script fixes

synthetichealth · Sep 13, 2024 · 540269d · 540269d
1 parent fb7d08c
commit 540269d
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Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/run_coherent_eyes.sh b/run_coherent_eyes.sh
@@ -1,4 +1,5 @@
 #!/bin/bash
+set -e
 
 basedir=`pwd`
 
@@ -28,6 +29,9 @@ run_population () {
 }
 
 
+python3 -m venv ./venv/
+source ./venv/bin/activate
+python3 -m pip install -r src/main/python/coherent-data/requirements.txt
 
 rm -rf selected1000/ selected100/ selected10/
 
@@ -49,7 +53,7 @@ cat deleted_modules.txt | xargs rm -f
 # population 1
 # 1000 records with 5-year history and only relevant conditions enabled
 outputfolder="./output_population1000"
-rm -r $outputfolder
+rm -rf $outputfolder
 seed=12345
 location=Massachusetts
 years_of_history=5
@@ -68,7 +72,7 @@ cat deleted_modules.txt | xargs git restore
 # population 2
 # 100 records with 5 year history and all conditions enabled
 outputfolder="./output_population100"
-rm -r $outputfolder
+rm -rf $outputfolder
 seed=98765
 location=Virginia
 years_of_history=5
@@ -84,7 +88,7 @@ cp output_population100/fhir/*Information*.json selected100
 # population 3
 # 5-10 curated records with full history and all conditions enabled
 outputfolder="./output_population10"
-rm -r $outputfolder
+rm -rf $outputfolder
 seed=4444
 location=Washington
 years_of_history=0

diff --git a/src/main/python/coherent-data/requirements.txt b/src/main/python/coherent-data/requirements.txt
@@ -1,3 +1,4 @@
 pandas==1.5.3
+numpy==1.26.4
 pillow==10.2.0
 pydicom==2.4.4