From 3a140e5612085bc966901bb0c628198cecc02b41 Mon Sep 17 00:00:00 2001
From: David Sampson <davidcsampson@gmail.com>
Date: Wed, 8 Mar 2023 18:45:37 -0500
Subject: [PATCH 01/11] Renamed experimentOutput and fileOutpu

---
 apps/backend/app.py                           | 10 ++--
 apps/backend/modules/runner.py                | 49 ++++++++++---------
 apps/frontend/components/NewExp.tsx           |  8 +--
 .../stepComponents/InformationStep.tsx        |  8 +--
 apps/frontend/firebase/db.ts                  |  4 +-
 apps/frontend/pages/dashboard.tsx             |  2 +-
 6 files changed, 41 insertions(+), 40 deletions(-)

diff --git a/apps/backend/app.py b/apps/backend/app.py
index d0d112d9..ee47b36d 100644
--- a/apps/backend/app.py
+++ b/apps/backend/app.py
@@ -74,8 +74,8 @@ def run_batch(data):
     experiment = expRef.get().to_dict()
     print(f"Experiment info: {experiment}")
     experiment['id'] = expId
-    experimentOutput = experiment['fileOutput']
-    resultOutput = experiment['resultOutput']
+    trialExtraFile = experiment['trialExtraFile']
+    trialResult = experiment['trialResult']
     keepLogs = experiment['keepLogs']
     scatterPlot = experiment['scatter']
     dumbTextArea = experiment['consts']
@@ -84,7 +84,7 @@ def run_batch(data):
     #Downloading Experiment File
     os.makedirs(f'ExperimentFiles/{expId}')
     os.chdir(f'ExperimentFiles/{expId}')
-    if experimentOutput != '' or postProcess != '' or keepLogs:
+    if trialExtraFile != '' or postProcess != '' or keepLogs:
         print('There will be experiment outputs')
         os.makedirs('ResCsvs')
     print(f'Downloading file for {expId}')
@@ -124,7 +124,7 @@ def run_batch(data):
 
     try:
         #Running the Experiment
-        conduct_experiment(expId, expRef, experimentOutput, resultOutput, filepath, filetype, numExperimentsToRun)
+        conduct_experiment(expId, expRef, trialExtraFile, trialResult, filepath, filetype, numExperimentsToRun, keepLogs)
 
         # Post Processing
         if postProcess:
@@ -143,7 +143,7 @@ def run_batch(data):
         uploadBlob = firebaseBucket.blob(f"results/result{expId}.csv")
         uploadBlob.upload_from_filename('results.csv')
 
-        if experimentOutput != '' or postProcess:
+        if trialExtraFile != '' or postProcess:
             print('Uploading Result Csvs')
             try:
                 shutil.make_archive('ResultCsvs', 'zip', 'ResCsvs')
diff --git a/apps/backend/modules/runner.py b/apps/backend/modules/runner.py
index 35ca2ccd..d532b73a 100644
--- a/apps/backend/modules/runner.py
+++ b/apps/backend/modules/runner.py
@@ -14,16 +14,17 @@
 OUTPUT_INDICATOR_USING_CSVS = "In ResCsvs"
 
 
-def get_data(process: 'Popen[str]', trialRun: int):
+def get_data(process: 'Popen[str]', trialRun: int, keepLogs: bool):
     try:
         data = process.communicate()
-        os.chdir('ResCsvs')
-        with open(f"log{trialRun}.txt", 'w', encoding='utf8') as f:
-            f.write(data[0])
-            if data[1]:
-                f.write(data[1])
-            f.close()
-        os.chdir('..')
+        if keepLogs:
+            os.chdir('ResCsvs')
+            with open(f"log{trialRun}.txt", 'w', encoding='utf8') as f:
+                f.write(data[0])
+                if data[1]:
+                    f.write(data[1])
+                f.close()
+            os.chdir('..')
         print(data)
         if data[1]:
             print(f'errors returned from pipe is {data[1]}')
@@ -36,14 +37,14 @@ def get_data(process: 'Popen[str]', trialRun: int):
     return result
 
 
-def run_trial(experiment_path, config_path, filetype, trialRun: int):
+def run_trial(experiment_path, config_path, filetype, trialRun: int, keepLogs: bool):
     #make sure that the cwd is ExperimentsFiles/{ExperimentId}
     if filetype == 'python':
         with Popen(['python', experiment_path, config_path], stdout=PIPE, stdin=PIPE, stderr=PIPE, encoding='utf8') as process:
-            return get_data(process, trialRun)
+            return get_data(process, trialRun, keepLogs)
     elif filetype == 'java':
         with Popen(['java', '-jar', experiment_path, config_path], stdout=PIPE, stdin=PIPE, stderr=PIPE, encoding='utf8') as process:
-            return get_data(process, trialRun)
+            return get_data(process, trialRun, keepLogs)
 
 
 def get_first_line_of_trial_results_csv(filename):
@@ -76,7 +77,7 @@ def add_to_output_batch(fileOutput, ExpRun):
         raise FileHandlingError("Failed to copy results csv") from err
 
 
-def conduct_experiment(expId, expRef, experimentOutput, resultOutput, filepath, filetype, numTrialsToRun):
+def conduct_experiment(expId, expRef, trialExtraFile, trialResult, filepath, filetype, numTrialsToRun, keepLogs):
     print(f"Running Experiment {expId}")
 
     passes = 0
@@ -90,11 +91,11 @@ def conduct_experiment(expId, expRef, experimentOutput, resultOutput, filepath,
         expRef.update({"startedAtEpochMillis": int(startSeconds * 1000)})
         try:
             print("Running the first trial...")
-            firstTrial = run_trial(filepath, f'configFiles/{0}.ini', filetype, 0)
-            if resultOutput == '':
+            firstTrial = run_trial(filepath, f'configFiles/{0}.ini', filetype, 0, keepLogs)
+            if trialResult == '':
                 writer.writerow(["Experiment Run", "Result"] + paramNames)
             else:
-                if (output := get_first_line_of_trial_results_csv(resultOutput)) is None:
+                if (output := get_first_line_of_trial_results_csv(trialResult)) is None:
                     raise InternalTrialFailedError("Nothing returned when trying to get header results (David, improve this error message please)")
                 writer.writerow(["Experiment Run"] + output + paramNames)
         except Exception as err:
@@ -122,31 +123,31 @@ def conduct_experiment(expId, expRef, experimentOutput, resultOutput, filepath,
             #Running the rest of the experiments
 
             print(f"Continuing now running {numTrialsToRun}")
-            if experimentOutput != '':
-                add_to_output_batch(experimentOutput, 0)
+            if trialExtraFile != '':
+                add_to_output_batch(trialExtraFile, 0)
                 firstTrial = OUTPUT_INDICATOR_USING_CSVS
-            if resultOutput == '':
+            if trialResult == '':
                 writer.writerow(["0", firstTrial] + get_configs_ordered(f'configFiles/{0}.ini', paramNames))
             else:
-                if (output := get_output_results(resultOutput)) is None:
+                if (output := get_output_results(trialResult)) is None:
                     raise InternalTrialFailedError("Nothing returned when trying to get first non-header line of results (the first run?) (David, improve this error message please)")
                 writer.writerow(["0"] + output + get_configs_ordered(f'configFiles/{0}.ini', paramNames))
             for i in range(1, numTrialsToRun + 1):
                 try:
-                    response_data = run_trial(filepath, f'configFiles/{i}.ini', filetype, i)
+                    response_data = run_trial(filepath, f'configFiles/{i}.ini', filetype, i, keepLogs)
                 except InternalTrialFailedError:
                     print('The trial failed for some internal reason?')  # TODO should this halt all further experiment runs?
                     fails += 1
                     expRef.update({'fails': fails})
                     continue
 
-                if experimentOutput != '':
+                if trialExtraFile != '':
                     response_data = OUTPUT_INDICATOR_USING_CSVS
-                    add_to_output_batch(experimentOutput, i)
-                if resultOutput == '':
+                    add_to_output_batch(trialExtraFile, i)
+                if trialResult == '':
                     writer.writerow([i, response_data] + get_configs_ordered(f'configFiles/{i}.ini', paramNames))
                 else:
-                    output = get_output_results(resultOutput)
+                    output = get_output_results(trialResult)
                     if output is None:
                         raise InternalTrialFailedError("Nothing returned when trying to get first non-header line of results (the rest of the runs?) (David, improve this error message please)")
                     writer.writerow([i] + output + get_configs_ordered(f'configFiles/{i}.ini', paramNames))
diff --git a/apps/frontend/components/NewExp.tsx b/apps/frontend/components/NewExp.tsx
index ec459ce5..73e19156 100644
--- a/apps/frontend/components/NewExp.tsx
+++ b/apps/frontend/components/NewExp.tsx
@@ -66,8 +66,8 @@ const NewExp = ({ formState, setFormState, copyID, setCopyId, ...rest }) => {
 			parameters: formList([] as any[]), // TODO type for parameters will remove the need for `any` here
 			name: '',
 			description: '',
-			fileOutput: '',
-			resultOutput: '',
+			trialExtraFile: '',
+			trialResult: '',
 			scatterIndVar: '',
 			scatterDepVar: '',
 			dumbTextArea: '',
@@ -90,8 +90,8 @@ const NewExp = ({ formState, setFormState, copyID, setCopyId, ...rest }) => {
 						parameters: formList(params),
 						name: expInfo['name'],
 						description: expInfo['description'],
-						fileOutput: expInfo['fileOutput'],
-						resultOutput: expInfo['resultOutput'],
+						trialExtraFile: expInfo['trialExtraFile'],
+						trialResult: expInfo['trialResult'],
 						verbose: expInfo['verbose'],
 						nWorkers: expInfo['workers'],
 						scatter: expInfo['scatter'],
diff --git a/apps/frontend/components/stepComponents/InformationStep.tsx b/apps/frontend/components/stepComponents/InformationStep.tsx
index 04d200aa..82e41391 100644
--- a/apps/frontend/components/stepComponents/InformationStep.tsx
+++ b/apps/frontend/components/stepComponents/InformationStep.tsx
@@ -25,22 +25,22 @@ export const InformationStep = ({ form, ...props }) => {
 					</div>
 				</InputSection>
 
-				<InputSection header={'File Output'}>
+				<InputSection header={'Trial\'s Extra File'}>
 					<div className='sm:col-span-4'>
 						<input
 							type='text'
 							placeholder='Name and extension of the output CSV file'
-							{...form.getInputProps('fileOutput')}
+							{...form.getInputProps('trialExtraFile')}
 							className='block w-full rounded-md border-gray-300 shadow-sm focus:border-blue-500 focus:ring-blue-500 sm:text-sm'
 						/>
 					</div>
 				</InputSection>
-				<InputSection header={'Result Output'}>
+				<InputSection header={'Trial Result'}>
 					<div className='sm:col-span-4'>
 						<input
 							type='text'
 							placeholder='Name and extension of the experiment results file'
-							{...form.getInputProps('resultOutput')}
+							{...form.getInputProps('trialResult')}
 							className='block w-full rounded-md border-gray-300 shadow-sm focus:border-blue-500 focus:ring-blue-500 sm:text-sm'
 						/>
 					</div>
diff --git a/apps/frontend/firebase/db.ts b/apps/frontend/firebase/db.ts
index 06f0ad3f..08c98949 100644
--- a/apps/frontend/firebase/db.ts
+++ b/apps/frontend/firebase/db.ts
@@ -18,8 +18,8 @@ export const submitExperiment = async (values, userId) => {
 		verbose: values.verbose,
 		workers: values.nWorkers,
 		expId: newExperiment.id,
-		fileOutput: values.fileOutput,
-		resultOutput: values.resultOutput,
+		trialExtraFile: values.trialExtraFile,
+		trialResult: values.trialResult,
 		keepLogs: values.keepLogs,
 		scatter: values.scatter,
 		scatterIndVar: values.scatterIndVar,
diff --git a/apps/frontend/pages/dashboard.tsx b/apps/frontend/pages/dashboard.tsx
index 40a7f161..f67cf1de 100644
--- a/apps/frontend/pages/dashboard.tsx
+++ b/apps/frontend/pages/dashboard.tsx
@@ -198,7 +198,7 @@ const ExpLog = ({ projectinit, setFormState, setCopyId }) => {
 					</button> :
 					null
 				}
-				{project['finished'] == true && (project['fileOutput'] || project['scatter'] || project['keepLogs']) ?
+				{project['finished'] == true && (project['trialExtraFile'] || project['scatter'] || project['keepLogs']) ?
 					<button type= "button" data-id={project.expId}
 						className='inline-flex items-center justify-center px-4 py-2 border border-transparent shadow-sm text-sm font-medium rounded-md text-white bg-blue-600 hover:bg-blue-700 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-blue-500 xl:w-full'
 						onClick={downloadExpZip}>

From 39387cdb7267a3fde774c74e300c529b586f28a7 Mon Sep 17 00:00:00 2001
From: David Sampson <davidcsampson@gmail.com>
Date: Wed, 8 Mar 2023 22:11:21 -0500
Subject: [PATCH 02/11] Added print logs for when we raise an error, also added
 another case for python file types

---
 apps/backend/app.py                             | 7 +++++--
 apps/backend/modules/runner.py                  | 1 -
 example_experiments/python/genetic_algorithm.py | 4 ++--
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/apps/backend/app.py b/apps/backend/app.py
index ee47b36d..97bdf4db 100644
--- a/apps/backend/app.py
+++ b/apps/backend/app.py
@@ -17,7 +17,6 @@
 from modules.output.plots import generateScatterPlot
 from modules.configs import generate_config_files
 
-
 try:
     import magic  # Crashes on windows if you're missing the 'python-magic-bin' python package
 except ImportError:
@@ -98,17 +97,21 @@ def run_batch(data):
         filedata = firebaseBucket.blob(filepath)
         filedata.download_to_filename(filepath)
     except Exception as err:
+        print(f"Error {err} occurred while trying to download experiment file")
         raise GladosInternalError('Failed to download experiment files') from err
+    print(f"Downloaded {filepath} to ExperimentFiles/{expId}/{filepath}")
 
     #Determining FileType
     rawfiletype = magic.from_file(filepath)
+    print(rawfiletype)
     filetype = 'unknown'
-    if 'Python script' in rawfiletype:
+    if 'Python script' in rawfiletype or 'python3' in rawfiletype:
         filetype = 'python'
     elif 'Java archive data (JAR)' in rawfiletype:
         filetype = 'java'
 
     if filetype == 'unknown':
+        print(f"{rawfiletype} could not be mapped to python or java, if it should consider updating the matching statements")
         raise NotImplementedError("Unknown experiment file type")
     print(f"Raw Filetype: {rawfiletype}\n Filtered Filetype: {filetype}")
 
diff --git a/apps/backend/modules/runner.py b/apps/backend/modules/runner.py
index d532b73a..1df12063 100644
--- a/apps/backend/modules/runner.py
+++ b/apps/backend/modules/runner.py
@@ -25,7 +25,6 @@ def get_data(process: 'Popen[str]', trialRun: int, keepLogs: bool):
                     f.write(data[1])
                 f.close()
             os.chdir('..')
-        print(data)
         if data[1]:
             print(f'errors returned from pipe is {data[1]}')
             return PIPE_OUTPUT_ERROR_MESSAGE
diff --git a/example_experiments/python/genetic_algorithm.py b/example_experiments/python/genetic_algorithm.py
index 9a15f460..19e9cf8b 100644
--- a/example_experiments/python/genetic_algorithm.py
+++ b/example_experiments/python/genetic_algorithm.py
@@ -28,7 +28,7 @@
 p: int, default: 60, min: 60, max: 100, step: 20 this is the population variable
 gl: int, default: 1, min: 1, max: 20, step: 1 this is the genomeLength variable
 mr: float, default: 0.2, min: 0.1, max: 0.8, step: 0.1 this is the mutationrate variable
-s: int, default: 1, min: 1, max: 1, step: 1 this is the seed variable
+seed: int, default: 1, min: 1, max: 1, step: 1 this is the seed variable
 
 PostProcess:
 Scatter Plot: checked
@@ -105,7 +105,7 @@ def main():
     population = int(config["DEFAULT"]["p"])
     genomelength = int(config["DEFAULT"]["gl"])
     mutationrate = float(config["DEFAULT"]["mr"])
-    seed = int(config["DEFAULT"]["s"])
+    seed = int(config["DEFAULT"]["seed"])
     random.seed(seed)
     #generate initial population
     chroms = generateChroms(population, genomelength)

From e553969e3623bbd2a8297641a7e0715addabbcd0 Mon Sep 17 00:00:00 2001
From: Robb <computerguy440+gh@gmail.com>
Date: Thu, 9 Mar 2023 00:03:36 -0500
Subject: [PATCH 03/11] Top level error catch that should be able to print info
 about any error we fail to catch via other approaches

---
 apps/backend/app.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/apps/backend/app.py b/apps/backend/app.py
index 97bdf4db..d7f04114 100644
--- a/apps/backend/app.py
+++ b/apps/backend/app.py
@@ -47,13 +47,14 @@
 flaskApp = Flask(__name__)
 CORS(flaskApp)
 
-runner = ProcessPoolExecutor(1)
+MAX_WORKERS = 1
+runner = ProcessPoolExecutor(MAX_WORKERS)
 
 
 ### FLASK API ENDPOINT
 @flaskApp.post("/experiment")
 def recv_experiment():
-    runner.submit(run_batch, request.get_json())
+    runner.submit(handle_exceptions_from_run, request.get_json())
     return 'OK'
 
 
@@ -62,6 +63,15 @@ def glados_custom_flask_error(error):
     return jsonify(error.to_dict()), error.status_code
 
 
+def handle_exceptions_from_run(data):
+    try:
+        run_batch(data)
+    except Exception as err:
+        print(f"Unexpected exception while trying to run the experiment, this was not caught by our own code and needs to be handled better: {err}")
+        logging.exception(err)
+        raise err
+
+
 def run_batch(data):
     print(f'Run_Batch starting with data {data}')
     experiments = firebaseDb.collection('Experiments')

From 9b2ff05f6bbfe79993cbf715982785d8150ecb02 Mon Sep 17 00:00:00 2001
From: Robb <computerguy440+gh@gmail.com>
Date: Thu, 9 Mar 2023 00:50:40 -0500
Subject: [PATCH 04/11] Extract methods for readability

---
 apps/backend/app.py                  | 124 ++++++++++++++++-----------
 apps/backend/modules/output/plots.py |   8 +-
 2 files changed, 76 insertions(+), 56 deletions(-)

diff --git a/apps/backend/app.py b/apps/backend/app.py
index d7f04114..7993cf7e 100644
--- a/apps/backend/app.py
+++ b/apps/backend/app.py
@@ -76,10 +76,12 @@ def run_batch(data):
     print(f'Run_Batch starting with data {data}')
     experiments = firebaseDb.collection('Experiments')
 
-    #Parsing the argument data
+    # Obtain most basic experiment info
     expId = data['experiment']['id']
     print(f'received {expId}')
     expRef = experiments.document(expId)
+
+    # Parsing the argument data
     experiment = expRef.get().to_dict()
     print(f"Experiment info: {experiment}")
     experiment['id'] = expId
@@ -93,36 +95,10 @@ def run_batch(data):
     #Downloading Experiment File
     os.makedirs(f'ExperimentFiles/{expId}')
     os.chdir(f'ExperimentFiles/{expId}')
-    if trialExtraFile != '' or postProcess != '' or keepLogs:
-        print('There will be experiment outputs')
-        os.makedirs('ResCsvs')
-    print(f'Downloading file for {expId}')
-    try:
-        filepath = experiment['file']
-    except KeyError:
-        filepath = f'experiment{expId}'
-        print(f"No filepath specified so defaulting to {filepath}")
-    print(f"Downloading {filepath} to ExperimentFiles/{expId}/{filepath}")
-    try:
-        filedata = firebaseBucket.blob(filepath)
-        filedata.download_to_filename(filepath)
-    except Exception as err:
-        print(f"Error {err} occurred while trying to download experiment file")
-        raise GladosInternalError('Failed to download experiment files') from err
-    print(f"Downloaded {filepath} to ExperimentFiles/{expId}/{filepath}")
+    filepath = download_experiment_files(expId, experiment, trialExtraFile, keepLogs, postProcess)
 
-    #Determining FileType
-    rawfiletype = magic.from_file(filepath)
-    print(rawfiletype)
-    filetype = 'unknown'
-    if 'Python script' in rawfiletype or 'python3' in rawfiletype:
-        filetype = 'python'
-    elif 'Java archive data (JAR)' in rawfiletype:
-        filetype = 'java'
-
-    if filetype == 'unknown':
-        print(f"{rawfiletype} could not be mapped to python or java, if it should consider updating the matching statements")
-        raise NotImplementedError("Unknown experiment file type")
+    #Determining experiment FileType -> how we need to execute it
+    rawfiletype, filetype = determine_experiment_file_type(filepath)
     print(f"Raw Filetype: {rawfiletype}\n Filtered Filetype: {filetype}")
 
     #Generating Configs from hyperparameters
@@ -140,30 +116,10 @@ def run_batch(data):
         conduct_experiment(expId, expRef, trialExtraFile, trialResult, filepath, filetype, numExperimentsToRun, keepLogs)
 
         # Post Processing
-        if postProcess:
-            print("Beginning post processing")
-            try:
-                if scatterPlot:
-                    print("Creating Scatter Plot")
-                    depVar = experiment['scatterDepVar']
-                    indVar = experiment['scatterIndVar']
-                    generateScatterPlot(indVar, depVar, 'results.csv', expId)
-            except KeyError as err:
-                raise GladosInternalError("Error during plot generation") from err
+        post_process_experiment(expId, experiment, scatterPlot, postProcess)
 
         #Uploading Experiment Results
-        print('Uploading Results to the frontend')
-        uploadBlob = firebaseBucket.blob(f"results/result{expId}.csv")
-        uploadBlob.upload_from_filename('results.csv')
-
-        if trialExtraFile != '' or postProcess:
-            print('Uploading Result Csvs')
-            try:
-                shutil.make_archive('ResultCsvs', 'zip', 'ResCsvs')
-                uploadBlob = firebaseBucket.blob(f"results/result{expId}.zip")
-                uploadBlob.upload_from_filename('ResultCsvs.zip')
-            except Exception as err:
-                raise GladosInternalError("Error uploading to firebase") from err
+        upload_experiment_results(expId, trialExtraFile, postProcess)
     except ExperimentAbort as err:
         print(f'Experiment {expId} critical failure, not doing any result uploading or post processing')
         logging.exception(err)
@@ -178,6 +134,70 @@ def run_batch(data):
         os.chdir('../..')
 
 
+def determine_experiment_file_type(filepath):
+    rawfiletype = magic.from_file(filepath)
+    print(rawfiletype)
+    filetype = 'unknown'
+    if 'Python script' in rawfiletype or 'python3' in rawfiletype:
+        filetype = 'python'
+    elif 'Java archive data (JAR)' in rawfiletype:
+        filetype = 'java'
+
+    if filetype == 'unknown':
+        print(f"{rawfiletype} could not be mapped to python or java, if it should consider updating the matching statements")
+        raise NotImplementedError("Unknown experiment file type")
+    return rawfiletype, filetype
+
+
+def download_experiment_files(expId, experiment, trialExtraFile, keepLogs, postProcess):
+    if trialExtraFile != '' or postProcess != '' or keepLogs:
+        print('There will be experiment outputs')
+        os.makedirs('ResCsvs')
+    print(f'Downloading file for {expId}')
+    try:
+        filepath = experiment['file']
+    except KeyError:
+        filepath = f'experiment{expId}'
+        print(f"No filepath specified so defaulting to {filepath}")
+    print(f"Downloading {filepath} to ExperimentFiles/{expId}/{filepath}")
+    try:
+        filedata = firebaseBucket.blob(filepath)
+        filedata.download_to_filename(filepath)
+    except Exception as err:
+        print(f"Error {err} occurred while trying to download experiment file")
+        raise GladosInternalError('Failed to download experiment files') from err
+    print(f"Downloaded {filepath} to ExperimentFiles/{expId}/{filepath}")
+    return filepath
+
+
+def upload_experiment_results(expId, trialExtraFile, postProcess):
+    print('Uploading Results to the frontend')
+    uploadBlob = firebaseBucket.blob(f"results/result{expId}.csv")
+    uploadBlob.upload_from_filename('results.csv')
+
+    if trialExtraFile != '' or postProcess:
+        print('Uploading Result Csvs')
+        try:
+            shutil.make_archive('ResultCsvs', 'zip', 'ResCsvs')
+            uploadBlob = firebaseBucket.blob(f"results/result{expId}.zip")
+            uploadBlob.upload_from_filename('ResultCsvs.zip')
+        except Exception as err:
+            raise GladosInternalError("Error uploading to firebase") from err
+
+
+def post_process_experiment(expId, experiment, scatterPlot, postProcess):
+    if postProcess:
+        print("Beginning post processing")
+        try:
+            if scatterPlot:
+                print("Creating Scatter Plot")
+                depVar = experiment['scatterDepVar']
+                indVar = experiment['scatterIndVar']
+                generateScatterPlot(indVar, depVar, 'results.csv', expId)
+        except KeyError as err:
+            raise GladosInternalError("Error during plot generation") from err
+
+
 if __name__ == '__main__':
     logging.getLogger().setLevel(logging.INFO)
     os.chdir('/app/GLADOS_HOME')
diff --git a/apps/backend/modules/output/plots.py b/apps/backend/modules/output/plots.py
index 1c4e276a..394d4c81 100644
--- a/apps/backend/modules/output/plots.py
+++ b/apps/backend/modules/output/plots.py
@@ -17,14 +17,14 @@ def generateScatterPlot(independentVar, dependantVar, resultFile, expId):
             x.append(float(row[indIndex]))
             y.append(float(row[depIndex]))
 
-    fig, ax = plt.subplots()
+    figure, axes = plt.subplots()
     print(np.array(x))
     print(np.array(y))
     m, b = np.polyfit(np.array(x), np.array(y), 1)
-    sc = ax.scatter(x,y)
+    sc = axes.scatter(x,y)
     plt.plot(x, m*np.array(x) + b)
-    ax.set_ylabel(dependantVar, loc='top')
-    ax.set_xlabel(independentVar, loc='left')
+    axes.set_ylabel(dependantVar, loc='top')
+    axes.set_xlabel(independentVar, loc='left')
     try:
         os.chdir('ResCsvs')
         plt.savefig(f'scatter{expId}.png')

From 2ba09f402f4837d85ce2fb3fc9800649ca6429fb Mon Sep 17 00:00:00 2001
From: Robb <computerguy440+gh@gmail.com>
Date: Thu, 9 Mar 2023 01:03:46 -0500
Subject: [PATCH 05/11] Increased log message clarity

---
 apps/backend/modules/runner.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/apps/backend/modules/runner.py b/apps/backend/modules/runner.py
index 1df12063..2ac1d311 100644
--- a/apps/backend/modules/runner.py
+++ b/apps/backend/modules/runner.py
@@ -28,11 +28,11 @@ def get_data(process: 'Popen[str]', trialRun: int, keepLogs: bool):
         if data[1]:
             print(f'errors returned from pipe is {data[1]}')
             return PIPE_OUTPUT_ERROR_MESSAGE
-    except Exception as e:
-        print(e)
-        raise InternalTrialFailedError("Encountered another exception while reading pipe") from e
+    except Exception as err:
+        print("Encountered another exception while reading pipe: {err}")
+        raise InternalTrialFailedError("Encountered another exception while reading pipe") from err
     result = data[0].split('\n')[0]
-    print(f"result data: {result}")
+    print(f"trial#{trialRun} result data: {result}")
     return result
 
 
@@ -121,7 +121,7 @@ def conduct_experiment(expId, expRef, trialExtraFile, trialResult, filepath, fil
         if numTrialsToRun > 0:
             #Running the rest of the experiments
 
-            print(f"Continuing now running {numTrialsToRun}")
+            print(f"Continuing with running the {numTrialsToRun} other trials...")
             if trialExtraFile != '':
                 add_to_output_batch(trialExtraFile, 0)
                 firstTrial = OUTPUT_INDICATOR_USING_CSVS
@@ -156,4 +156,4 @@ def conduct_experiment(expId, expRef, trialExtraFile, trialResult, filepath, fil
                 else:
                     fails += 1
                     expRef.update({'fails': fails})
-        print("Finished running Experiments")
+        print("Finished running Trials")

From 456852fcd7cb07a83faf0ebf7b04d8eae9669bf2 Mon Sep 17 00:00:00 2001
From: Robb <computerguy440+gh@gmail.com>
Date: Thu, 9 Mar 2023 01:06:52 -0500
Subject: [PATCH 06/11] Docs update

---
 Monorepo.wiki | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Monorepo.wiki b/Monorepo.wiki
index 297cf828..49bbaf95 160000
--- a/Monorepo.wiki
+++ b/Monorepo.wiki
@@ -1 +1 @@
-Subproject commit 297cf828047f4391a475d4cf826e403d7f9cc49d
+Subproject commit 49bbaf95cf48c8ddb1dc88c48e3be14197c616f8

From 21d4c29c42135d54cde7dbe395e0a21d19e3072b Mon Sep 17 00:00:00 2001
From: Robb <computerguy440+gh@gmail.com>
Date: Thu, 9 Mar 2023 01:36:24 -0500
Subject: [PATCH 07/11] Running an Experiment docs update

---
 Monorepo.wiki | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Monorepo.wiki b/Monorepo.wiki
index 49bbaf95..e9d075cc 160000
--- a/Monorepo.wiki
+++ b/Monorepo.wiki
@@ -1 +1 @@
-Subproject commit 49bbaf95cf48c8ddb1dc88c48e3be14197c616f8
+Subproject commit e9d075cc7166b910714d632cc28a35b2c858243d

From 0f88a119ffbc2e97c854d75739cab824e3aaf8d6 Mon Sep 17 00:00:00 2001
From: David Sampson <davidcsampson@gmail.com>
Date: Fri, 10 Mar 2023 16:53:16 -0500
Subject: [PATCH 08/11] Update
 apps/frontend/components/stepComponents/InformationStep.tsx

Co-authored-by: Rob B <computerguy440+gh@gmail.com>
---
 apps/frontend/components/stepComponents/InformationStep.tsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/apps/frontend/components/stepComponents/InformationStep.tsx b/apps/frontend/components/stepComponents/InformationStep.tsx
index 82e41391..a53dc91a 100644
--- a/apps/frontend/components/stepComponents/InformationStep.tsx
+++ b/apps/frontend/components/stepComponents/InformationStep.tsx
@@ -25,7 +25,7 @@ export const InformationStep = ({ form, ...props }) => {
 					</div>
 				</InputSection>
 
-				<InputSection header={'Trial\'s Extra File'}>
+				<InputSection header={"Trial's Extra File"}>
 					<div className='sm:col-span-4'>
 						<input
 							type='text'

From b1f6f930422e4092810f1ef78068d9542dd7f6f6 Mon Sep 17 00:00:00 2001
From: David Sampson <davidcsampson@gmail.com>
Date: Fri, 10 Mar 2023 16:56:11 -0500
Subject: [PATCH 09/11] Updated example experiments

---
 example_experiments/python/addNumsWithCsv.py    | 12 ++++++------
 example_experiments/python/genetic_algorithm.py |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/example_experiments/python/addNumsWithCsv.py b/example_experiments/python/addNumsWithCsv.py
index 10a1a22a..4464b009 100644
--- a/example_experiments/python/addNumsWithCsv.py
+++ b/example_experiments/python/addNumsWithCsv.py
@@ -8,23 +8,23 @@
 and telling the system to gather the data from that file.
 
 There are two different ways to gather additional information from an experiment
-    - Result Output: Gathers the designated file that a run of the file generates and places in a zip to be uploaded when
+    - Trial's Extra File: Gathers the designated file that a run of the file generates and places in a zip to be uploaded when
         the experiment completes
-    - File Output: Integrates the information from a 2 line csv of headers and values that the file run generates
+    - Trial Result: Integrates the information from a 2 line csv of headers and values that the file run generates
         and adds them to the result csv that is being uploaded
 
 How to tell if they worked
-    - Result Output: You can download a zip file that contains the different output files specified
-    - File Output: The result csv downloaded has been expanded with information from the specified file
+    - Trial's Extra File: You can download a zip file that contains the different output files specified
+    - Trial Result: The result csv downloaded has been expanded with information from the specified file
 
 
 Example settings for a run that demonstrates this:
 
 Info:
 If you want a collection of each CSV this experiment runs:
-    Result Output: AddNumResult.csv
+    Trial's Extra File: AddNumResult.csv
 If you want the information from each CSV to be included in the resultCsv
-    File Output: AddNumResult.csv
+    Trial Result: AddNumResult.csv
 Both can be used at the same time
 
 Parameters:
diff --git a/example_experiments/python/genetic_algorithm.py b/example_experiments/python/genetic_algorithm.py
index 19e9cf8b..893ee963 100644
--- a/example_experiments/python/genetic_algorithm.py
+++ b/example_experiments/python/genetic_algorithm.py
@@ -21,7 +21,7 @@
 Example settings for a run that demonstrates this:
 
 Info:
-File Output: geneticRes.csv
+Trial's Extra File: geneticRes.csv
 
 Parameters: -The parameters are shortened to make it easier to fill out
 g: int, default: 1, min: 1, max: 10, step: 1 this is the generations variable

From 882698045e1a96a61e3f60bdf9831fce347852d9 Mon Sep 17 00:00:00 2001
From: Robb <computerguy440+gh@gmail.com>
Date: Fri, 10 Mar 2023 17:00:34 -0500
Subject: [PATCH 10/11] Move legacy tests out to a folder

---
 apps/backend/{tests/legacy => legacy-tests}/conftest.py        | 0
 apps/backend/legacy-tests/readme.md                            | 3 +++
 .../legacy => legacy-tests}/test_app_input_integration.py      | 0
 apps/backend/{tests/legacy => legacy-tests}/test_app_unit.py   | 0
 4 files changed, 3 insertions(+)
 rename apps/backend/{tests/legacy => legacy-tests}/conftest.py (100%)
 create mode 100644 apps/backend/legacy-tests/readme.md
 rename apps/backend/{tests/legacy => legacy-tests}/test_app_input_integration.py (100%)
 rename apps/backend/{tests/legacy => legacy-tests}/test_app_unit.py (100%)

diff --git a/apps/backend/tests/legacy/conftest.py b/apps/backend/legacy-tests/conftest.py
similarity index 100%
rename from apps/backend/tests/legacy/conftest.py
rename to apps/backend/legacy-tests/conftest.py
diff --git a/apps/backend/legacy-tests/readme.md b/apps/backend/legacy-tests/readme.md
new file mode 100644
index 00000000..e482c29b
--- /dev/null
+++ b/apps/backend/legacy-tests/readme.md
@@ -0,0 +1,3 @@
+# Legacy Tests
+
+TODO These tests are from the first team, we don't use them any more, they should be removed as soon as we're done pulling inspiration from them.
diff --git a/apps/backend/tests/legacy/test_app_input_integration.py b/apps/backend/legacy-tests/test_app_input_integration.py
similarity index 100%
rename from apps/backend/tests/legacy/test_app_input_integration.py
rename to apps/backend/legacy-tests/test_app_input_integration.py
diff --git a/apps/backend/tests/legacy/test_app_unit.py b/apps/backend/legacy-tests/test_app_unit.py
similarity index 100%
rename from apps/backend/tests/legacy/test_app_unit.py
rename to apps/backend/legacy-tests/test_app_unit.py

From 835c1a58a35a9a19c486b0b93a4b4d89ea8c72b3 Mon Sep 17 00:00:00 2001
From: David Sampson <davidcsampson@gmail.com>
Date: Fri, 10 Mar 2023 17:09:40 -0500
Subject: [PATCH 11/11] Fixed A mistake

---
 example_experiments/python/genetic_algorithm.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/example_experiments/python/genetic_algorithm.py b/example_experiments/python/genetic_algorithm.py
index 893ee963..05ed8973 100644
--- a/example_experiments/python/genetic_algorithm.py
+++ b/example_experiments/python/genetic_algorithm.py
@@ -21,7 +21,7 @@
 Example settings for a run that demonstrates this:
 
 Info:
-Trial's Extra File: geneticRes.csv
+Trial Result: geneticRes.csv
 
 Parameters: -The parameters are shortened to make it easier to fill out
 g: int, default: 1, min: 1, max: 10, step: 1 this is the generations variable