Experiment anon field

.bcipy/README.md

@@ -0,0 +1,36 @@
+# Experiments and Fields
+
+BciPy experiments and fields allow users to collect metadata that may be integrated alongside core BciPy data. This is particularly useful when the experiment has completed and a researcher wants to curate their files for sharing with the community.
+
+## Experiments
+
+An experiment defines the name, summary and fields to collect. At this level, the requirement for collection during every task and whether or not to anonymize later will be set. The anonymization does not encrypt the data at rest, but instead defines how to handle the field later when uploading/sharing. The registered experiments are defined in `.bcipy/experiment/experiments.json` in the following format:
+
+```js
+{ 
+    name: { 
+        fields : {
+            name: "",
+            required: bool,
+            anonymize: bool
+        },
+        summary: "" 
+        }
+}
+```
+
+## Fields
+
+A field is a unit of data collection for an experiment. It has a name, help text and type. The type will determine how it is collected and validated. The registered fields are defined in `.bcipy/field/fields.json` in the following format:
+
+
+```js
+{
+    name: {
+        help_text: "",
+        type: "FieldType"
+        }
+}
+```
+
+where FieldType may be str, bool, int, or float.

.gitignore

@@ -24,6 +24,5 @@ htmlcov/
 bcipy.egg-info/
 build/
 dist/
-.bcipy/*
 
-bcipy/parameters/parameters_*
+bcipy/parameters/parameters_*

README.md

@@ -34,15 +34,15 @@ Memmott, T., Koçanaoğulları, A., Lawhead, M., Klee, D., Dudy, S., Fried-Oken,
 
 ## Dependencies
 ---------------
-This project requires Psychopy, Python v 3.6.5, and other packages. See requirements.txt. When possible integration with other open source libraries will be done.
+This project requires Python > 3.6.5 and other packages defined in the requirements.txt.
 
 
 ## Installation
 ---------------
 
 #### BCI Setup
 
-In order to run BCI suite on your computer, first install **Python 3.6.5** [from here.](https://www.python.org/downloads/)
+In order to run BCI suite on your computer, first install **Python 3** [from here.](https://www.python.org/downloads/)
 
 You must install Docker and Docker-Machine to use the Language Model developed by CSLU. There are instructions in the language model directory for getting the image you need (think of it as a callable server). You'll also need to download and load the language model [images](https://drive.google.com/drive/folders/1OYpUYASAceb60b2c5obyYytEZ0AZrajY?usp=sharing). If not using or rolling your own, set fake_lm to true in the parameters.json file.
 
@@ -133,7 +133,7 @@ Use this resource for examples: http://docs.python-guide.org/en/latest/writing/s
 ## Testing
 ----------
 
-When writing tests, put them in the correct module, in a tests folder, and prefix the file and test itself with `test` in order for pytest to discover it. See other module tests for examples!
+When writing tests, put them in the correct module, in a tests folder, and prefix the file and test itself with `test_` in order for pytest to discover it. See other module tests for examples!
 
 Development requirements must be installed before running: `pip install dev_requirements.txt`
 
@@ -153,7 +153,7 @@ py.test acquisition
 To generate test coverage metrics, in the command line:
 
 ```bash
-coverage run --branch --source=bcipy -m pytest
+coverage run --branch --source=bcipy -m pytest --mpl -k "not slow"
 
 #Generate a command line report
 coverage report

bcipy/gui/experiments/ExperimentField.py

@@ -8,7 +8,6 @@
 from PyQt5.QtCore import Qt
 from PyQt5.QtWidgets import (
     QHBoxLayout,
-    QMessageBox,
     QPushButton,
     QScrollArea,
     QVBoxLayout,
@@ -17,7 +16,9 @@
 
 from bcipy.gui.gui_main import (
     AlertMessageType,
+    AlertMessageResponse,
     AlertResponse,
+    MessageBox,
     app,
     BoolInput,
     DirectoryInput,
@@ -47,6 +48,7 @@ class ExperimentFieldCollection(QWidget):
         'directorypath': DirectoryInput
     }
     require_mark = '*'
+    alert_timeout = 10
     save_data = {}
 
     def __init__(self, title: str, width: int, height: int, experiment_name: str, save_path: str, file_name: str):
@@ -95,6 +97,7 @@ def field_input(self, field_name: str, field_type: str, help_tip: str, required:
         """
 
         form_input = self.type_inputs.get(field_type, TextInput)
+
         if required:
             field_name += self.require_mark
         return form_input(
@@ -107,7 +110,7 @@ def field_input(self, field_name: str, field_type: str, help_tip: str, required:
     def build_assets(self) -> None:
         """Build Assets.
 
-        Build any needed assests for the Experiment Field Widget. Currently, only a form is needed.
+        Build any needed assets for the Experiment Field Widget. Currently, only a form is needed.
         """
         self.build_form()
 
@@ -124,7 +127,8 @@ def check_input(self) -> bool:
                     title='BciPy Alert',
                     message=f'Required field {name.strip(self.require_mark)} must be filled out!',
                     message_type=AlertMessageType.CRIT,
-                    okay_or_cancel=True)
+                    message_response=AlertMessageResponse.OCE,
+                    message_timeout=self.alert_timeout)
                 return False
         return True
 
@@ -171,36 +175,39 @@ def build_save_data(self) -> None:
                 title='Error',
                 message=f'Error saving data. Invalid value provided. \n {e}',
                 message_type=AlertMessageType.WARN,
-                okay_or_cancel=True
+                message_response=AlertMessageResponse.OCE,
+                message_timeout=self.alert_timeout
             )
 
     def write_save_data(self) -> None:
         save_experiment_field_data(self.save_data, self.save_path, self.file_name)
         self.throw_alert_message(
             title='Success',
             message=(
-                f'Data sucessfully written to: \n\n{self.save_path}/{self.file_name} \n\n\n'
-                'Please close this window to start the task!'),
+                f'Data successfully written to: \n\n{self.save_path}/{self.file_name} \n\n\n'
+                'Please wait or close this window to start the task!'),
             message_type=AlertMessageType.INFO,
-            okay_or_cancel=True
+            message_response=AlertMessageResponse.OCE,
+            message_timeout=self.alert_timeout,
         )
 
     def throw_alert_message(self,
                             title: str,
                             message: str,
                             message_type: AlertMessageType = AlertMessageType.INFO,
-                            okay_to_exit: bool = False,
-                            okay_or_cancel: bool = False) -> QMessageBox:
+                            message_response: AlertMessageResponse = AlertMessageResponse.OTE,
+                            message_timeout: float = 0) -> MessageBox:
         """Throw Alert Message."""
 
-        msg = QMessageBox()
+        msg = MessageBox()
         msg.setWindowTitle(title)
         msg.setText(message)
         msg.setIcon(message_type.value)
+        msg.setTimeout(message_timeout)
 
-        if okay_to_exit:
+        if message_response is AlertMessageResponse.OTE:
             msg.setStandardButtons(AlertResponse.OK.value)
-        elif okay_or_cancel:
+        elif message_response is AlertMessageResponse.OCE:
             msg.setStandardButtons(AlertResponse.OK.value | AlertResponse.CANCEL.value)
 
         return msg.exec_()
@@ -267,7 +274,6 @@ def start_app() -> None:
     from bcipy.helpers.system_utils import DEFAULT_EXPERIMENT_ID
 
     parser = argparse.ArgumentParser()
-    # save path
 
     # experiment_name
     parser.add_argument('-p', '--path', default='.',
@@ -292,7 +298,7 @@ def start_app() -> None:
     file_name = args.filename
 
     bcipy_gui = app(sys.argv)
-    # todo change height based on field #?
+
     ex = MainPanel(
         title='Experiment Field Collection',
         height=250,