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.

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

[ENH] Add a script to generate csv files #46

Merged
merged 2 commits into from
Jan 17, 2019

Conversation

oesteban
Copy link
Member

First, convert bson to json using mongodb's tool. Second, use this script to generate csv tables.

First, convert bson to json using mongodb's tool. Second, use this
script to generate csv tables.
@oesteban oesteban requested a review from rwblair January 12, 2019 16:27

data = defaultdict(emptylist, {})
for entry in dictlist:
md5sum = entry['provenance']['md5sum']
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

dumps from the rating collection don't have a provenance field, md5sum should exist at the top level of the object.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yep, you need to use the flag --no-dedup for those. Probably the flag could use a renaming.

import json

import numpy as np
import pandas as pd
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

pandas and numpy aren't requirements for eve, maybe add them to the requirements.txt so the main docker container can run the tool? Otherwise I'm not opposed to a requirements file for the tools directory since it seems it might be used outside the containers.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yeah, I see this more as a place to have the script, not as a dependency.

@rwblair
Copy link
Contributor

rwblair commented Jan 17, 2019

You know the dependencies and how to call it, I'm merging.

@rwblair rwblair merged commit 954ada1 into nipreps:master Jan 17, 2019
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants