diff cp_common_functions.py @ 2:534ed7b8ca34 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cp_common_functions.py	Thu Apr 16 05:44:16 2020 -0400
@@ -0,0 +1,61 @@
+INDENTATION = "    "
+LINE_NUM_MODULES = 4
+
+def get_json_value(json_input, keys_path):
+    """Returns the value specified in keys_path (using dot notation) or an empty string if the key doesn't exist"""
+    if not isinstance(json_input, dict):
+        return ""
+    keys = keys_path.split(".")
+    try:
+        value = json_input[keys[0]]
+        for key in keys[1:]:
+            value = value[key]
+        return value
+    except KeyError:
+        return ""
+
+
+def concat_conditional(a, b):
+    if a == "" or b == "":
+        return ""
+    else:
+        return f"{a}_{b}"
+
+        
+def get_total_number_of_modules(pipeline_lines):
+    """Gets the number of modules from the header of the previous pipeline"""
+    number_of_modules = pipeline_lines[LINE_NUM_MODULES].strip().split(':')[1]
+    return int(number_of_modules)
+
+
+def get_pipeline_lines(input_pipeline):
+    """Returns a list with the lines in the .cppipe file"""
+    with open(input_pipeline) as f:
+        lines = f.readlines()
+    return lines
+
+
+def update_module_count(pipeline_lines, count):
+    """Updates the number of modules in the .cppipe header"""
+    module_count_entry = pipeline_lines[LINE_NUM_MODULES].strip().split(':')[0]
+    pipeline_lines[4] = f"{module_count_entry}:{count}\n"
+    return pipeline_lines
+
+
+def write_pipeline(filename, lines_pipeline):
+    """Writes the lines composing the pipeline into a file"""
+    with open(filename, "w") as f:
+        f.writelines(lines_pipeline)
+
+
+def build_header(module_name, module_number):
+    """Creates the first line of a module given the name and module number"""
+    result = "|".join([f"{module_name}:[module_num:{module_number}",
+                       "svn_version:\\'Unknown\\'",
+                       "variable_revision_number:4",
+                       "show_window:False",
+                       "notes:\\x5B\\x5D",
+                       "batch_state:array(\\x5B\\x5D, dtype=uint8)",
+                       "enabled:True",
+                       "wants_pause:False]\n"])
+    return result