Implement database access

.github/workflows/build.yml

@@ -1,6 +1,8 @@
 name: build
 on:
   push:
+    branches:
+      - main
     tags:
       - 'v*.*.*'
 jobs:

CHANGELOG.rst

@@ -9,6 +9,21 @@ Changelog <https://keepachangelog.com/en/1.0.0/>`_, and this project
 adheres to `Semantic
 Versioning <https://semver.org/spec/v2.0.0.html>`_.
 
+[v0.5.9 unreleased]
+-------------------
+
+In Progress
+======
+
+- a database interface
+
+[v0.5.8]
+--------
+
+Hotfix
+======
+
+- plot figure saving fixed
 
 [v0.5.7]
 --------

db/create.py

@@ -0,0 +1,92 @@
+import sqlite3
+from sqlite3 import Error
+
+PATH = r".\db\example.db"
+
+# flake8: noqa
+
+
+def create_connection():
+    """create a database connection to a database that resides
+    in the memory
+    """
+    conn = None
+    try:
+        conn = sqlite3.connect(PATH)
+    except Error as e:
+        print(e)
+    finally:
+        return conn
+
+
+def create_table(conn, create_table_sql):
+    """create a table from the create_table_sql statement
+    :param conn: Connection object
+    :param create_table_sql: a CREATE TABLE statement
+    :return:
+    """
+    try:
+        c = conn.cursor()
+        c.execute(create_table_sql)
+    except Error as e:
+        print(e)
+
+
+def main():
+    # trailing commas will throw a syntax error !?
+
+    sql_create_projects_table = """
+        CREATE TABLE IF NOT EXISTS projects (
+            id integer PRIMARY KEY,
+            name text NOT NULL
+        );
+        """
+
+    sql_create_tests_table = """
+        CREATE TABLE IF NOT EXISTS tests (
+            id integer PRIMARY KEY,
+            name text NOT NULL,
+            project_id integer NOT NULL,
+            FOREIGN KEY (project_id) REFERENCES projects (id)
+        );
+        """
+
+    sql_create_readings_table = """
+        CREATE TABLE IF NOT EXISTS readings (
+            id integer PRIMARY KEY,
+            name text NOT NULL,
+            pump_1 integer NOT NULL,
+            pump_2 integer NOT NULL,
+            test_id integer NOT NULL,
+            FOREIGN KEY (test_id) REFERENCES tests (id)
+        );
+        """
+
+    sql_create_groups_table = """
+        CREATE TABLE IF NOT EXISTS groups (
+            id integer NOT NULL,
+            listID NOT NULL,
+            name text NOT NULL,
+        )
+        """
+
+    # create a database connection
+    conn = create_connection()
+    # create tables
+    if conn is not None:
+        # create projects table
+        print("projects")
+        create_table(conn, sql_create_projects_table)
+
+        print("tasks")
+        # create tasks table
+        create_table(conn, sql_create_tests_table)
+    else:
+        print("Error! cannot create the database connection.")
+
+    conn.commit()
+    conn.close()
+
+
+if __name__ == "__main__":
+    main()

db/sampledb.json

@@ -0,0 +1,42 @@
+{
+    "_default": {
+        "1": {
+            "uuid":"uuid",
+            "name": "project",
+            "customer": "customer",
+            "productionCo": "productionCo",
+            "submittedBy": "submittedBy",
+            "field": "field",
+            "sample": "sample",
+            "sampleDate": "sampleDate",
+            "recDate": "recDate",
+            "compDate": "compDate",
+            "analyst": "analyst",
+            "numbers": "numbers",
+            "notes": "notes",
+            "tests": [
+                {
+                    "name": "testname",
+                    "reportAs":"label",
+                    "isBlank": true,
+                    "chemical": "chemical",
+                    "rate": 100,
+                    "clarity": "clarity",
+                    "toConsider": "toConsider",
+                    "includeOnRep": "includeOnRep",
+                    "obsBaseline": 75,
+                    "notes": "notes",
+                    "result": 100,
+                    "readings":[
+                        {
+                            "average": 2,
+                            "pump 1": 1,
+                            "pump 2": 3,
+                            "elapsedMin": "stamp"
+                        }
+                    ]
+                }
+            ]
+        }
+    }
+}

db/sampledb.yaml

@@ -0,0 +1,33 @@
+---
+_default:
+  '1':
+    uuid: uuid
+    name: project
+    customer: customer
+    productionCo: productionCo
+    submittedBy: submittedBy
+    field: field
+    sample: sample
+    sampleDate: sampleDate
+    recDate: recDate
+    compDate: compDate
+    analyst: analyst
+    numbers: numbers
+    notes: notes
+    tests:
+    - name: testname
+      reportAs: label
+      isBlank: true
+      chemical: chemical
+      rate: 100
+      clarity: clarity
+      toConsider: toConsider
+      includeOnRep: includeOnRep
+      obsBaseline: 75
+      notes: notes
+      result: 100
+      readings:
+      - average: 2
+        pump 1: 1
+        pump 2: 3
+        elapsedMin: stamp

db/schema.sql

@@ -0,0 +1,44 @@
+--
+-- File generated with SQLiteStudio v3.3.3 on Wed Jun 30 07:22:45 2021
+--
+-- Text encoding used: System
+--
+PRAGMA foreign_keys = off;
+BEGIN TRANSACTION;
+
+-- Table: projects
+CREATE TABLE projects (
+    id   INTEGER PRIMARY KEY,
+    name TEXT    NOT NULL
+);
+
+
+-- Table: readings
+CREATE TABLE readings (
+    id      INTEGER PRIMARY KEY,
+    test_id INTEGER REFERENCES tests (id) ON DELETE CASCADE
+                                          ON UPDATE CASCADE
+                    NOT NULL
+);
+
+
+-- Table: reports
+CREATE TABLE reports (
+    id      INTEGER PRIMARY KEY,
+    test_id         REFERENCES tests (id) ON DELETE CASCADE
+                                          ON UPDATE CASCADE
+);
+
+
+-- Table: tests
+CREATE TABLE tests (
+    id         INTEGER PRIMARY KEY,
+    project_id         REFERENCES projects (id) ON DELETE CASCADE
+                                                ON UPDATE CASCADE
+                       NOT NULL,
+    name       TEXT    NOT NULL
+);
+
+
+COMMIT TRANSACTION;
+PRAGMA foreign_keys = on;

pyproject.toml

@@ -1,10 +1,11 @@
 [tool.poetry]
 name = "scalewiz"
-version = "0.5.7"
+version = "0.5.8"
 description = "A graphical user interface for chemical performance testing designed to work with Teledyne SSI MX-class HPLC pumps."
 readme = "README.rst"
-license = "GPL-3.0-or-later"
+license = "GPL-3.0"
 authors = ["Alex Whittington <[email protected]>"]
+repository = "https://github.com/teauxfu/scalewiz"
 packages = [
     {include = "scalewiz"}
 ]
@@ -29,6 +30,7 @@ pandas = "^1.2.2"
 py-hplc = "^1.0.1"
 tomlkit = "^0.7.0"
 appdirs = "^1.4.4"
+tinydb = "^4.4.0"
 
 [tool.poetry.scripts]
 scalewiz = "scalewiz.__main__:main"

requirements.txt

@@ -154,6 +154,9 @@ pytz==2021.1; python_full_version >= "3.7.1" \
 six==1.16.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.7" \
     --hash=sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254 \
     --hash=sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926
+tinydb==4.4.0; python_version >= "3.5" and python_version < "4.0" \
+    --hash=sha256:30b0f718ebb288e42d2f69f3e1b18928739f25153e6b5308a234e95c1673de71 \
+    --hash=sha256:d57c29524ecacc081ebc24f96e0d787bba11dc20d52634a32a709b878be3545a
 tkcalendar==1.6.1 \
     --hash=sha256:9d3a80816a7b32d64fab696fa3d2a007fb23c87953267d5e343a38ff4cd7c15c \
     --hash=sha256:c3ac34ab268734377ce73407893e8a5765e288aecbbb55136fb3ccea98006a96 \

scalewiz/__init__.py

@@ -4,10 +4,13 @@
 
 from typing import TYPE_CHECKING
 
+from tinydb import TinyDB
+
 if TYPE_CHECKING:
     from tkinter import Tk
 
 from scalewiz.helpers.configuration import get_config
 
 ROOT: Tk = None
 CONFIG: dict = get_config()
+DATABASE: TinyDB = TinyDB(CONFIG["recents"]["database"])

scalewiz/components/evaluation_window.py

@@ -119,7 +119,7 @@ def save(self) -> None:
         )
         parent_dir = Path(self.editor_project.path.get()).parent
         plot_output = Path(parent_dir, plot_output).resolve()
-        self.plot_view.fig.savefig(plot_output)
+        self.plot_view.fig.savefig(str(plot_output))
         self.editor_project.plot.set(str(plot_output))
         # update log
         log_output = (

scalewiz/helpers/configuration.py

@@ -16,6 +16,18 @@
 
 CONFIG_DIR = Path(user_config_dir("ScaleWiz", "teauxfu"))
 CONFIG_FILE = Path(CONFIG_DIR, "config.toml")
+DATABASE_FILE = Path(CONFIG_DIR, "db.json")
+
+
+def ensure_database() -> None:
+    """Ensures a database file exists."""
+    # make sure we have a place to store data
+    if DATABASE_FILE.is_file():
+        LOGGER.info("Found an existing database file %s", DATABASE_FILE)
+    else:
+        LOGGER.info("No database file found. Making one now at %s", DATABASE_FILE)
+        with DATABASE_FILE.open("w") as dbfile:
+            dbfile.write("")
 
 
 def ensure_config() -> None:
@@ -34,6 +46,8 @@ def ensure_config() -> None:
             "No config file found in %s. Making one now at %s", CONFIG_DIR, CONFIG_FILE
         )
         init_config()
+    ensure_database()
+    update_config("recents", "database", str(DATABASE_FILE))
 
 
 def init_config() -> None:
@@ -84,6 +98,7 @@ def generate_default() -> document:
     recents = table()
     recents["analyst"] = "teauxfu"
     recents["project"] = ""
+    recents["database"] = str(DATABASE_FILE)
     doc["recents"] = recents
     doc["recents"].comment("these will get updated between user sessions")
 
@@ -124,7 +139,6 @@ def generate_default() -> document:
 
 def open_config() -> None:
     """Opens the config file."""
-    ensure_config()
     if CONFIG_FILE.is_file():
         os.startfile(CONFIG_FILE)
 
@@ -134,6 +148,8 @@ def get_config() -> dict[str, Union[float, int, str]]:
     ensure_config()
     with CONFIG_FILE.open("r") as file:
         config = loads(file.read())
+    if "database" not in config["recents"]:
+        config["recents"]["database"] = str(DATABASE_FILE)
     return config
 
 
@@ -145,7 +161,6 @@ def update_config(table: str, key: str, value: Union[float, int, str]) -> None:
         key (str): the key to update
         value (Union[float, int, str]): the new value of `key`
     """
-    ensure_config()
     doc = loads(CONFIG_FILE.open("r").read())
     if table in doc.keys() and key in doc[table].keys():
         doc[table][key] = value