Merge pull request 'kc-covid19-zipcode' (#2) from kc-covid19-zipcode into main

Reviewed-on: http://git.prasket.net/prasket/api.seattlematrix.org/pulls/2

.gitignore

@@ -1,2 +1,4 @@
-covid-19*
-.vscode
+.vscode
+test.py
+output
+creds.py

Pipfile

@@ -8,6 +8,7 @@ pylint = "*"
 
 [packages]
 psycopg2 = "*"
+flask = "*"
 
 [requires]
 python_version = "3.7"

Pipfile.lock

@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
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+            "sha256": "da16bb60c1de007d8f94358351fd693711e6cabca5199ddb2b0c14d9da227c5a"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -16,6 +16,73 @@
         ]
     },
     "default": {
+        "click": {
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+                "sha256:cd5df75523866410809ca100dc9681e301e3c27567cf498077e8551b6d20e42f",
+                "sha256:cdb132fc825c38e1aeec2c8aa9338310d29d337bebbd7baa06889d09a60a1fa2",
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@@ -34,6 +101,13 @@
             ],
             "index": "pypi",
             "version": "==2.8.5"
+        },
+        "werkzeug": {
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+            "version": "==1.0.1"
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     "develop": {

README.md

@@ -2,7 +2,6 @@
 
 API to help make public data easier to access. Idea started with need for King County, WA COVID-19 data in API format while only having an excel file for source data. 
 
-
 ## Development Setup
 
 ### Datastore
@@ -20,12 +19,41 @@ docker ps # to find the CONTAINER ID
 docker exec -it 05b3a3471f6f bash
 ```
 
+From the shell login to the db and setup initial user and database
+
+```bash
+psql -U postgres
+```
+
+Create your creds.py from the creds_sample.py
+
+```bash
+cp creds_sample.py creds.py
+```
+
+Edit creds.py with correct info for your db.
+
+More info coming soon on using the scripts in database/ to create tables and load them with data. 
+
 ### Development Env.
 
-I am using Python 3.7 
+Project is using Python 3.7 
 
-I use [pipenv](https://pipenv.pypa.io/en/latest/) when I develop with Python. 
+In the project we use [pipenv](https://pipenv.pypa.io/en/latest/) when developing. 
 
 ```bash
 pipenv install && pipenv shell
 ```
+### Production
+
+When running on Debian server libpq-dev is required, this is postgresl library. 
+
+```bash
+sudo apt-get install libpq-dev
+```
+
+### Data Available
+
+- King County, Washington COVID-19 Data
+    - [King County, WS Covid-19 by ZipCode](https://api.seattlematrix.org/v1/kingcounty/covid-19/zipcode/all)
+    - sample source url https://www.kingcounty.gov/depts/health/covid-19/data/~/media/depts/health/communicable-diseases/documents/C19/data/covid-data-extract-geography-august-24.ashx

api.py

@@ -0,0 +1,46 @@
+import flask
+from flask import request, jsonify
+import psycopg2
+import json
+
+app = flask.Flask(__name__)
+app.config["DEBUG"] = True
+import creds
+
+# Assign secrets to variables, should look into making this 
+# a function. Plan to move this to Vault from creds file.
+dbhost = creds.dblogin['host']
+database = creds.dblogin['db']
+username = creds.dblogin['username']
+password = creds.dblogin['password']
+port = creds.dblogin['port']
+
+@app.route('/', methods=['GET'])
+def home():
+    # TODO: Look into putting all this into a template or something.
+    return """<h1>Public API offered by the team at Seattle Matrix</h1> <p>This \
+        site is a collection of api's from various public sources collected \
+        by the team at <a href="https://seattlematrix.org" target="_blank">SeattleMatrix.org</a>.</p> Current Data: \
+        </br><a href="https://api.seattlematrix.org/v1/kingcounty/covid-19/zipcode/all" target="_blank">King County, WA Covid-19 By ZipCode</a> - Current Dates: 20200810, 20200824, 20200831
+        """
+
+# A route to return all of the available records for King County COVID-19
+@app.route('/v1/kingcounty/covid-19/zipcode/all', methods=['GET'])
+def api_zipcode_all():
+    """ This route returns all the data in the king_county_covid19_zip
+    table. This data is currently manually updated. 
+    """
+    conn = psycopg2.connect(f"host={dbhost} dbname={database} user={username} password={password} port={port} sslmode='require'")
+    cur = conn.cursor()
+    cur.execute("select row_to_json(king_county_covid19_zip) from king_county_covid19_zip;")
+    rows = cur.fetchall()
+    # FIXME: returning row throws an error and jsonify returns double nested 
+    # json result need to figure this out.
+    return jsonify(rows)
+
+if __name__ == "__main__":
+    app.run(host='0.0.0.0')
+
+# TODO: Create route for filtering on zipcode and date 
+# TODO: Put all above into function for covid-19 data 
+# TODO: Look into making a Class for db connection

create_covid-19_zip.py

@@ -1,19 +0,0 @@
-import psycopg2
-conn = psycopg2.connect("host='localhost' dbname='king_county_wa' user='postgres' password='postgres'" )
-
-cur = conn.cursor()
-cur.execute("""
-	CREATE TABLE covid19_zip(
-	zipcode varchar(5),
-	population int4,
-	tests int4,
-	test_Rate varchar(10),
-	positives int4,
-	positive_rate varchar(10), 	
-	hospitalizations int4, 
-	hospitalization_rate varchar(10), 
-	deaths int4, 
-	death_rate varchar(10)
-)
-""")
-conn.commit()

creds_sample.py

@@ -0,0 +1,12 @@
+""" save this file as creds.py and update with your
+db information. I will be updating app to use Vault 
+for secrets soon.
+"""
+
+dblogin = {
+        'host' : 'localhost',
+        'port' : '5432',
+        'username' : 'username',
+        'password' : 'password',
+        'db' : 'db'
+}

database/create_covid-19_zip.py

@@ -0,0 +1,30 @@
+import psycopg2
+import creds
+
+# assign secrets to variables
+dbhost = creds.dblogin['host']
+database = creds.dblogin['db']
+username = creds.dblogin['username']
+password = creds.dblogin['password']
+port = creds.dblogin['port']
+
+conn = psycopg2.connect(f"host={dbhost} dbname={database} user={username} password={password} port={port} sslmode='require'")
+
+cur = conn.cursor()
+cur.execute("""
+	CREATE TABLE king_county_covid19_zip(
+    id SERIAL PRIMARY KEY,
+	date_added DATE NOT NULL DEFAULT CURRENT_DATE,
+	date_data DATE,
+	zipcode TEXT,
+	population INTEGER,
+	tests INTEGER,
+	test_rate TEXT,
+	positives INTEGER,
+	positive_rate TEXT, 	
+	hospitalizations INTEGER, 
+	hospitalization_rate TEXT, 
+	deaths INTEGER, 
+	death_rate TEXT)
+""")
+conn.commit()

database/load_db.py

@@ -0,0 +1,33 @@
+import psycopg2
+import csv
+from datetime import datetime
+import creds
+
+# assign secrets to variables
+dbhost = creds.dblogin['host']
+database = creds.dblogin['db']
+username = creds.dblogin['username']
+password = creds.dblogin['password']
+port = creds.dblogin['port']
+
+conn = psycopg2.connect(f"host={dbhost} dbname={database} user={username} password={password} port={port} sslmode='require'")
+
+cur = conn.cursor()
+
+# take the source data csv and upload to the database. 
+# using date variable to choose file
+data_date = "20200831"
+source_file = "./source_data/covid-19_" +data_date+"_zip.csv"
+
+with open(source_file, 'r') as f:
+    reader = csv.reader(f)
+    next(reader) # Skip the header row.
+    for row in reader:
+        cur.execute(
+        "INSERT INTO king_county_covid19_zip(date_data, zipcode, population, tests, test_rate, \
+         positives, positive_rate, hospitalizations, hospitalization_rate, deaths, death_rate) \
+         VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s)", 
+         (data_date,row[0],row[1],row[2],row[3],row[4],row[5],row[6],row[7],row[8],row[9])
+        )
+
+conn.commit()

database/source_data/covid-19_20200810_zip.csv

@@ -0,0 +1,85 @@
+Location_Name,Population,Tests,Test_Rate,Positives,Positive_Rate,Hospitalizations,Hospitalization_Rate,Deaths,Death_Rate
+00000,2226300,337664,  15167.05,16749,    752.32,2043,     91.77,676,     30.36
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+98199,21488,3852,    179.26,57,      2.65,4,      0.19,1,      0.05
+98224,310,14,     45.16,1,      3.23,0,      0.00,0,      0.00
+98288,374,39,    104.28,0,      0.00,0,      0.00,0,      0.00
+98354,7419,60,      8.09,6,      0.81,1,      0.13,1,      0.13
+98422,21107,4,      0.19,3,      0.14,1,      0.05,0,      0.00

database/source_data/covid-19_20200824_zip.csv

@@ -0,0 +1,85 @@
+Location_Name,Population,Tests,Test_Rate,Positives,Positive_Rate,Hospitalizations,Hospitalization_Rate,Deaths,Death_Rate
+00000,2226300,343578,  15432.69,18824,    845.53,2182,     98.01,711,     31.94
+98001,35948,5107,    142.07,435,     12.10,43,      1.20,7,      0.19
+98002,35106,6236,    177.63,649,     18.49,71,      2.02,13,      0.37
+98003,49587,8287,    167.12,971,     19.58,91,      1.84,19,      0.38
+98004,34755,6552,    188.52,232,      6.68,32,      0.92,11,      0.32
+98005,20154,2810,    139.43,121,      6.00,16,      0.79,0,      0.00
+98006,38904,5409,    139.03,148,      3.80,14,      0.36,4,      0.10
+98007,28612,3027,    105.79,175,      6.12,27,      0.94,11,      0.38
+98008,26113,3517,    134.68,220,      8.42,39,      1.49,16,      0.61
+98010,5549,729,    131.38,31,      5.59,1,      0.18,1,      0.18
+98011,34504,4135,    119.84,161,      4.67,27,      0.78,12,      0.35
+98014,7630,976,    127.92,21,      2.75,3,      0.39,0,      0.00
+98019,12209,1449,    118.68,37,      3.03,0,      0.00,1,      0.08
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+98023,50842,7271,    143.01,570,     11.21,52,      1.02,8,      0.16
+98024,6000,803,    133.83,20,      3.33,1,      0.17,0,      0.00
+98027,30108,4958,    164.67,221,      7.34,45,      1.49,25,      0.83
+98028,23193,3735,    161.04,143,      6.17,28,      1.21,9,      0.39
+98029,29254,4538,    155.12,107,      3.66,12,      0.41,12,      0.41
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+98107,29219,7717,    264.11,111,      3.80,8,      0.27,4,      0.14
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+98118,49108,11377,    231.67,595,     12.12,62,      1.26,11,      0.22
+98119,26126,5935,    227.17,86,      3.29,6,      0.23,1,      0.04
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+98134,675,414,    613.33,17,     25.19,3,      4.44,0,      0.00
+98136,16216,4165,    256.85,78,      4.81,6,      0.37,3,      0.19
+98144,32523,9509,    292.38,358,     11.01,58,      1.78,20,      0.61
+98146,29292,5057,    172.64,352,     12.02,41,      1.40,12,      0.41
+98148,10823,1677,    154.95,131,     12.10,18,      1.66,3,      0.28
+98155,34534,6970,    201.83,286,      8.28,47,      1.36,24,      0.69
+98164,157,3972,  25299.36,9,     57.32,0,      0.00,1,      6.37
+98166,21840,3947,    180.72,196,      8.97,27,      1.24,4,      0.18
+98168,36076,6291,    174.38,644,     17.85,49,      1.36,7,      0.19
+98177,20330,4526,    222.63,143,      7.03,31,      1.52,21,      1.03
+98178,26649,4931,    185.04,308,     11.56,28,      1.05,7,      0.26
+98188,25097,5094,    202.97,428,     17.05,41,      1.63,7,      0.28
+98195,0,40,       .,4,       .,0,       .,0,       .
+98198,36960,6225,    168.43,523,     14.15,49,      1.33,6,      0.16
+98199,21488,4913,    228.64,61,      2.84,3,      0.14,1,      0.05
+98224,310,16,     51.61,1,      3.23,0,      0.00,0,      0.00
+98288,374,46,    122.99,0,      0.00,0,      0.00,0,      0.00
+98354,7419,65,      8.76,6,      0.81,1,      0.13,2,      0.27
+98422,21107,7,      0.33,4,      0.19,2,      0.09,0,      0.00

database/source_data/covid-19_20200831_zip.csv

@@ -0,0 +1,85 @@
+Location_Name,Population,Tests,Test_Rate,Positives,Positive_Rate,Hospitalizations,Hospitalization_Rate,Deaths,Death_Rate
+00000,2226300,361435,  16234.78,19665,    883.30,2229,    100.12,720,     32.34
+98001,35948,4520,    125.74,460,     12.80,46,      1.28,8,      0.22
+98002,35106,5255,    149.69,669,     19.06,69,      1.97,12,      0.34
+98003,49587,7308,    147.38,1043,     21.03,100,      2.02,24,      0.48
+98004,34755,5554,    159.80,235,      6.76,30,      0.86,9,      0.26
+98005,20154,2432,    120.67,129,      6.40,17,      0.84,0,      0.00
+98006,38904,4763,    122.43,155,      3.98,14,      0.36,4,      0.10
+98007,28612,2748,     96.04,182,      6.36,27,      0.94,12,      0.42
+98008,26113,3115,    119.29,224,      8.58,39,      1.49,16,      0.61
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+98011,34504,3565,    103.32,161,      4.67,27,      0.78,12,      0.35
+98014,7630,890,    116.64,24,      3.15,5,      0.66,0,      0.00
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+98023,50842,6359,    125.07,612,     12.04,53,      1.04,7,      0.14
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+98195,0,38,       .,4,       .,0,       .,0,       .
+98198,36960,5321,    143.97,550,     14.88,50,      1.35,6,      0.16
+98199,21488,4230,    196.85,64,      2.98,3,      0.14,1,      0.05
+98224,310,14,     45.16,1,      3.23,0,      0.00,0,      0.00
+98288,374,34,     90.91,0,      0.00,0,      0.00,0,      0.00
+98354,7419,59,      7.95,5,      0.67,1,      0.13,2,      0.27
+98422,21107,6,      0.28,3,      0.14,1,      0.05,0,      0.00

load_db.py

@@ -1,17 +0,0 @@
-import psycopg2
-import csv
-conn = psycopg2.connect("host='localhost' dbname='king_county_wa' user='postgres' password='postgres'" )
-
-cur = conn.cursor()
-
-with open('covid-19_zip.csv', 'r') as f:
-    reader = csv.reader(f)
-    next(reader) # Skip the header row.
-    for row in reader:
-        #print(row)
-        cur.execute(
-        "INSERT INTO covid19_zip VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s, %s)", row
-        )
-conn.commit()
-
-cur.execute('SELECT * FROM covid19_zip')