Mercurial > repos > bgruening > cp_common
diff cp_common_functions.py @ 2:3c3cd68d6d5a draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
author | bgruening |
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date | Thu, 16 Apr 2020 05:29:02 -0400 |
parents | |
children | e7273daa5ae2 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cp_common_functions.py Thu Apr 16 05:29:02 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