feat: initial project structure and implementation

crategen/cli.py

@@ -1,24 +1,30 @@
-import json
 import click
+import json
 from crategen.converter_manager import ConverterManager
 
 @click.command()
-@click.option('--input', 'input_file', type=click.Path(exists=True), required=True, help='Path to the input file.')
-@click.option('--output', 'output_file', type=click.Path(), required=True, help='Path to the output file.')
-@click.option('--conversion-type', 'conversion_type', type=click.Choice(['tes_to_wrroc', 'wes_to_wrroc']), required=True, help='Type of conversion.')
-def cli(input_file, output_file, conversion_type):
-    with open(input_file, 'r') as f:
-        data = json.load(f)
-
+@click.option('--input', prompt='Input file', help='Path to the input JSON file.')
+@click.option('--output', prompt='Output file', help='Path to the output JSON file.')
+@click.option('--conversion-type', prompt='Conversion type', type=click.Choice(['tes-to-wrroc', 'wes-to-wrroc']), help='Type of conversion to perform.')
+def cli(input, output, conversion_type):
+    """
+    Command Line Interface for converting TES/WES to WRROC.
+    """
     manager = ConverterManager()
 
-    if conversion_type == 'tes_to_wrroc':
+    # Load input data from JSON file
+    with open(input, 'r') as input_file:
+        data = json.load(input_file)
+
+    # Perform the conversion based on the specified type
+    if conversion_type == 'tes-to-wrroc':
         result = manager.convert_tes_to_wrroc(data)
-    elif conversion_type == 'wes_to_wrroc':
+    elif conversion_type == 'wes-to-wrroc':
         result = manager.convert_wes_to_wrroc(data)
-
-    with open(output_file, 'w') as f:
-        json.dump(result, f, indent=2)
+
+    # Save the result to the output JSON file
+    with open(output, 'w') as output_file:
+        json.dump(result, output_file, indent=4)
 
 if __name__ == '__main__':
     cli()

crategen/converter_manager.py

@@ -2,7 +2,6 @@
 from .converters.wes_converter import WESConverter
 
 class ConverterManager:
-
     def __init__(self):
         self.tes_converter = TESConverter()
         self.wes_converter = WESConverter()
@@ -12,9 +11,3 @@ def convert_tes_to_wrroc(self, tes_data):
 
     def convert_wes_to_wrroc(self, wes_data):
         return self.wes_converter.convert_to_wrroc(wes_data)
-
-    def convert_wrroc_to_tes(self, wrroc_data):
-        return self.tes_converter.convert_from_wrroc(wrroc_data)
-
-    def convert_wrroc_to_wes(self, wrroc_data):
-        return self.wes_converter.convert_from_wrroc(wrroc_data)

crategen/converters/tes_converter.py

@@ -1,41 +1,52 @@
 from .abstract_converter import AbstractConverter
-import datetime
+from ..utils.formatting import convert_to_iso8601
 
 class TESConverter(AbstractConverter):
 
     def convert_to_wrroc(self, tes_data):
-        # Implement the conversion logic from TES to WRROC
+        # Validate and extract data with defaults
+        id = tes_data.get("id", "")
+        name = tes_data.get("name", "")
+        description = tes_data.get("description", "")
+        executors = tes_data.get("executors", [{}])
+        inputs = tes_data.get("inputs", [])
+        outputs = tes_data.get("outputs", [])
+        creation_time = tes_data.get("creation_time", "")
+        end_time = tes_data.get("end_time", "")
+
+        # Convert to WRROC
         wrroc_data = {
-            "@id": tes_data["id"],
-            "name": tes_data.get("name", ""),
-            "description": tes_data.get("description", ""),
-            "instrument": tes_data["executors"][0]["image"] if tes_data.get("executors") else None,
-            "object": [{"@id": input.get("url"), "name": input.get("path")} for input in tes_data.get("inputs", [])],
-            "result": [{"@id": output.get("url"), "name": output.get("path")} for output in tes_data.get("outputs", [])],
-            "startTime": self.convert_to_iso8601(tes_data.get("creation_time")),
-            "endTime": self.convert_to_iso8601(tes_data.get("end_time")),
+            "@id": id,
+            "name": name,
+            "description": description,
+            "instrument": executors[0].get("image", None) if executors else None,
+            "object": [{"@id": input.get("url", ""), "name": input.get("path", "")} for input in inputs],
+            "result": [{"@id": output.get("url", ""), "name": output.get("path", "")} for output in outputs],
+            "startTime": convert_to_iso8601(creation_time),
+            "endTime": convert_to_iso8601(end_time),
         }
         return wrroc_data
 
     def convert_from_wrroc(self, wrroc_data):
-        # Implement the conversion logic from WRROC to TES
+        # Validate and extract data with defaults
+        id = wrroc_data.get("@id", "")
+        name = wrroc_data.get("name", "")
+        description = wrroc_data.get("description", "")
+        instrument = wrroc_data.get("instrument", "")
+        object_data = wrroc_data.get("object", [])
+        result_data = wrroc_data.get("result", [])
+        start_time = wrroc_data.get("startTime", "")
+        end_time = wrroc_data.get("endTime", "")
+
+        # Convert from WRROC to TES
         tes_data = {
-            "id": wrroc_data["@id"],
-            "name": wrroc_data.get("name", ""),
-            "description": wrroc_data.get("description", ""),
-            "executors": [{"image": wrroc_data.get("instrument")}],
-            "inputs": [{"url": obj["@id"], "path": obj["name"]} for obj in wrroc_data.get("object", [])],
-            "outputs": [{"url": res["@id"], "path": res["name"]} for res in wrroc_data.get("result", [])],
-            "creation_time": wrroc_data.get("startTime"),
-            "end_time": wrroc_data.get("endTime"),
+            "id": id,
+            "name": name,
+            "description": description,
+            "executors": [{"image": instrument}],
+            "inputs": [{"url": obj.get("@id", ""), "path": obj.get("name", "")} for obj in object_data],
+            "outputs": [{"url": res.get("@id", ""), "path": res.get("name", "")} for res in result_data],
+            "creation_time": start_time,
+            "end_time": end_time,
         }
         return tes_data
-
-    def convert_to_iso8601(self, timestamp):
-        if timestamp:
-            try:
-                return datetime.datetime.strptime(timestamp, "%Y-%m-%dT%H:%M:%SZ").isoformat() + "Z"
-            except ValueError:
-                # Handle incorrect format or other issues
-                return None
-        return None

crategen/converters/wes_converter.py

@@ -1,39 +1,46 @@
 from .abstract_converter import AbstractConverter
-import datetime
+from ..utils.formatting import convert_to_iso8601
 
 class WESConverter(AbstractConverter):
 
     def convert_to_wrroc(self, wes_data):
-        # Implement the conversion logic from WES to WRROC
+        # Validate and extract data with defaults
+        run_id = wes_data.get("run_id", "")
+        name = wes_data.get("run_log", {}).get("name", "")
+        state = wes_data.get("state", "")
+        start_time = wes_data.get("run_log", {}).get("start_time", "")
+        end_time = wes_data.get("run_log", {}).get("end_time", "")
+        outputs = wes_data.get("outputs", {})
+
+        # Convert to WRROC
         wrroc_data = {
-            "@id": wes_data.get("run_id", ""),
-            "name": wes_data.get("run_log", {}).get("name", ""),
-            "status": wes_data.get("state", ""),
-            "startTime": self.convert_to_iso8601(wes_data.get("run_log", {}).get("start_time")),
-            "endTime": self.convert_to_iso8601(wes_data.get("run_log", {}).get("end_time")),
-            "result": [{"@id": output.get("location", ""), "name": output.get("name", "")} for output in wes_data.get("outputs", [])],
+            "@id": run_id,
+            "name": name,
+            "status": state,
+            "startTime": convert_to_iso8601(start_time),
+            "endTime": convert_to_iso8601(end_time),
+            "result": [{"@id": output.get("location", ""), "name": output.get("name", "")} for output in outputs],
         }
         return wrroc_data
 
     def convert_from_wrroc(self, wrroc_data):
-        # Implement the conversion logic from WRROC to WES
+        # Validate and extract data with defaults
+        run_id = wrroc_data.get("@id", "")
+        name = wrroc_data.get("name", "")
+        start_time = wrroc_data.get("startTime", "")
+        end_time = wrroc_data.get("endTime", "")
+        state = wrroc_data.get("status", "")
+        result_data = wrroc_data.get("result", [])
+
+        # Convert from WRROC to WES
         wes_data = {
-            "run_id": wrroc_data.get("@id", ""),
+            "run_id": run_id,
             "run_log": {
-                "name": wrroc_data.get("name", ""),
-                "start_time": wrroc_data.get("startTime", ""),
-                "end_time": wrroc_data.get("endTime", ""),
+                "name": name,
+                "start_time": start_time,
+                "end_time": end_time,
             },
-            "state": wrroc_data.get("status", ""),
-            "outputs": [{"location": res.get("@id", ""), "name": res.get("name", "")} for res in wrroc_data.get("result", [])],
+            "state": state,
+            "outputs": [{"location": res.get("@id", ""), "name": res.get("name", "")} for res in result_data],
         }
         return wes_data
-
-    def convert_to_iso8601(self, timestamp):
-        if timestamp:
-            try:
-                return datetime.datetime.strptime(timestamp, "%Y-%m-%dT%H:%M:%SZ").isoformat() + "Z"
-            except ValueError:
-                # Handle incorrect format or other issues
-                return None
-        return None

crategen/utils/formatting.py

@@ -0,0 +1,34 @@
+import datetime
+
+def convert_to_iso8601(timestamp):
+    """
+    Convert a given timestamp to ISO 8601 format.
+    Handles multiple formats including RFC 3339, ISO 8601 with and without fractional seconds.
+
+    Args:
+        timestamp (str): The timestamp to be converted.
+
+    Returns:
+        str: The converted timestamp in ISO 8601 format, or None if the input format is incorrect.
+    """
+    if timestamp:
+        # List of supported formats
+        formats = [
+            "%Y-%m-%dT%H:%M:%S.%fZ",    # RFC 3339 with fractional seconds
+            "%Y-%m-%dT%H:%M:%SZ",       # RFC 3339 without fractional seconds
+            "%Y-%m-%dT%H:%M:%S%z",      # ISO 8601 with timezone
+            "%Y-%m-%dT%H:%M:%S.%f%z",   # ISO 8601 with fractional seconds and timezone
+        ]
+        for fmt in formats:
+            try:
+                dt = datetime.datetime.strptime(timestamp, fmt)
+                iso_format = dt.isoformat()
+                # Strip fractional seconds if not needed
+                if '.' in iso_format:
+                    iso_format = iso_format.split('.')[0]
+                return iso_format + 'Z'
+            except ValueError:
+                continue
+        # Handle incorrect format or other issues
+        return None
+    return None