Skip to content

Commit fdb10f5

Browse files
sandereggsanderegg
authored
#5 kember postprocessing (#157)
* added link def in configuration * removed int from available types. changed float to number * refactoring get value * changed type from int to integer * added exception for invalid item type error added exception for s3 transfer error * typo * nodeports now able to upload files and folders to S3 * pylint * Makefile usable from Windows bash * renamed methods * fixed type * fixed tests after renaming int to integer * added default values for SIMCORE_NODE_UUID and SIMCORE_PIPELINE_ID * moved environment variable inside init function * typo * added minio as a fixture * added unit tests that use minio * removed empty file * renamed minio fixture, pylint * fixed issue with converting booleans added test with setters * fixed conversions added test for folderûrl * pylint * moved getting env variable in init function * moved file to test folder moved json encoding/decoding of db configuration in io module removed unnecessary test_postgres module * simplifications * renamed io module to dbmanager * removed unnecessary test * get the ip directly from docker * moved creation of env variables to a better location use docker API to get the IP and port * skip 2 tests that do not run on travis * added Dockerfile for kember postpro case extended docker-compose accordingly * completed all graphs * create dummy file * fixed figure 7 and partly 6 * completed figure 1 with annotations * all plots but figure 5 missing now * autorun notebook completeted heatmap code * added button to show/hide raw code added auto slicing of data with a max display of 50k points for now all graphs are in now * code cleanup * added Makefile, docker-compose for jupyter notebook solo * makefile similar to root makefile * fix development dummy file * use jupyter notebook 1.3 * make pylint happy * fixed JS added hide_input * sort lines according to review @manuel
1 parent 4b0da86 commit fdb10f5

16 files changed

+781
-54761
lines changed

‎packages/simcore-sdk/requirements.txt

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
1+
mock==2.0.0
2+
networkx==2.1
13
psycopg2==2.7.4
24
sqlalchemy==1.2.8
3-
networkx==2.1
45
tenacity==4.12.0
5-
mock==2.0.0

‎services/dy-2Dgraph/TestingDBConnectionwithSimcoreSDK.ipynb

Lines changed: 0 additions & 278 deletions
This file was deleted.

‎services/dy-2Dgraph/use-cases/Makefile

Lines changed: 29 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -2,10 +2,25 @@ VERSION := $(shell cat /proc/version)
22
# SAN this is a hack so that docker-compose works in the linux virtual environment under Windows
33
ifneq (,$(findstring Microsoft,$(VERSION)))
44
export DOCKER_COMPOSE=docker-compose.exe
5+
export DOCKER=docker.exe
56
else
67
export DOCKER_COMPOSE=docker-compose
8+
export DOCKER=docker
79
endif
810

11+
all:
12+
@echo 'run `make build-devel` to build your dev environment'
13+
@echo 'run `make up-devel` to start your dev environment.'
14+
@echo 'see Makefile for further targets'
15+
16+
build-devel:
17+
${DOCKER_COMPOSE} -f docker-compose.yml -f docker-compose.devel.yml build --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"`
18+
19+
rebuild-devel:
20+
${DOCKER_COMPOSE} -f docker-compose.yml -f docker-compose.devel.yml build --no-cache --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"`
21+
22+
up-devel:
23+
${DOCKER_COMPOSE} -f docker-compose.yml -f docker-compose.devel.yml up
924

1025
build:
1126
${DOCKER_COMPOSE} -f docker-compose.yml build --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"`
@@ -18,15 +33,17 @@ up:
1833

1934
down:
2035
${DOCKER_COMPOSE} -f docker-compose.yml down
21-
22-
build-devel:
23-
${DOCKER_COMPOSE} -f docker-compose.yml -f docker-compose.devel.yml build --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"`
24-
25-
rebuild-devel:
26-
${DOCKER_COMPOSE} -f docker-compose.yml -f docker-compose.devel.yml build --no-cache --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"`
27-
28-
up-devel:
29-
${DOCKER_COMPOSE} -f docker-compose.yml -f docker-compose.devel.yml up
30-
31-
down-devel:
32-
${DOCKER_COMPOSE} -f docker-compose.yml -f docker-compose.devel.yml down
36+
${DOCKER_COMPOSE} -f docker-compose.yml -f docker-compose.devel.yml down
37+
38+
SERVICES_VERSION=1.0
39+
40+
push_service_images:
41+
${DOCKER} login masu.speag.com
42+
${DOCKER} tag use-cases_cc-0d:latest masu.speag.com/simcore/services/dynamic/cc-0d-viewer:${SERVICES_VERSION}
43+
${DOCKER} push masu.speag.com/simcore/services/dynamic/cc-0d-viewer:${SERVICES_VERSION}
44+
${DOCKER} tag use-cases_cc-1d:latest masu.speag.com/simcore/services/dynamic/cc-1d-viewer:${SERVICES_VERSION}
45+
${DOCKER} push masu.speag.com/simcore/services/dynamic/cc-1d-viewer:${SERVICES_VERSION}
46+
${DOCKER} tag use-cases_cc-2d:latest masu.speag.com/simcore/services/dynamic/cc-2d-viewer:${SERVICES_VERSION}
47+
${DOCKER} push masu.speag.com/simcore/services/dynamic/cc-2d-viewer:${SERVICES_VERSION}
48+
${DOCKER} tag use-cases_kember:latest masu.speag.com/simcore/services/dynamic/kember-viewer:${SERVICES_VERSION}
49+
${DOCKER} push masu.speag.com/simcore/services/dynamic/kember-viewer:${SERVICES_VERSION}

‎services/dy-2Dgraph/use-cases/cc/Dockerfile

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
FROM masu.speag.com/simcore/services/jupyter-base-notebook:1.2 AS common
1+
FROM masu.speag.com/simcore/services/jupyter-base-notebook:1.3 AS common
22

33
LABEL maintainer="sanderegg"
44

‎services/dy-2Dgraph/use-cases/cc/requirements.txt

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
1-
psycopg2-binary==2.7.4
2-
sqlalchemy==1.2.8
1+
jupyter_contrib_nbextensions==0.5.0
2+
jupyter_dashboards==0.7.0
3+
matplotlib==2.2.2
34
minio==4.0.0
45
networkx==2.1
5-
tenacity==4.12.0
6-
plotly==2.6.0
7-
matplotlib==2.2.2
8-
tqdm==4.23.4
96
pandas==0.22.0
10-
jupyter_contrib_nbextensions==0.5.0
11-
jupyter_dashboards==0.7.0
7+
plotly==2.6.0
8+
psycopg2-binary==2.7.4
9+
sqlalchemy==1.2.8
10+
tenacity==4.12.0
11+
tqdm==4.23.4

0 commit comments

Comments
 (0)