Skip to content

Update mimic_ingest.py#4

Open
cbarina wants to merge 3 commits intoClarityNLP:masterfrom
cbarina:patch-2
Open

Update mimic_ingest.py#4
cbarina wants to merge 3 commits intoClarityNLP:masterfrom
cbarina:patch-2

Conversation

@cbarina
Copy link
Copy Markdown

@cbarina cbarina commented Mar 31, 2022

Removed references to external server to pick up person_source_value (this isn't anywhere in the person table in latest (mimic-iii v1.4))

Changed csv file open to start with .gz file (what is provided from physionet.org site for mimic-iii)

Changed solr_url to match localhost install

Fixed issues where remaining rows beyond last full chunk weren't getting posted to solr

Small updates to progress print() statements to clarify progress (out of total rows) and HTTP response (200)

cbarina added 3 commits March 31, 2022 18:00
Removed references to external server to pick up person_source_value (this isn't anywhere in the person table in latest (mimic-iii v1.4))

Changed csv file open to start with .gz file (what is provided from physionet.org site for mimic-iii)

Changed solr_url to match localhost install

Small updates to progress print() statements to clarify progress (out of total rows) and HTTP response (200)
add'l tweaks after realizing some elements were hard to understand/hard-coded
code wasn't handling remaining rows/posting to server; this was fixed
also made user parameter for document source more obvious and next to other user parameters
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.

1 participant