1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/1ae7433d67d9/ changeset: 1ae7433d67d9 user: dannon date: 2012-02-28 17:00:16 summary: Workflows: Additional rename options available to Rename Datasets action -- from Dave Walton. Syntax: #{inputs_file_variable | option 1 | option n} where: input_file_variable = is the name of a module input variable | = the delimiter for added options. Optional if no options. options = basename, upper, lower basename = keep all of the file name except the extension (everything before the final ".") upper = force the file name to upper case lower = force the file name to lower case Example: #{input1 | basename | upper} affected #: 1 file
diff -r c2cb11dd86d8b6fd8799a3b0fa6d685eae0c5e98 -r 1ae7433d67d9a954a8f5043962b72becf4f55473 lib/galaxy/jobs/actions/post.py --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -126,10 +126,73 @@ verbose_name = "Rename Dataset"
@classmethod - def execute(cls, app, sa_session, action, job, replacement_dict): + def execute(cls, app, sa_session, action, job, replacement_dict): # Prevent renaming a dataset to the empty string. if action.action_arguments and action.action_arguments.has_key('newname') and action.action_arguments['newname'] != '': new_name = action.action_arguments['newname'] + + # TODO: Unify and simplify replacement options. + # Add interface through workflow editor UI + + # The following if statement will process a request to rename + # using an input file name. + # TODO: Replace all matching code with regex + # Proper syntax is #{input_file_variable | option 1 | option n} + # where + # input_file_variable = is the name of an module input variable + # | = the delimiter for added options. Optional if no options. + # options = basename, upper, lower + # basename = keep all of the file name except the extension + # (everything before the final ".") + # upper = force the file name to upper case + # lower = force the file name to lower case + # suggested additions: + # "replace" option so you can replace a portion of the name, + # support multiple #{name} in one rename action... + + if new_name.find("#{") > -1: + to_be_replaced = "" + # This assumes a single instance of #{variable} will exist + start_pos = new_name.find("#{") + 2 + end_pos = new_name.find("}") + to_be_replaced = new_name[start_pos:end_pos] + input_file_var = to_be_replaced + # Pull out the piped controls and store them for later + # parsing. + tokens = to_be_replaced.split("|") + operations = [] + if len(tokens) > 1: + input_file_var = tokens[0].strip() + for i in range(1, len(tokens)): + operations.append(tokens[i].strip()) + + replacement = "" + # Lookp through inputs find one with "to_be_replaced" input + # variable name, and get the replacement name + for input_assoc in job.input_datasets: + if input_assoc.name == input_file_var: + replacement = input_assoc.dataset.name + + # Do operations on replacement + # Any control that is not defined will be ignored. + # This should be moved out to a class or module function + for operation in operations: + # Basename returns everything prior to the final '.' + if operation == "basename": + fields = replacement.split(".") + replacement = fields[0] + if len(fields) > 1: + temp = "" + for i in range(1, len(fields) - 1): + temp += "." + fields[i] + replacement += temp + elif operation == "upper": + replacement = replacement.upper() + elif operation == "lower": + replacement = replacement.lower() + + new_name = new_name.replace("#{%s}" % to_be_replaced, replacement) + if replacement_dict: for k, v in replacement_dict.iteritems(): new_name = new_name.replace("${%s}" % k, v)
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