Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/alondhe/achilles_v4
https://github.com/alondhe/achilles_v4
Last synced: 12 days ago
JSON representation
- Host: GitHub
- URL: https://github.com/alondhe/achilles_v4
- Owner: alondhe
- License: apache-2.0
- Created: 2018-02-07T18:50:13.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2018-02-07T18:53:08.000Z (almost 7 years ago)
- Last Synced: 2023-03-10T07:02:44.989Z (almost 2 years ago)
- Language: HTML
- Size: 340 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README-impala.md
- License: LICENSE
Awesome Lists containing this project
README
Make sure you have Impala running on a cluster with the Common Data Model data loaded
as described in [https://github.com/OHDSI/CommonDataModel/tree/master/Impala](https://github.com/OHDSI/CommonDataModel/tree/master/Impala).
Before running Achilles, create a database for the Achilles tables:
```bash
impala-shell -q 'CREATE DATABASE achilles'
```
Download the Impala JDBC drivers from the [Cloudera website](http://www.cloudera.com/downloads/connectors/impala/jdbc/2-5-36.html), and install them in a local
directory called _~/impala-drivers/Cloudera_ImpalaJDBC4_2.5.36_.
In R, use the following commands to install the Impala development version of Achilles. I used Docker to get all the pre-reqs (and ran `docker run -it --rm -v ~/impala-drivers/:/impala-drivers achilles_achilles bash`).
```r
install.packages("devtools")
library(devtools)
install_github("tomwhite/SqlRender", ref="impala-timestamp")
library(SqlRender)
install_github("ohdsi/DatabaseConnector")
install_github("ohdsi/Achilles")
```
To run Achilles for a single, simple analysis, try:
```r
library(Achilles)
connectionDetails <- createConnectionDetails(dbms="impala",
server="bottou01.sjc.cloudera.com",
schema="omop_cdm_parquet",
pathToDriver = "/impala-drivers/Cloudera_ImpalaJDBC4_2.5.36")
achillesResults <- achilles(connectionDetails, cdmDatabaseSchema="omop_cdm_parquet",
resultsDatabaseSchema="achilles", sourceName="Impala trial", runHeel = FALSE,
cdmVersion = "5", vocabDatabaseSchema="omop_cdm_parquet", analysisIds = c(1))
```
Have a look at the output:
```bash
impala-shell -q 'select * from achilles.achilles_results'
```
The following is a more complex analysis:
```r
achillesResults <- achilles(connectionDetails, cdmDatabaseSchema="omop_cdm_parquet",
resultsDatabaseSchema="achilles", sourceName="Impala trial", runHeel = FALSE,
cdmVersion = "5", vocabDatabaseSchema="omop_cdm_parquet", analysisIds = c(105))
```
This is how you can run a set of analyses, by exclusion:
```r
allAnalyses=getAnalysisDetails()$analysis_id
subset1=setdiff(allAnalyses,c(110))
subset2=Filter(function(X) { X > 0 }, subset1)
achillesResults <- achilles(connectionDetails, cdmDatabaseSchema="omop_cdm_parquet",
resultsDatabaseSchema="achilles", sourceName="Impala trial", runHeel = FALSE, createTable = FALSE,
cdmVersion = "5", vocabDatabaseSchema="omop_cdm_parquet",
analysisIds = subset2)
```
Note that `createTable` has been set to `FALSE` so that the initial tables are not
created, to save time.
Finally, run all of the analyses with:
```r
achillesResults <- achilles(connectionDetails, cdmDatabaseSchema="omop_cdm_parquet",
resultsDatabaseSchema="achilles", sourceName="Impala trial", runHeel = FALSE,
cdmVersion = "5", vocabDatabaseSchema="omop_cdm_parquet")
```
You can uninstall packages with
```r
remove.packages("Achilles")
remove.packages("DatabaseConnector")
remove.packages("SqlRender")
```
If you want to delete all the Achilles results use the following:
```bash
impala-shell -q 'drop database achilles cascade'
```
Heel implementation for Impala
Currently only Achilles precomputations are fully developed for Impala. No work was done on the Heel component of Achilles
```bash
impala-shell -q 'drop database achilles cascade'
```