Scicat metadata parsing

rfi_file_monitor/metadataparser.py

@@ -0,0 +1,23 @@
+from abc import ABC, abstractmethod
+
+
+class MetadataParser(ABC):
+    """Each file will need it's own metadata parser, as every import library works in different ways.
+    This class aims to standardise the function names across each file loader."""
+
+    NAME = "Metadataparser"
+
+    def __init__(self):
+        self.metadata = []
+
+    @classmethod
+    @abstractmethod
+    def supports_file(cls, file: str):
+        """This method allows you to add the file types that the method supports"""
+        raise NotImplementedError
+
+    @classmethod
+    @abstractmethod
+    def extract_metadata(cls, capture_metadata, file):
+        """extracts metadata, for a given set of vars"""
+        raise NotImplementedError

rfi_file_monitor/metadataparsers/csv_metadata_parser.py

@@ -0,0 +1,40 @@
+from rfi_file_monitor.metadataparser import MetadataParser
+from itertools import takewhile
+import re
+import logging
+
+logger = logging.getLogger(__name__)
+
+
+class CsvMetadataParser(MetadataParser):
+    NAME = "CSV Parser"
+
+    @classmethod
+    def supports_file(cls, file: str):
+        if file.endswith("csv") or file.endswith("tsv"):
+            return True
+        return False
+
+    @classmethod
+    def extract_metadata(cls, capture_metadata, file):
+        # check for metadata stored as comments
+
+        with open(file, "r") as fobj:
+            # takewhile returns an iterator over all the lines
+            # that start with the comment string
+            headiter = takewhile(lambda s: s.startswith("#"), fobj)
+            # you may want to process the headers differently,
+            # but here we just convert it to a list
+            metadata = list(headiter)
+
+        scicat_metadata = {}
+        for line in metadata:
+            line = line.strip("#")
+            line = line.strip("\n")
+            for i in capture_metadata:
+                if i in line:
+                    splitline = re.split(r'[ ,|;"=]+', line)
+                    splitline = [part for part in splitline if part != ""]
+                    scicat_metadata[splitline[0]] = splitline[1]
+
+        return scicat_metadata