Create symlink latest. Add jobID parser.

Author: kuchtact

sample_inputs/sample_run/GTC4/test_0001node/Status/latest

@@ -0,0 +1 @@
+123456789.0123/

scripts/parse_file.py

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+import copy
+
+class ParseJobID:
+    def parse_file(self, file_path):
+        with open(file_path) as file:
+            file_contents = [line for line in file]
+
+        jobID = None
+        for l in file_contents:
+            try:
+                jobID = int(l.strip())
+                break
+            except:
+                continue
+        if jobID is not None:
+            return jobID
+        else:
+            raise Exception("No jobid found in " + file_path)
+
+
+class ParseRGTInput:
+    def parse_file(self, file_path, verbose=False):
+        with open(file_path) as file:
+            file_contents = [line for line in file]
+
+        unchanged_contents = copy.deepcopy(file_contents)
+        # This is used to raise errors and find what line is the problem.
+        file_contents = list(enumerate(file_contents))
+        if verbose:
+            print("Removing commented lines.")
+        file_contents = self.remove_commented(file_contents)
+
+        if verbose:
+            print("Splitting lines.")
+        try:
+            file_contents = self.split_lines(file_contents)
+        except SyntaxError as e:
+            raise Exception(e.toString(unchanged_contents))
+
+        if verbose:
+            print("Parsing variables.")
+        try:
+            path_to_tests, test_list = self.parse_vars(file_contents)
+        except SyntaxError as e:
+            raise Exception(e.toString(unchanged_contents))
+
+        return path_to_tests, test_list
+
+
+    def parse_vars(self, file_contents):
+        test_list = []
+        path_to_tests = None
+        for line_tup in file_contents:
+            line_num = line_tup[0]
+            var = line_tup[1]["var"]
+            vals = line_tup[1]["vals"]
+
+            if var.lower() == "path_to_tests":
+                if len(vals) == 0:
+                    raise SyntaxError(message="No path to tests.", line_num=line_num)
+                elif len(vals) > 1:
+                    raise SyntaxError(message="Too many paths to tests.", line_num=line_num)
+                path_to_tests = vals[0]
+            elif var.lower() == "test":
+                if len(vals) < 2:
+                    raise SyntaxError(message="Need both program name and test name.", line_num=line_num)
+                elif len(vals) > 2:
+                    raise SyntaxError(message="Too many values after test. Only need program name and test name.", line_num=line_num)
+                test_list.append({"program": vals[0], "test": vals[1]})
+            else:
+                raise SyntaxError(message="Incorrect variable to set. Should be either 'path_to_tests' or 'test'.", line_num=line_num)
+
+        if path_to_tests == None:
+            raise Exception("No path to tests found.")
+        return path_to_tests, test_list
+
+
+    def remove_commented(self, file_contents):
+        contents = []
+        for line_tup in file_contents:
+            line = line_tup[1]
+            if len(line.lstrip()) > 0:
+                if line.lstrip()[0] != "#":
+                    contents.append((line_tup[0], line.lstrip()))
+        return contents
+
+
+    def split_lines(self, file_contents):
+        contents = []
+        for line_tup in file_contents:
+            line = line_tup[1]
+            line_num = line_tup[0]
+            line = line.split('=')
+            if len(line) < 2:
+                raise SyntaxError(message="Not enough '='.", line_num=line_num)
+            elif len(line) > 2:
+                raise SyntaxError(message="Too many '='.", line_num=line_num)
+
+            line = [l.split() for l in line]
+            if len(line[0]) == 0:
+                raise SyntaxError(message="Nothing before '='.", line_num=line_num)
+            elif len(line[0]) > 1:
+                raise SyntaxError(message="Too many space separated items before '='.", line_num=line_num)
+
+            if len(line[1]) == 0:
+                raise SyntaxError(message="Nothing after '='.", line_num=line_num)
+            elif len(line[1]) > 2:
+                raise SyntaxError(message="Too many space separated items after '='.", line_num=line_num)
+
+            line_dic = {"var": line[0][0], "vals": line[1]}
+            contents.append((line_num, line_dic))
+        return contents
+
+
+class SyntaxError(Exception):
+    def __init__(self, message, line_num=-1):
+        super().__init__(message)
+        self.message = message
+        self.line_num = line_num
+
+    def toString(self, unchanged_contents):
+        new_message = self.message
+        if self.line_num != -1:
+            new_message += "\nline " + str(self.line_num) + ":\t" + unchanged_contents[self.line_num]
+        return new_message
+
+
+if __name__ == '__main__':
+    rgtin_path = "/Users/cameronkuchta/Documents/GitHub/harmony/sample_inputs/rgt.input.master"
+    job_id_path = "/Users/cameronkuchta/Documents/GitHub/harmony/sample_inputs/sample_run/GTC4/test_0001node/Status/123456789.0123/job_id.txt"
+    parseID = ParseJobID()
+    print(parseID.parse_file(job_id_path))