firatozdemir

firatozdemir

Member Since 7 years ago

Switzerland

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5 contributions in the last year

Pinned
⚡ Extending Pretrained Segmentation Networkswith Additional Anatomical Structures
⚡ Read data from google spreadsheets
⚡ Computation using data flow graphs for scalable machine learning
⚡ Public code for our submission to the 2017 ACDC Cardiac Segmentation challenge
⚡ PermafrostAnalytics - Repository for the Hackathon on the 28 - 30. November 2019. For further information, please contact *[email protected]*.
Activity
Oct
26
2 days ago
started
started time in 2 days ago
Sep
27
1 month ago
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issue

firatozdemir issue SwissDataScienceCenter/renku-python

firatozdemir
firatozdemir

bug: ci/cd fails for previously successful renku==0.14.1 spec. only renku==1.0.0.pre1 works

Describe the bug CI/CD pipeline failing for a project with renku==0.14.1 although it passed 3 months ago (with no changes).

Link to project Project where I observed the behavior

Reproduce Here is the successful build log from 3months ago, using renku==0.14.1.
Fail log for the same commit that fails today, using renku==0.14.1.
Success log for the same project if I update renku version to renku==1.0.0.pre1.

For reference, here is the root of error (seems like missing package rdflib-jsonld<0.6.0,>=0.5.0):

ERROR: Command errored out with exit status 1:
 command: /home/jovyan/.local/pipx/venvs/renku/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ey4tcloy/rdflib-jsonld_2056368f122a489fa203be534966777b/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ey4tcloy/rdflib-jsonld_2056368f122a489fa203be534966777b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-_rg_2j4b
     cwd: /tmp/pip-install-ey4tcloy/rdflib-jsonld_2056368f122a489fa203be534966777b/
Complete output (1 lines):
error in rdflib-jsonld setup command: use_2to3 is invalid.
----------------------------------------
 WARNING: Discarding https://files.pythonhosted.org/packages/f5/17/45e137be0d93b70827fe5529c0400731344a978bc792193d7d9152e6dbe4/rdflib-jsonld-0.5.0.tar.gz#sha256=4f7d55326405071c7bce9acf5484643bcb984eadb84a6503053367da207105ed (from https://pypi.org/simple/rdflib-jsonld/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
 ERROR: Could not find a version that satisfies the requirement rdflib-jsonld<0.6.0,>=0.5.0 (from renku) (from versions: 0.2, 0.3, 0.4.0, 0.5.0, 0.6.0, 0.6.1, 0.6.2)
 ERROR: No matching distribution found for rdflib-jsonld<0.6.0,>=0.5.0
 Error installing renku from spec 'renku==0.14.1'.

Expected behavior Previously succeeding build should still succeed with the same renku build it worked before. Otherwise previously working projects would fail image builds.

Run environment (please complete the following information):

  • renku-python: 0.14.1 and 0.16.1 fails, 1.0.0.pre1 succeeds
  • Python version: 3.7
  • local terminal OR renkulab interactive environment? renkulab ci/cd
  • if renkulab, specify RStudio / Jupyterlab / Other & browser [e.g. chrome, safari]: tried on renkulab

Additional context This is not an issue for my project, but perhaps it ends up being one for other older projects that track attention one of these days.

Sep
24
1 month ago
Activity icon
issue

firatozdemir issue SwissDataScienceCenter/renku-python

firatozdemir
firatozdemir

Bug (error) trying to import renku dataset to a renku project

Description renku dataset import possibly broken on master branch.
Another potential explanation of the issue is that renku datasets not registered to knowledge graph on master branch.
Another potential explanation of the issue is that changes in the structure of renku graph cause one of the above two hypothesis.

Links to projects Main renku project.
Second renku project where the dataset exists.
Third renku project from last stable release where a working dataset exists.

To Reproduce Steps to reproduce the behavior:

  1. Clone renku-python master branch, build it. After, clone my renku project. Then try to import dataset from another renku project.
git clone [email protected]:SwissDataScienceCenter/renku-python.git
cd renku-python
pip install .[all]
cd ..
git clone [email protected]:firat.ozdemir/tmp_renku_proj.git tmp_
cd tmp_

Dataset from stable renku release is located on this renku project. Dataset name: sample-small-dataset, project name: stable-small-oa-dataset

renku dataset import https://renkulab.io/projects/firat.ozdemir/stable-small-oa-dataset/datasets/sample-small-dataset

Returns

Processing commits 2/2 4d09f5e8958c9fc78d303f953850095aeda12178 Successfully applied 1 migrations. CHECKSUM NAME SIZE (MB) TYPE


ae45879be9926ed516c542290bff9ccf98bac656 small_sim_dataset2.h5 16000000.00 h5 Warning: Do you wish to download this version? [y/N]: N

This command succeeds. renku dataset import can import the dataset from a stable release renku project. Now try it again with a renku project from master branch.
A dataset from master branch of renku-python is located on this renku project. Dataset name: small-oa-dataset-proj, project name: small-oa-dataset

renku dataset import https://renkulab.io/projects/firat.ozdemir/small-oa-dataset/datasets/small-oa-dataset-proj

Returns

Error: Cannot fetch dataset with name 'small-oa-dataset-proj' from 'https://renkulab.io/knowledge-graph/projects/firat.ozdemir/small-oa-dataset'

Expected behavior One would expect the same prompt to ask whether to download the found version of the imported dataset or not.

Run environment (please complete the following information):

  • renku-python version: 0.16.1.dev51+gb8b124b1
  • Python version: 3.9.0
  • local terminal OR renkulab interactive environment? local
  • if renkulab, specify RStudio / Jupyterlab / Other & browser [e.g. chrome, safari] No

Additional context I noticed that I can also import dataset from stable renku release after finding the node @id that matches @type: "http://schema.org/Dataset:
image

renku dataset import https://renkulab.io/datasets/b12ce2d3-7bf4-4576-ba54-6a6a35d94e2b  

Accordingly, I attempted finding the same field for the dataset from the 2nd project.

renku graph export --full --format json-ld

image

Then I try the same:

renku dataset import https://renkulab.io/datasets/21fa6797e39a4f1e9344776436399977

I get the error: image

Error: Resource not found in knowledge graph: https://renkulab.io/datasets/21fa6797e39a4f1e9344776436399977

Final note: Knowledge Graph integration is active on all 3 projects.