2es.py from python3 to pypy3 for speed #139

Draft
wants to merge 1 commit into
base: master
Choose a base branch
from
Draft

Switch *_postgres2es.py from python3 to pypy3 for speed #139

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 1 addition & 3 deletions python/Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM ghcr.io/opendrr/python-env
FROM ghcr.io/anthonyfok/python-env:debian-sid-20201012

LABEL maintainer="Joost van Ulden <[email protected]>"

Expand All @@ -8,8 +8,6 @@ COPY . .

#RUN chmod +x docker-entrypoint.sh && chmod +x add_data.sh
RUN chmod +x add_data.sh && \
apt-get update && \
apt-get install -y dos2unix eatmydata git git-lfs jq time && \
dos2unix add_data.sh
#ENTRYPOINT ["/usr/src/app/docker-entrypoint.sh"]
CMD ./add_data.sh
44 changes: 22 additions & 22 deletions python/add_data.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -790,10 +790,10 @@ export_to_elasticsearch() {
# shellcheck disable=SC2154
if [ "$loadPsraModels" = true ]; then
LOG "Creating PSRA indices in Elasticsearch"
RUN python3 psra_postgres2es.py
RUN python3 hmaps_postgres2es.py
RUN python3 uhs_postgres2es.py
RUN python3 srcLoss_postgres2es.py
RUN pypy3 psra_postgres2es.py
RUN pypy3 hmaps_postgres2es.py
RUN pypy3 uhs_postgres2es.py
RUN pypy3 srcLoss_postgres2es.py

LOG "Creating PSRA Kibana Index Patterns"
RUN curl -X POST -H "Content-Type: application/json" "${KIBANA_ENDPOINT}/s/gsc-cgc/api/saved_objects/index-pattern/opendrr_psra_indicators_s" -H "kbn-xsrf: true" -d '{ "attributes": { "title":"opendrr_psra_indicators_s"}}'
Expand All @@ -808,8 +808,8 @@ export_to_elasticsearch() {
if [[ "$loadDsraScenario" = true ]]; then
for eqscenario in ${EQSCENARIO_LIST[*]}; do
LOG "Creating Elasticsearch indexes for DSRA"
RUN python3 dsra_postgres2es.py --eqScenario="$eqscenario" --dbview="all_indicators" --idField="building"
RUN python3 dsra_postgres2es.py --eqScenario="$eqscenario" --dbview="all_indicators" --idField="sauid"
RUN pypy3 dsra_postgres2es.py --eqScenario="$eqscenario" --dbview="all_indicators" --idField="building"
RUN pypy3 dsra_postgres2es.py --eqScenario="$eqscenario" --dbview="all_indicators" --idField="sauid"

# LOG "Creating DSRA Kibana Index Patterns"
# Need to develop saved object workflow for automated index patern generation
Expand All @@ -824,7 +824,7 @@ done
# if [[ "$loadHazardThreat" = true ]]; then
# # All Indicators
# LOG "Creating Elasticsearch indexes for Hazard Threat"
# RUN python3 hazardThreat_postgres2es.py --type="all_indicators" --aggregation="sauid" --geometry=geom_poly --idField="Sauid"
# RUN pypy3 hazardThreat_postgres2es.py --type="all_indicators" --aggregation="sauid" --geometry=geom_poly --idField="Sauid"

# LOG "Creating Hazard Threat Kibana Index Patterns"
# RUN curl -X POST -H "Content-Type: application/json" "${KIBANA_ENDPOINT}/s/gsc-cgc/api/saved_objects/index-pattern/opendrr_hazard_threat_all_indicators_s" -H "kbn-xsrf: true" -d '{ "attributes": { "title":"opendrr_hazard_threat_all_indicators_s"}}'
Expand All @@ -834,8 +834,8 @@ done
# shellcheck disable=SC2154
if [[ $loadPhysicalExposure = true ]]; then
LOG "Creating Elasticsearch indexes for Physical Exposure"
RUN python3 exposure_postgres2es.py --aggregation="building" --geometry=geom_point
RUN python3 exposure_postgres2es.py --aggregation="sauid" --geometry=geom_poly
RUN pypy3 exposure_postgres2es.py --aggregation="building" --geometry=geom_point
RUN pypy3 exposure_postgres2es.py --aggregation="sauid" --geometry=geom_poly

LOG "Creating Exposure Kibana Index Patterns"
RUN curl -X POST -H "Content-Type: application/json" "${KIBANA_ENDPOINT}/s/gsc-cgc/api/saved_objects/index-pattern/opendrr_nhsl_physical_exposure_all_indicators_s" -H "kbn-xsrf: true" -d '{ "attributes": { "title":"opendrr_nhsl_physical_exposure_all_indicators_s"}}'
Expand All @@ -847,7 +847,7 @@ done
# 2021/09/21 DR - Keeping Hazard Threah and Risk Dynamics out of ES for the time being
# if [[ $loadRiskDynamics = true ]]; then
# LOG "Creating Elasticsearch indexes for Risk Dynamics"
# RUN python3 riskDynamics_postgres2es.py --type="all_indicators" --aggregation="sauid" --geometry=geom_point --idField="ghslID"
# RUN pypy3 riskDynamics_postgres2es.py --type="all_indicators" --aggregation="sauid" --geometry=geom_point --idField="ghslID"

# LOG "Creating Risk Dynamics Kibana Index Patterns"
# RUN curl -X POST -H "Content-Type: application/json" "${KIBANA_ENDPOINT}/s/gsc-cgc/api/saved_objects/index-pattern/opendrr_nhsl_risk_dynamics_all_indicators" -H "kbn-xsrf: true" -d '{ "attributes": { "title":"opendrr_nhsl_risk_dynamics_all_indicators"}}'
Expand All @@ -857,12 +857,12 @@ done
# shellcheck disable=SC2154
if [[ $loadSocialFabric = true ]]; then
LOG "Creating Elasticsearch indexes for Social Fabric"
RUN python3 socialFabric_postgres2es.py --aggregation="sauid" --geometry=geom_poly --sortfield="Sauid"
RUN python3 socialFabric_postgres2es.py --aggregation="hexgrid_5km" --geometry=geom --sortfield="gridid_5"
RUN python3 socialFabric_postgres2es.py --aggregation="hexgrid_10km" --geometry=geom --sortfield="gridid_10"
RUN python3 socialFabric_postgres2es.py --aggregation="hexgrid_25km" --geometry=geom --sortfield="gridid_25"
RUN python3 socialFabric_postgres2es.py --aggregation="hexgrid_50km" --geometry=geom --sortfield="gridid_50"
RUN python3 socialFabric_postgres2es.py --aggregation="hexgrid_100km" --geometry=geom --sortfield="gridid_100"
RUN pypy3 socialFabric_postgres2es.py --aggregation="sauid" --geometry=geom_poly --sortfield="Sauid"
RUN pypy3 socialFabric_postgres2es.py --aggregation="hexgrid_5km" --geometry=geom --sortfield="gridid_5"
RUN pypy3 socialFabric_postgres2es.py --aggregation="hexgrid_10km" --geometry=geom --sortfield="gridid_10"
RUN pypy3 socialFabric_postgres2es.py --aggregation="hexgrid_25km" --geometry=geom --sortfield="gridid_25"
RUN pypy3 socialFabric_postgres2es.py --aggregation="hexgrid_50km" --geometry=geom --sortfield="gridid_50"
RUN pypy3 socialFabric_postgres2es.py --aggregation="hexgrid_100km" --geometry=geom --sortfield="gridid_100"

LOG "Creating Social Fabric Kibana Index Patterns"
RUN curl -X POST -H "Content-Type: application/json" "${KIBANA_ENDPOINT}/s/gsc-cgc/api/saved_objects/index-pattern/opendrr_nhsl_social_fabric_all_indicators_s" -H "kbn-xsrf: true" -d '{ "attributes": { "title":"opendrr_nhsl_social_fabric_all_indicators_s"}}'
Expand All @@ -877,12 +877,12 @@ done
# shellcheck disable=SC2154
if [[ $loadHexGrid = true ]]; then
LOG "Creating Elasticsearch indexes for Hexgrids"
RUN python3 hexgrid_5km_postgres2es.py
RUN python3 hexgrid_10km_postgres2es.py
RUN python3 hexgrid_25km_postgres2es.py
RUN python3 hexgrid_50km_postgres2es.py
RUN python3 hexgrid_100km_postgres2es.py
RUN python3 hexgrid_sauid_postgres2es.py
RUN pypy3 hexgrid_5km_postgres2es.py
RUN pypy3 hexgrid_10km_postgres2es.py
RUN pypy3 hexgrid_25km_postgres2es.py
RUN pypy3 hexgrid_50km_postgres2es.py
RUN pypy3 hexgrid_100km_postgres2es.py
RUN pypy3 hexgrid_sauid_postgres2es.py

LOG "Creating HexGrid Kibana Index Patterns"
RUN curl -X POST -H "Content-Type: application/json" "${KIBANA_ENDPOINT}/s/gsc-cgc/api/saved_objects/index-pattern/opendrr_hexgrid_5km" -H "kbn-xsrf: true" -d '{ "attributes": { "title":"opendrr_hexgrid_5km"}}'
Expand Down
8 changes: 6 additions & 2 deletions python/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
#!/usr/bin/python3
# =================================================================
# SPDX-License-Identifier: MIT
#
Expand All @@ -9,10 +8,15 @@
# =================================================================

import configparser
import psycopg2
import json
import decimal

import platform
if platform.python_implementation() == "PyPy":
import psycopg2cffi as psycopg2
else:
import psycopg2

from elasticsearch import Elasticsearch
from elasticsearch import helpers

Expand Down