chore: adds a simple rule to transform the cli.

bitia/dsl.py

 __author__ = "Dilawar Singh"
 __email__ = "dilawar@subcom.tech"
 
-import pyparsing as pp
+import typing as T
 from urllib.parse import urlparse
 
+import pyparsing as pp
+
 ppc = pp.pyparsing_common
 
+
+class FileWithLocation:
+    def __init__(self, filename: str, location: T.Optional[str] = None):
+        self.filename = filename
+        self.location = location
+
+    def __repr__(self):
+        return str((self.filename, self.location))
+
+    def url(self):
+        return self.location.geturl()
+
+    @staticmethod
+    def from_tokens(_s, _loc, toks):
+        loc = toks[-1]
+        assert 1 <= len(toks) <= 2, f"Either 1 or 2 tokens, got {toks}"
+        filename = loc.path if len(toks) == 1 else str(toks[0])
+        return FileWithLocation(filename, loc)
+
+
 p_start = pp.Literal("<").suppress()
 p_end = pp.Literal(">").suppress()
 p_pipe = pp.Literal("|").suppress()
 
 # fixme: filename can have no-printables?
-p_filepath = pp.Word(pp.printables.translate({ord(i): None for i in r"|"}))
+p_filepath = pp.Word(pp.printables.translate({ord(i): None for i in r"|"})).set_name(
+    "filepath"
+)
 
-p_url = pp.Word(pp.printables.translate({ord(i): None for i in r"<>"}))
+p_url = pp.Word(pp.printables.translate({ord(i): None for i in r"<>"})).set_name("url")
 p_url.setParseAction(lambda xs: list(map(urlparse, xs)))
 
-p_file_with_url = p_start + p_filepath + p_pipe + p_url + p_end
+p_file_with_url = p_start + pp.Optional(p_filepath + p_pipe) + p_url + p_end
+p_file_with_url.set_name("file_with_location")
+p_file_with_url.set_parse_action(FileWithLocation.from_tokens)
 #  p_file_with_url.set_debug()
 
 
-class DLS:
+class DSL:
     """Domain Spefic Langauge for BiTIA"""
 
     def __init__(self):
         pass
 
-    @classmethod
-    def transform_line(cls, line: str) -> str:
+    @staticmethod
+    def transform_line(line: str) -> str:
         """Transform a simple line"""
+        # rule 1: search for p_file_with_url and replace those.
+        to_replace: T.Dict[str, str] = {}
+        download_lines = set()
+        for tokens, start, end in p_file_with_url.scan_string(line):
+            download_lines.add(f"bitia-runner tools make-available {tokens[0].url()}")
+            to_replace[line[start:end]] = tokens[0].filename
+        for k, v in to_replace.items():
+            line = line.replace(k, v)
+        return "\n".join(download_lines) + "\n" + line
+
+
+def test_simple_cli_with_dsl():
+    """Test the full dsl"""
+    lines = [
+        "# samtools sort -n Col0_C1.100k.bam -o out.sort.bam",
+        "samtools sort -n <Col0_C1.100k.bam|https://figshare.com/ndownloader/files/2133244> -o out.sort.bam",
+        "# samtools fastq Col0_C1.100k.bam",
+        "samtools fastq <Col0_C1.100k.bam|https://figshare.com/ndownloader/files/2133244>",
+        "# fastqc SRR20076358_1.fastq.gz",
+        "fastqc <ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/058/SRR20076358/SRR20076358_1.fastq.gz>",
+    ]
+    for line in lines:
+        newline = DSL.transform_line(line)
+        print("\n--")
+        print(f"\told={line}\n\tnew={newline}")
 
 
 def test_parser():
     """tests"""
     assert not p_start.parse_string("<")
     assert not p_end.parse_string(">")
-    a = p_url.parse_string("https://subcom.tech/a.txt")
+    a = p_url.parse_string("https://subcom.tech/a.txt#sha256=3319eqeqda")
+    print(11, a)
     assert a
+    assert a[0].scheme == "https"
+    assert a[0].fragment == "sha256=3319eqeqda"
+    assert a[0].path == "/a.txt"
 
-    a = p_url.parse_string("https://subcom.tech/a.txt#sha256=3319eqeqda")
+    a = p_file_with_url.parse_string("<foo.txt|http://example.com/foo.txt>")
+    print(12, a)
     assert a
 
-    a = p_file_with_url.parse_string("<foo|http://a.com/foo>")
+    a = p_file_with_url.parse_string("<http://example.com/foo.txt>")
     assert a
+    print(a)
 
 
 if __name__ == "__main__":
+    test_simple_cli_with_dsl()
     test_parser()