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MannLabs / CKG

Clinical Knowledge Graph (CKG) is a platform with twofold objective: 1) build a graph database with experimental data and data imported from diverse biomedical databases 2) automate knowledge discovery making use of all the information contained in the graph
MIT License
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Graph algorithms unavailable for neo4j 4.0 #22

Closed scarltee closed 4 years ago

scarltee commented 4 years ago

Hi,

I am trying to install CKG on a macbook machine. It seems that currently one can only download neo4j 4.0 or 3.5.18+, where graph algorithms seem to be unavailable.

When I try to build from terminal with python builder.py -b full -u neo4j, it returns: Traceback (most recent call last): File "builder.py", line 14, in from graphdb_builder.builder import importer, loader ModuleNotFoundError: No module named 'graphdb_builder'

Is there a way around it? Thanks!

albsantosdel commented 4 years ago

Hi, There are two issues: 1) Neo4j version. The current Neo4j release is 4.0.5 and as you mention, the graph algorithm plugin is still not available. However, if you install the Neo4j Desktop application (https://neo4j.com/download/neo4j-desktop/?edition=desktop&flavour=osx&release=1.2.9&offline=true) when you create a local graph, it will let you choose the version of Neo4j that you want to use (CKG uses 3.5.14). 2) ModuleNotFoundError. It seems that your PYTHONPATH has not been updated. I recommend you to follow the instructions here: https://ckg.readthedocs.io/en/latest/intro/getting-started-with-build.html#add-ckg-to-bashrc

scarltee commented 4 years ago

Thanks! Issues solved.

sitashmarajbhandari7879 commented 3 years ago

Hello, when I try to build Neo4j Graph database in windows I keep getting this error

1 1

(CKG_ENV) C:\Users\sitas\CKG\src\graphdb_builder\builder>python builder.py -b full -u neo4j

Traceback (most recent call last): File "builder.py", line 14, in from graphdb_builder.builder import importer, loader File "C:\Users\sitas\CKG\src\graphdb_builder\builder\importer.py", line 20, in from graphdb_builder.users import users_controller as uh File "C:\Users\sitas\CKG\src\graphdb_builder\users\users_controller.py", line 8, in from passlib.hash import bcrypt File "C:\Users\sitas\CKG_ENV\lib\site-packages\passlib\hash.py", line 25, in from passlib.registry import _proxy File "C:\Users\sitas\CKG_ENV\lib\site-packages\passlib\registry.py", line 12, in from passlib.ifc import PasswordHash File "C:\Users\sitas\CKG_ENV\lib\site-packages\passlib\ifc.py", line 10, in from passlib.utils.decor import deprecated_method File "C:\Users\sitas\CKGENV\lib\site-packages\passlib\utils_init.py", line 845, in from time import clock as timer ImportError: cannot import name 'clock' from 'time' (unknown location)

can anyone please help me? I am new to neo4j and CKG