annotate env/lib/python3.9/site-packages/planemo/training/tool_input.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

"""Module contains code for the ToolInput class, dealing with the description of tool in workflow and XML."""

from planemo import templates
from planemo.io import info


INPUT_PARAM = """
>{{space}}- *"{{param_label}}"*: `{{param_value}}`
"""

INPUT_FILE_TEMPLATE = """
>{{space}}- {{ '{%' }} icon {{icon}} {{ '%}' }} *"{{input_name}}"*: {{input_value}}
"""

INPUT_SECTION = """
>{{space}}- In *"{{section_label}}"*:
"""

INPUT_ADD_REPEAT = """
>{{space}}- {{ '{%' }} icon param-repeat {{ '%}' }} *"Insert {{repeat_label}}"*
"""

SPACE = '    '


class ToolInput(object):
    """Class to describe a tool input / parameter and its value from a workflow."""

    def __init__(self, tool_inp_desc, wf_param_values, wf_steps, level, should_be_there=False, force_default=False):
        """Init an instance of ToolInput."""
        self.name = tool_inp_desc['name']
        if 'type' not in tool_inp_desc:
            raise ValueError("No type for the parameter %s" % tool_inp_desc['name'])
        self.type = tool_inp_desc['type']
        self.tool_inp_desc = tool_inp_desc
        self.level = level
        self.wf_param_values = wf_param_values
        self.wf_steps = wf_steps
        self.formatted_desc = ''
        self.force_default = force_default

        if self.name not in self.wf_param_values:
            if not should_be_there:
                info("%s not in workflow" % self.name)
            else:
                raise ValueError("%s not in workflow" % (self.name))
        else:
            self.wf_param_values = self.wf_param_values[self.name]

    def get_formatted_inputs(self):
        """Format the inputs of a step."""
        inputlist = ''
        inps = []
        if isinstance(self.wf_param_values, list):
            # multiple input (not collection)
            icon = 'param-files'
            for i in self.wf_param_values:
                inps.append('`%s` %s' % (
                    i['output_name'],
                    get_input_tool_name(i['id'], self.wf_steps)))
        else:
            inp = self.wf_param_values
            if 'id' in inp:
                # sinle input or collection
                inp_type = self.wf_steps[str(inp['id'])]['type']
                if 'collection' in inp_type:
                    icon = 'param-collection'
                else:
                    icon = 'param-file'
                inps = ['`%s` %s' % (
                    inp['output_name'],
                    get_input_tool_name(inp['id'], self.wf_steps))]
        if len(inps) > 0:
            inputlist += templates.render(INPUT_FILE_TEMPLATE, **{
                "icon": icon,
                "input_name": self.tool_inp_desc['label'],
                "input_value": ', '.join(inps),
                "space": SPACE * self.level
            })
        return inputlist

    def get_lower_param_desc(self):
        """Get the formatted description of the paramaters in the 'inputs' of the tool description."""
        sub_param_desc = ''
        for inp in self.tool_inp_desc["inputs"]:
            tool_inp = ToolInput(
                inp,
                self.wf_param_values,
                self.wf_steps,
                self.level + 1)
            sub_param_desc += tool_inp.get_formatted_desc()
        return sub_param_desc

    def get_formatted_section_desc(self):
        """Format the description (label and value) for parameters in a section."""
        section_paramlist = ''
        sub_param_desc = self.get_lower_param_desc()
        if sub_param_desc != '':
            section_paramlist += templates.render(INPUT_SECTION, **{
                'space': SPACE * self.level,
                'section_label': self.tool_inp_desc['title']})
            section_paramlist += sub_param_desc
        return section_paramlist

    def get_formatted_conditional_desc(self):
        """Format the description (label and value) for parameters in a conditional."""
        conditional_paramlist = ''
        # Get conditional parameter
        inp = ToolInput(
            self.tool_inp_desc['test_param'],
            self.wf_param_values,
            self.wf_steps,
            self.level,
            should_be_there=True,
            force_default=True)
        conditional_paramlist = inp.get_formatted_desc()
        cond_param = inp.wf_param_values

        # Get parameters in the when and their values
        tmp_tool_inp_desc = self.tool_inp_desc
        for case in tmp_tool_inp_desc['cases']:
            if case['value'] == cond_param and len(case['inputs']) > 0:
                self.tool_inp_desc = case
                conditional_paramlist += self.get_lower_param_desc()
        self.tool_inp_desc = tmp_tool_inp_desc
        return conditional_paramlist

    def get_formatted_repeat_desc(self):
        """Format the description (label and value) for parameters in a repeat."""
        repeat_paramlist = ''
        if self.wf_param_values != '[]':
            tool_inp = {}
            for inp in self.tool_inp_desc["inputs"]:
                tool_inp.setdefault(inp['name'], inp)
            tmp_wf_param_values = self.wf_param_values
            cur_level = self.level
            for ind, param in enumerate(tmp_wf_param_values):
                self.wf_param_values = param
                self.level = cur_level + 1
                paramlist_in_repeat = self.get_lower_param_desc()
                if paramlist_in_repeat != '':
                    # add first click
                    repeat_paramlist += templates.render(INPUT_ADD_REPEAT, **{
                        'space': SPACE * (self.level),
                        'repeat_label': self.tool_inp_desc['title']})
                    repeat_paramlist += paramlist_in_repeat
                self.level = cur_level
            self.wf_param_values = tmp_wf_param_values

        repeat_desc = ''
        if repeat_paramlist != '':
            repeat_desc += templates.render(INPUT_SECTION, **{
                'space': SPACE * self.level,
                'section_label': self.tool_inp_desc['title']}) + repeat_paramlist
        return repeat_desc

    def get_formatted_other_param_desc(self):
        """Get value of a 'simple' parameter if different from the default value, None otherwise."""
        param_value = None
        if self.tool_inp_desc['value'] == self.wf_param_values and not self.force_default:
            param_value = None
        elif self.type == 'boolean':
            if bool(self.tool_inp_desc['value']) == self.wf_param_values:
                param_value = None
            else:
                param_value = 'Yes' if self.wf_param_values else 'No'
        elif self.type == 'select':
            param_values = []
            for opt in self.tool_inp_desc['options']:
                if opt[1] == self.wf_param_values:
                    param_values.append(opt[0])
            param_value = ', '.join(param_values)
        elif self.type == 'data_column':
            param_value = "c%s" % self.wf_param_values
        else:
            param_value = self.wf_param_values

        param_desc = ''
        if param_value is not None:
            param_desc = templates.render(INPUT_PARAM, **{
                'space': SPACE * self.level,
                'param_label': self.tool_inp_desc['label'],
                'param_value': param_value})
        return param_desc

    def get_formatted_desc(self):
        """Get the formatted description (ready for hands-on tutorial) of the parameter."""
        if self.wf_param_values:
            if self.type == 'data' or self.type == 'data_collection':
                self.formatted_desc += self.get_formatted_inputs()
            elif self.type == 'section':
                self.formatted_desc += self.get_formatted_section_desc()
            elif self.type == 'conditional':
                self.formatted_desc += self.get_formatted_conditional_desc()
            elif self.type == 'repeat':
                self.formatted_desc += self.get_formatted_repeat_desc()
            else:
                self.formatted_desc += self.get_formatted_other_param_desc()
        return self.formatted_desc


def get_input_tool_name(step_id, steps):
    """Get the string with the name of the tool that generated an input."""
    inp_provenance = ''
    inp_prov_id = str(step_id)
    if inp_prov_id in steps:
        name = steps[inp_prov_id]['name']
        if 'Input dataset' in name:
            inp_provenance = "(%s)" % name
        else:
            inp_provenance = "(output of **%s** {%% icon tool %%})" % name
    return inp_provenance


def get_empty_input():
    """Get the string for an empty input."""
    return templates.render(INPUT_FILE_TEMPLATE, **{
        'space': 1 * SPACE,
        'icon': 'param-file',
        'input_name': 'Input file',
        'input_value': 'File'
    })


def get_empty_param():
    """Get the string for an empty param."""
    return templates.render(INPUT_PARAM, **{
        'space': 1 * SPACE,
        'param_label': 'Parameter',
        'param_value': 'a value'
    })