flowcraft/generator/inspect.py
def _update_process_stats(self):
        """Updates the process stats with the information from the processes

        This method is called at the end of each static parsing of the nextflow
        trace file. It re-populates the :attr:`process_stats` dictionary
        with the new stat metrics.
        """

        good_status = ["COMPLETED", "CACHED"]

        for process, vals in self.trace_info.items():

            # Update submission status of tags for each process
            vals = self._update_tag_status(process, vals)

            # Update process resources
            self._update_process_resources(process, vals)

            self.process_stats[process] = {}

            inst = self.process_stats[process]

            # Get number of completed samples
            inst["completed"] = "{}".format(
                len([x for x in vals if x["status"] in good_status]))

            # Get average time
            try:
                time_array = [self._hms(x["realtime"]) for x in vals]
                mean_time = round(sum(time_array) / len(time_array), 1)
                mean_time_str = strftime('%H:%M:%S', gmtime(mean_time))
                inst["realtime"] = mean_time_str
            # When the realtime column is not present
            except KeyError:
                inst["realtime"] = "-"

            # Get cumulative cpu/hours
            try:
                cpu_hours = [self._cpu_load_parser(
                    x["cpus"], x["%cpu"], x["realtime"]) for x in vals]
                inst["cpuhour"] = round(sum(cpu_hours), 2)
            # When the realtime, cpus or %cpus column are not present
            except KeyError:
                inst["cpuhour"] = "-"

            # Assess resource warnings
            inst["cpu_warnings"], inst["mem_warnings"] = \
                self._assess_resource_warnings(process, vals)

            # Get maximum memory
            try:
                rss_values = [self._size_coverter(x["rss"]) for x in vals
                              if x["rss"] != "-"]
                if rss_values:
                    max_rss = round(max(rss_values))
                    rss_str = self._size_compress(max_rss)
                else:
                    rss_str = "-"
                inst["maxmem"] = rss_str
            except KeyError:
                inst["maxmem"] = "-"

            # Get read size
            try:
                rchar_values = [self._size_coverter(x["rchar"]) for x in vals
                                if x["rchar"] != "-"]
                if rchar_values:
                    avg_rchar = round(sum(rchar_values) / len(rchar_values))
                    rchar_str = self._size_compress(avg_rchar)
                else:
                    rchar_str = "-"
            except KeyError:
                rchar_str = "-"
            inst["avgread"] = rchar_str

            # Get write size
            try:
                wchar_values = [self._size_coverter(x["wchar"]) for x in vals
                                if x["wchar"] != "-"]
                if wchar_values:
                    avg_wchar = round(sum(wchar_values) / len(wchar_values))
                    wchar_str = self._size_compress(avg_wchar)
                else:
                    wchar_str = "-"
            except KeyError:
                wchar_str = "-"
            inst["avgwrite"] = wchar_str
def _update_process_stats(self):
        """Updates the process stats with the information from the processes

        This method is called at the end of each static parsing of the nextflow
        trace file. It re-populates the :attr:`process_stats` dictionary
        with the new stat metrics.
        """

        good_status = ["COMPLETED", "CACHED"]

        for process, vals in self.trace_info.items():

            # Update submission status of tags for each process
            vals = self._update_tag_status(process, vals)

            # Update process resources
            self._update_process_resources(process, vals)

            self.process_stats[process] = {}

            inst = self.process_stats[process]

            # Get number of completed samples
            inst["completed"] = "{}".format(
                len([x for x in vals if x["status"] in good_status]))

            # Get average time
            try:
                time_array = [self._hms(x["realtime"]) for x in vals]
                mean_time = round(sum(time_array) / len(time_array), 1)
                mean_time_str = strftime('%H:%M:%S', gmtime(mean_time))
                inst["realtime"] = mean_time_str
            # When the realtime column is not present
            except KeyError:
                inst["realtime"] = "-"

            # Get cumulative cpu/hours
            try:
                cpu_hours = [self._cpu_load_parser(
                    x["cpus"], x["%cpu"], x["realtime"]) for x in vals]
                inst["cpuhour"] = round(sum(cpu_hours), 2)
            # When the realtime, cpus or %cpus column are not present
            except KeyError:
                inst["cpuhour"] = "-"

            # Assess resource warnings
            inst["cpu_warnings"], inst["mem_warnings"] = \
                self._assess_resource_warnings(process, vals)

            # Get maximum memory
            try:
                rss_values = [self._size_coverter(x["rss"]) for x in vals
                              if x["rss"] != "-"]
                if rss_values:
                    max_rss = round(max(rss_values))
                    rss_str = self._size_compress(max_rss)
                else:
                    rss_str = "-"
                inst["maxmem"] = rss_str
            except KeyError:
                inst["maxmem"] = "-"

            # Get read size
            try:
                rchar_values = [self._size_coverter(x["rchar"]) for x in vals
                                if x["rchar"] != "-"]
                if rchar_values:
                    avg_rchar = round(sum(rchar_values) / len(rchar_values))
                    rchar_str = self._size_compress(avg_rchar)
                else:
                    rchar_str = "-"
            except KeyError:
                rchar_str = "-"
            inst["avgread"] = rchar_str

            # Get write size
            try:
                wchar_values = [self._size_coverter(x["wchar"]) for x in vals
                                if x["wchar"] != "-"]
                if wchar_values:
                    avg_wchar = round(sum(wchar_values) / len(wchar_values))
                    wchar_str = self._size_compress(avg_wchar)
                else:
                    wchar_str = "-"
            except KeyError:
                wchar_str = "-"
            inst["avgwrite"] = wchar_str
Updates the process stats with the information from the processes

        This method is called at the end of each static parsing of the nextflow
        trace file. It re-populates the :attr:`process_stats` dictionary
        with the new stat metrics.