removed unused files, began adjusting docker-composes so that they will work together.

RxMix/testing.py

@@ -1,7 +0,0 @@
-import RxMixInABox as rx 
-a = rx.FindRxcuiByString("Levothyroxine")
-print(a)
-
-
-
-c= rx.get_brands_from_ingredients(a[0])

assorted/examining the db.sql

@@ -1,44 +0,0 @@
-SELECT why_stopped FROM ctgov.studies
-WHERE why_stopped IS NOT NULL
-LIMIT 100;
-
-SELECT study_type, count(*) from ctgov.studies
-group by study_type;
-
-SELECT is_fda_regulated_drug, count(*) from ctgov.studies
-GROUP BY is_fda_regulated_drug;
-
-
-
-/*
-Note that there is a decent number of trials that have expanded access
-*/
-SELECT 
-	study_type
-	, phase
-	, has_expanded_access
-	, has_dmc
-	, count(*) 
-FROM ctgov.studies
-WHERE 
-	is_fda_regulated_drug is true
-	AND
-	study_type = 'Interventional'
-	AND 
-	start_date > date('2007-01-01')
-group by study_type, phase, has_expanded_access, has_dmc;
-
-
-
-
-/*
- Find different mesh terms as assigned by clinicaltrials.gov
- */
-select * from ctgov.browse_conditions
-order by nct_id desc,mesh_type
-limit 200;
-
-select * from ctgov.browse_interventions
-order by nct_id desc
-limit 200;
-

classifications/classify_terminations.py

@@ -1,48 +0,0 @@
-import psycopg2 as psyco
-import pandas as pd
-import nltk
-from nltk.corpus import stopwords
-from sklearn.feature_extraction.text import TfidfVectorizer
-from sklearn.cluster import KMeans
-import re
-
-
-def preporcess_text(text):
-    
-    text = text.lower()
-    text = re.sub("[^A-Za-z]+", " ", text)
-    #make tokens
-    tokens = nltk.word_tokenize(text)
-
-    #remove stopwords
-    tokens = [ w for w in tokens if not w in stopwords.words("english")]
-
-    #rejoin
-    return " ".join(tokens).strip()
-
-if __name__ == "__main__":
-    conn = psyco.connect(dbname="aact_db", user="analysis", host="localhost", password="test")
-
-    curse = conn.cursor()
-
-    curse.execute("SELECT why_stopped FROM ctgov.studies WHERE why_stopped IS NOT NULL LIMIT 2000;")
-    results = curse.fetchall()
-
-    curse.close()
-    conn.close()
-
-    data = pd.DataFrame(results, columns = ["corpus"])
-    data["cleaned"] = data.corpus.apply(preporcess_text)
-
-    vectorizer = TfidfVectorizer(sublinear_tf=True)
-
-    X = vectorizer.fit_transform(data.cleaned)
-
-    kmeans = KMeans(n_clusters=10, random_state=11021585)
-    kmeans.fit(X)
-
-    data["cluster"] = kmeans.labels_
-
-    print(data.groupby(["cluster"])["cleaned"].count())
-
-    

classifications/readme.md

@@ -1 +0,0 @@
-I believe this is for a ml classification or reasons for terminations.

containers/RxNav-In-a-box/docker-compose.yml

@@ -7,9 +7,9 @@ services:
     expose:
     - "3306"
     volumes:
-      - ./rxnav-in-a-box/mysql:/docker-entrypoint-initdb.d:ro
+      - ./RxNav-In-a-box/rxnav-in-a-box/mysql:/docker-entrypoint-initdb.d:ro
-      - ./rxnav_data:/
+      - ./RxNav-In-a-box/rxnav_data:/
     environment:
       MYSQL_RANDOM_ROOT_PASSWORD: "yes"
-      MYSQL_USER: webuser
+      MYSQL_USER: ${MYSQL_USER}
-      MYSQL_PASSWORD: 9521354c77aa
+      MYSQL_PASSWORD: ${MYSQL_PASSWORD}

containers/docker-compose.yaml

@@ -0,0 +1,39 @@
+version: '3'
+
+networks:
+  pharmaceutical_research: #because it helps to have a way to link specifically to this. 
+
+services:
+  aact_db:
+    image: postgres:14-alpine
+    networks:
+      - pharmaceutical_research
+    container_name: aact_db
+    #restart: always #restart after crashes
+    environment:
+      POSTGRES_USER: ${POSTGRES_USER}
+      POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
+      POSTGRES_DB: ${POSTGRES_DB}
+    ports:
+      - "5432:5432" #host:container
+    volumes: #host:container is the format.
+      # this is persistant storage for the database  
+      - ./db_store/:/var/lib/postgresql/
+      # this is the database dump to restore from
+      - ./aact_downloads/postgres_data.dmp:/mnt/host_data/postgres_data.dmp
+      # this is the folder containing entrypoint info.
+      - ./docker-entrypoint-initdb.d/:/docker-entrypoint-initdb.d/
+
+
+  rxnav-db:
+    image: mariadb:10.4
+    restart: "no"
+    ports:
+      - "3306":"3306"
+    volumes:
+      - ./RxNav-In-a-box/rxnav-in-a-box/mysql:/docker-entrypoint-initdb.d:ro
+      - ./RxNav-In-a-box/rxnav_data:/
+    environment:
+      MYSQL_RANDOM_ROOT_PASSWORD: "yes"
+      MYSQL_USER: ${MYSQL_USER}
+      MYSQL_PASSWORD: ${MYSQL_PASSWORD}

sample.env

@@ -1,5 +0,0 @@
-#Env file for setting up db and 
-DBNAME="aact_db"
-DBUSER="root"
-DBHOST="localhost"
-DBPASS="root"