flowcraft/generator/engine.py
def _update_secondary_channels(self, p):
        """Given a process, this method updates the
        :attr:`~Process.secondary_channels` attribute with the corresponding
        secondary inputs of that channel.

        The rationale of the secondary channels is the following:

            - Start storing any secondary emitting channels, by checking the
              `link_start` list attribute of each process. If there are
              channel names in the link start, it adds to the secondary
              channels dictionary.
            - Check for secondary receiving channels, by checking the
              `link_end` list attribute. If the link name starts with a
              `__` signature, it will created an implicit link with the last
              process with an output type after the signature. Otherwise,
              it will check is a corresponding link start already exists in
              the at least one process upstream of the pipeline and if so,
              it will update the ``secondary_channels`` attribute with the
              new link.

        Parameters
        ----------
        p : flowcraft.Process.Process
        """

        # Check if the current process has a start of a secondary
        # side channel
        if p.link_start:
            logger.debug("[{}] Found secondary link start: {}".format(
                p.template, p.link_start))
            for l in p.link_start:
                # If there are multiple link starts in the same lane, the
                # last one is the only one saved.
                if l in self.secondary_channels:
                    self.secondary_channels[l][p.lane] = {"p": p, "end": []}
                else:
                    self.secondary_channels[l] = {p.lane: {"p": p, "end": []}}

        # check if the current process receives a secondary side channel.
        # If so, add to the links list of that side channel
        if p.link_end:
            logger.debug("[{}] Found secondary link end: {}".format(
                p.template, p.link_end))
            for l in p.link_end:

                # Get list of lanes from the parent forks.
                parent_forks = self._get_fork_tree(p.lane)

                # Parse special case where the secondary channel links with
                # the main output of the specified type
                if l["link"].startswith("__"):
                    self._set_implicit_link(p, l)
                    continue

                # Skip if there is no match for the current link in the
                # secondary channels
                if l["link"] not in self.secondary_channels:
                    continue

                for lane in parent_forks:
                    if lane in self.secondary_channels[l["link"]]:
                        self.secondary_channels[
                            l["link"]][lane]["end"].append("{}".format(
                                "{}_{}".format(l["alias"], p.pid)))

        logger.debug("[{}] Secondary links updated: {}".format(
            p.template, self.secondary_channels))
def _update_secondary_channels(self, p):
        """Given a process, this method updates the
        :attr:`~Process.secondary_channels` attribute with the corresponding
        secondary inputs of that channel.

        The rationale of the secondary channels is the following:

            - Start storing any secondary emitting channels, by checking the
              `link_start` list attribute of each process. If there are
              channel names in the link start, it adds to the secondary
              channels dictionary.
            - Check for secondary receiving channels, by checking the
              `link_end` list attribute. If the link name starts with a
              `__` signature, it will created an implicit link with the last
              process with an output type after the signature. Otherwise,
              it will check is a corresponding link start already exists in
              the at least one process upstream of the pipeline and if so,
              it will update the ``secondary_channels`` attribute with the
              new link.

        Parameters
        ----------
        p : flowcraft.Process.Process
        """

        # Check if the current process has a start of a secondary
        # side channel
        if p.link_start:
            logger.debug("[{}] Found secondary link start: {}".format(
                p.template, p.link_start))
            for l in p.link_start:
                # If there are multiple link starts in the same lane, the
                # last one is the only one saved.
                if l in self.secondary_channels:
                    self.secondary_channels[l][p.lane] = {"p": p, "end": []}
                else:
                    self.secondary_channels[l] = {p.lane: {"p": p, "end": []}}

        # check if the current process receives a secondary side channel.
        # If so, add to the links list of that side channel
        if p.link_end:
            logger.debug("[{}] Found secondary link end: {}".format(
                p.template, p.link_end))
            for l in p.link_end:

                # Get list of lanes from the parent forks.
                parent_forks = self._get_fork_tree(p.lane)

                # Parse special case where the secondary channel links with
                # the main output of the specified type
                if l["link"].startswith("__"):
                    self._set_implicit_link(p, l)
                    continue

                # Skip if there is no match for the current link in the
                # secondary channels
                if l["link"] not in self.secondary_channels:
                    continue

                for lane in parent_forks:
                    if lane in self.secondary_channels[l["link"]]:
                        self.secondary_channels[
                            l["link"]][lane]["end"].append("{}".format(
                                "{}_{}".format(l["alias"], p.pid)))

        logger.debug("[{}] Secondary links updated: {}".format(
            p.template, self.secondary_channels))
Given a process, this method updates the
        :attr:`~Process.secondary_channels` attribute with the corresponding
        secondary inputs of that channel.

        The rationale of the secondary channels is the following:

            - Start storing any secondary emitting channels, by checking the
              `link_start` list attribute of each process. If there are
              channel names in the link start, it adds to the secondary
              channels dictionary.
            - Check for secondary receiving channels, by checking the
              `link_end` list attribute. If the link name starts with a
              `__` signature, it will created an implicit link with the last
              process with an output type after the signature. Otherwise,
              it will check is a corresponding link start already exists in
              the at least one process upstream of the pipeline and if so,
              it will update the ``secondary_channels`` attribute with the
              new link.

        Parameters
        ----------
        p : flowcraft.Process.Process