Open SeeMJ opened 7 years ago
thanks for the report :)
looks like a bad interaction between virtualenv
and anaconda
. I was able to reproduce after installing anaconda. I will look into it.
this bug might be related
alternatively you can call setup.sh
without using pip
(that is: ./setup.sh --ccs --omop --psql
) and make sure all required packages are installed via anaconda (before doing so clean the directory using ./setup.sh --clean
and make sure the folder .venv
doesn't exist). It appears the anaconda guys argue that with their python you don't need virtualenv
so they likely won't fix the issue.
Thanks, Josua! I ran a complete fresh install as you recommended. But I still got the same error:
------------------ Console output:
186590cd8e57:patient-viz maggjin$ ./setup.sh --ccs --omop --psql
######################################################################## 100.0%
New python executable in .venv/bin/python
Installing setuptools, pip...
Complete output from command /Users/maggjin/Docum...viz/.venv/bin/python -c "import sys, pip; sys...d\"] + sys.argv[1:]))" setuptools pip:
Traceback (most recent call last):
File "
File
"/Users/maggjin/Documents/patient-viz/virtualenv-12.1.1/virtualenv_support/pip-6.1.1-py2.py3-none-any.whl/pip/init.py",
line 13, in
File
"/Users/maggjin/Documents/patient-viz/virtualenv-12.1.1/virtualenv_support/pip-6.1.1-py2.py3-none-any.whl/pip/utils/init.py",
line 14, in
File "/Users/maggjin/anaconda/lib/python2.7/zipfile.py", line 6, in
Oh my bad -- I forgot that --psql
needs pip
as well.
Please make sure to have psycopg2
installed if you want database access (that is the case with --omop
) and then run the command on a clean directory without --psql
:
./setup.sh --ccs --omop
Yes, I was able to install the project without complains. But when I tried to run the example: ./start.sh -p json/AEF023C2029F05BC.json --start there is no patient image loaded in the event panel, with error "Failed loading file json/AEF023C2029F05BC.json". Is it because I don't have patient's data? Are there any sample patient's data provided?
Thanks!
On Fri, May 19, 2017 at 10:36 AM, Josua Krause notifications@github.com wrote:
Oh my bad -- I forgot that --psql needs pip as well. Please make sure to have psycopg2 installed if you want database access (that is the case with --omop) and then run the command on a clean directory without --psql: ./setup.sh --ccs --omop
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/nyuvis/patient-viz/issues/59#issuecomment-302765350, or mute the thread https://github.com/notifications/unsubscribe-auth/AHvi_N3fX0lZ9o3WgY2TVugxmflg8Hryks5r7dMdgaJpZM4NdQWX .
yes, you have to download and process the example data. you can follow instructions here. keep in mind, that since you don't use pip
you have to write the full command and cannot rely on the short-cut --default
:
./setup.sh --icd9 --ccs --ndc --pnt --cms --do-convert --burst
This may take a while. Also, you don't have to clean up before executing the command. All those things will be created in addition to what you have already.
I was trying to install this project on my Mac. I have Anaconda v2.7 distribution installed. I have all the required packages installed as well. Here is the console output that I got by running
./setup.sh --default-omop
: