Merge pull request #4 from dbarrous/update-devcontainer-and-stub-code

Update .devcontainer config and Stub Code for Pipeline

.devcontainer/devcontainer.json

@@ -2,55 +2,73 @@
 // https://github.com/microsoft/vscode-dev-containers/tree/v0.183.0/containers/python-3
 {
 	"name": "Ubuntu 20.04 Python 3",
-	// Repo where this image's Dockerfile is maintained: https://github.com/HERMES-SOC/docker-lambda-base
-	"image": "public.ecr.aws/w5r9l1c8/swsoc-docker-lambda-base:latest",
-	"initializeCommand": "docker logout public.ecr.aws && docker pull public.ecr.aws/w5r9l1c8/swsoc-docker-lambda-base:latest",
-	// Set *default* container specific settings.json values on container create.
-	"settings": {
-		"python.pythonPath": "/usr/bin/python3",
-		"python.languageServer": "Pylance",
-		"python.linting.enabled": true,
-		"python.linting.pylintEnabled": true,
-		"python.formatting.blackPath": "/usr/local/bin/black",
-		"python.formatting.provider": "black",
-		"python.formatting.blackArgs": [
-			"--line-length",
-			"100"
-		],
-		"python.testing.unittestEnabled": false,
-		"python.testing.pytestEnabled": true,
-		"python.linting.lintOnSave": true,
-		"python.linting.flake8Enabled": true,
-		"editor.formatOnSave": true,
-		"python.linting.banditPath": "/usr/local/bin/bandit",
-		"python.linting.flake8Path": "/usr/local/bin/flake8",
-		"python.linting.mypyPath": "/usr/local/bin/mypy",
-		"python.linting.pycodestylePath": "/usr/local/bin/pycodestyle",
-		"python.linting.pydocstylePath": "/usr/local/bin/pydocstyle",
-		"python.linting.pylintPath": "/usr/bin/pylint",
-		"terminal.integrated.defaultProfile.linux": "bash (login)",
-		"terminal.integrated.profiles.linux": {
-			"bash (login)": {
-				"path": "bash"
-			}
-		}
+	// Repo where this image's Dockerfile is maintained: https://github.com/PADRESat/sdc_aws_base_docker_image
+	"image": "public.ecr.aws/w5r9l1c8/dev-padre-swsoc-docker-lambda-base:latest",
+	"initializeCommand": "docker logout public.ecr.aws && docker pull public.ecr.aws/w5r9l1c8/dev-padre-swsoc-docker-lambda-base:latest",
+	// If you want to run the production version of the container, comment out the image and initializeCommand lines above and uncomment the line below.
+	// "image": "public.ecr.aws/w5r9l1c8/padre-swsoc-docker-lambda-base:latest",
+	// "initializeCommand": "docker logout public.ecr.aws && docker pull public.ecr.aws/w5r9l1c8/swsoc-docker-lambda-base:latest",
+	"customizations": {
+		"vscode": {
+			// Set *default* container specific settings.json values on container create.
+			"settings": {
+				"python.pythonPath": "/usr/bin/python3",
+				"python.testing.unittestEnabled": false,
+				"python.testing.pytestEnabled": true,
+				"python.languageServer": "Pylance",
+
+				//PyLint Settings
+				"pylint.enabled": true,
+				"pylint.path": ["/usr/bin/pylint"],
+				"pylint.lintOnChange": true,
+
+				// Black Settings
+				"python.editor.defaultFormatter": "ms-python.black-formatter",
+    			"python.editor.formatOnSave": true,
+				"black-formatter.path": ["/usr/local/bin/black"],
+				"black-formatter.args": [
+					"--line-length",
+					"100"
+				],
+
+				// Flake8 Settings
+				"flake8.path": ["/usr/local/bin/flake8"],
+				"flake8.lintOnChange": true,
+
+				// Terminal Settings
+				"terminal.integrated.defaultProfile.linux": "bash (login)",
+				"terminal.integrated.profiles.linux": {
+					"bash (login)": {
+						"path": "bash"
+					}
+				}
+			},
+			// Add the IDs of extensions you want installed when the container is created.
+			"extensions": [
+				"ms-python.python",
+				"ms-python.vscode-pylance",
+				"ms-python.pylint",
+				"ms-python.black-formatter",
+				"ms-python.flake8",
+				"marklarah.pre-commit-vscode",
+				"ms-toolsai.jupyter",
+				"ms-toolsai.jupyter-renderers",
+				"ms-toolsai.jupyter-keymap",
+				"jithurjacob.nbpreviewer"
+			],
+		}	
 	},
-	// Add the IDs of extensions you want installed when the container is created.
-	"extensions": [
-		"ms-python.python",
-		"ms-python.vscode-pylance",
-		"marklarah.pre-commit-vscode",
-		"ms-toolsai.jupyter",
-		"ms-toolsai.jupyter-renderers",
-		"ms-toolsai.jupyter-keymap",
-		"jithurjacob.nbpreviewer"
-	],
+
 	// Mount to a volume if you'd like to persist data to your disk
-	// "mounts": ["source=<add your /path/on/host here>, target=/workspaces/hermes_core, type=bind"],
+	"mounts": [
+		"source=${localEnv:HOME}/.bash_profile,target=/home/vscode/.bashrc,type=bind,consistency=cached"
+	],
+
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.
 	// "forwardPorts": [],
+
 	// Use 'postCreateCommand' to run commands after the container is created.
-	//"postCreateCommand": "bash -i -c 'pip3 install --user .[all]'",
+	"postCreateCommand": "sudo pip3 uninstall padre_sharp -y",
 	// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
 	"remoteUser": "vscode"
 }

padre_sharp/calibration/calibration.py

@@ -1,11 +1,13 @@
 """
 A module for all things calibration.
 """
+
 from pathlib import Path
 import random
 
 from astropy.time import Time
 
+from swxsoc.util import util
 from padre_sharp import log
 
 __all__ = [
@@ -34,7 +36,7 @@ def process_file(data_filename: Path) -> list:
     log.info(f"Processing file {data_filename}.")
     output_files = []
 
-    #  calibrated_file = calibrate_file(data_filename)
+    calibrated_file = calibrate_file(data_filename)
     output_files.append(calibrated_file)
     #  data_plot_files = plot_file(data_filename)
     #  calib_plot_files = plot_file(calibrated_file)
@@ -74,15 +76,40 @@ def calibrate_file(data_filename: Path, output_level=2) -> Path:
         )
     )
 
-    calib_file = get_calibration_file(data_filename)
-    if calib_file is None:
-        raise ValueError("Calibration file for {} not found.".format(data_filename))
-    else:
-        calib_data = read_calibration_file(calib_file)
+    file_metadata = util.parse_science_filename(data_filename)
 
-    # example log messages
+    # Temporary directory
+    tmp_dir = Path("/tmp")
 
-    return None
+    if file_metadata is None:
+        log.error(f"Could not parse filename {data_filename}.")
+        return None
+
+    if file_metadata["level"] == "l0":
+        new_filename = tmp_dir / util.create_science_filename(
+            instrument=file_metadata["instrument"],
+            time=file_metadata["time"],
+            version=f"0.0.{file_metadata['version']}",
+            level="l1",
+        )
+        with open(new_filename, "w"):
+            pass
+
+    elif file_metadata["level"] == "l1":
+        new_filename = tmp_dir / util.create_science_filename(
+            instrument=file_metadata["instrument"],
+            time=file_metadata["time"],
+            version=file_metadata["version"],
+            level="ql",
+        )
+
+        with open(new_filename, "w"):
+            pass
+    else:
+        log.error(f"Could not calibrate file {data_filename}.")
+        raise ValueError(f"Cannot find calibration for file {data_filename}.")
+
+    return new_filename
 
 
 def get_calibration_file(time: Time) -> Path:

padre_sharp/tests/test_calibration.py

@@ -7,7 +7,7 @@ def test_calibrate_file():
         calib.calibrate_file("datafile_with_no_calib.cdf")
     assert (
         str(excinfo.value)
-        == "Calibration file for datafile_with_no_calib.cdf not found."
+        == "File datafile_with_no_calib.cdf not recognized. Not a valid mission name."
     )
 
 

padre_sharp/util/config.py

@@ -4,6 +4,7 @@
 This code is based on that provided by SunPy see
     licenses/SUNPY.rst
 """
+
 import os
 import shutil
 import configparser

padre_sharp/util/exceptions.py

@@ -7,6 +7,7 @@
 This code is based on that provided by SunPy see
     licenses/SUNPY.rst
 """
+
 import warnings
 
 __all__ = [

pyproject.toml

@@ -27,6 +27,7 @@ classifiers = [
 dependencies = [
   'astropy',
   'sunpy',
+  'swxsoc @ git+https://github.com/swxsoc/swxsoc.git@main',
 ]
 
 [project.optional-dependencies]