roc-film 1.13.5__py3-none-any.whl → 1.14.0__py3-none-any.whl

roc/film/tasks/check_dds.py

@@ -4,17 +4,17 @@
 """
 Contains task to check for SolO MOC DDS files.
 """
+
 import os
 from glob import glob
 
-from edds_process.response import \
-    count_packets
+from edds_process.response import count_packets
 
 from poppy.core.task import Task
 from poppy.core.logger import logger
 from poppy.core.target import FileTarget
 
-__all__ = ['CheckDds']
+__all__ = ["CheckDds"]
 
 
 class CheckDds(Task):
@@ -22,59 +22,59 @@ class CheckDds(Task):
     Task to check and load every SolO MOC DDS XML files found into
     a given input directory or list of files.
     """
-    plugin_name = 'roc.film'
-    name = 'check_dds'
+
+    plugin_name = "roc.film"
+    name = "check_dds"
 
     def add_targets(self):
-        self.add_output(identifier='dds_xml_files', many=True,
-                        target_class=FileTarget)
+        self.add_output(identifier="dds_xml_files", many=True, target_class=FileTarget)
 
     def run(self):
-
         # Get optional filters from input keywords
-        no_tmraw = self.pipeline.get('no_tmraw', default=False)
-        no_tcreport = self.pipeline.get('no_tcreport', default=False)
+        no_tmraw = self.pipeline.get("no_tmraw", default=False)
+        no_tcreport = self.pipeline.get("no_tcreport", default=False)
 
         if no_tmraw and no_tcreport:
-            logger.warning('"no-tmraw" and "no-tcreport" input keywords cannot be both '
-                           'set to True')
+            logger.warning(
+                '"no-tmraw" and "no-tcreport" input keywords cannot be both set to True'
+            )
             self.pipeline.exit()
 
         # Get input directory containing DDS file(s)
-        input_dir = self.pipeline.get('input_dir')
+        input_dir = self.pipeline.get("input_dir")
         if input_dir:
-            self.dds_xml_list = glob(os.path.join(input_dir, '*.xml'))
-        elif self.pipeline.get('dds_files'):
-            self.dds_xml_list = self.pipeline.get('dds_files')
+            self.dds_xml_list = glob(os.path.join(input_dir, "*.xml"))
+        elif self.pipeline.get("dds_files"):
+            self.dds_xml_list = self.pipeline.get("dds_files")
         else:
-            logger.warning(
-                'No valid input argument passed to the CheckDds Task')
+            logger.warning("No valid input argument passed to the CheckDds Task")
             self.pipeline.exit()
 
         # Filtering input DDS files
-        self.dds_xml_list = self.filtering_dds(self.dds_xml_list,
-                                               no_tcreport=no_tcreport,
-                                               no_tmraw=no_tmraw)
+        self.dds_xml_list = self.filtering_dds(
+            self.dds_xml_list, no_tcreport=no_tcreport, no_tmraw=no_tmraw
+        )
 
         # Check if no DDS file
         self.dds_xml_num = len(self.dds_xml_list)
         if self.dds_xml_num == 0:
             self.dds_packet_num_list = []
             self.dds_packet_num = 0
-            logger.warning(f'No input DDS file found')
+            logger.warning("No input DDS file found")
         else:
-            logger.debug('Getting total number of packets...')
-            self.dds_packet_num_list = [count_packets(current_dds)
-                                        for current_dds in self.dds_xml_list]
+            logger.debug("Getting total number of packets...")
+            self.dds_packet_num_list = [
+                count_packets(current_dds) for current_dds in self.dds_xml_list
+            ]
             self.dds_packet_num = sum(self.dds_packet_num_list)
-            logger.info(f'{self.dds_xml_num} DDS file(s) with {self.dds_packet_num} packets loaded')
+            logger.info(
+                f"{self.dds_xml_num} DDS file(s) with {self.dds_packet_num} packets loaded"
+            )
 
-        self.outputs['dds_xml_files'].filepath = self.dds_xml_list
+        self.outputs["dds_xml_files"].filepath = self.dds_xml_list
 
     @staticmethod
-    def filtering_dds(dds_xml_list,
-                      no_tmraw=False,
-                      no_tcreport=False):
+    def filtering_dds(dds_xml_list, no_tmraw=False, no_tcreport=False):
         """
         Filter input DDS files.
 
@@ -86,32 +86,26 @@ class CheckDds(Task):
 
         # Filtering input DDS file(s)
         for current_file in dds_xml_list:
-            file_pattern = os.path.splitext(
-                os.path.basename(current_file))[0].lower()
-            if 'tmraw' in file_pattern and not no_tmraw:
+            file_pattern = os.path.splitext(os.path.basename(current_file))[0].lower()
+            if "tmraw" in file_pattern and not no_tmraw:
                 output_list.append(current_file)
-                logger.debug(f'{current_file} added to the list')
-            elif 'tcreport' in file_pattern and not no_tcreport:
+                logger.debug(f"{current_file} added to the list")
+            elif "tcreport" in file_pattern and not no_tcreport:
                 output_list.append(current_file)
-                logger.debug(f'{current_file} added to the list')
+                logger.debug(f"{current_file} added to the list")
 
         return output_list
 
     def loop_generator(self, loop):
-
-        # Get pipeline
-        pipeline = loop.pipeline
-
         # Get list of dds XML files
-        dds_xml_list = loop.inputs['dds_xml_files'].filepath
+        dds_xml_list = loop.inputs["dds_xml_files"].filepath
         if dds_xml_list is None or len(dds_xml_list) == 0:
-            logger.info('No input DDS file for loop')
+            logger.info("No input DDS file for loop")
             return
 
         # Loop over each DDS file in the list
-        for i, dds_file_target in enumerate(loop.inputs['dds_xml_files']):
-
+        for i, dds_file_target in enumerate(loop.inputs["dds_xml_files"]):
             # pass DDS to first task in the pipeline workflow loop
-            dds_file_target.link('dds_xml')
+            dds_file_target.link("dds_xml")
 
             yield

roc/film/tasks/db_to_anc_bia_sweep_table.py

@@ -0,0 +1,381 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""Contains task to create the RPW ANC Bias sweep table CDF files."""
+
+import csv
+import os
+import uuid
+from datetime import datetime
+import pandas as pd
+from sqlalchemy import and_
+
+from poppy.core.logger import logger
+from poppy.core import TargetFileNotSaved
+from poppy.core.db.connector import Connector
+from poppy.core.generic.cache import CachedProperty
+from poppy.core.target import FileTarget
+from poppy.core.task import Task
+
+from roc.dingo.models.data import EventLog
+from roc.dingo.tools import valid_time, query_db, get_columns
+
+from roc.film import TIME_DAILY_STRFORMAT, TIME_ISO_STRFORMAT
+from roc.film.constants import (
+    PIPELINE_DATABASE,
+    TRYOUTS,
+    SQL_LIMIT,
+    TIME_WAIT_SEC,
+    BIA_SWEEP_TABLE_PACKETS,
+)
+from roc.film.tools import get_datasets
+from roc.film.tools.file_helpers import get_output_dir, is_output_dir, generate_filepath
+from roc.film.tools.metadata import set_logical_file_id
+
+__all__ = ["DbToAncBiaSweepTable"]
+
+
+class DbToAncBiaSweepTable(Task):
+    """
+    Task to generate ANC bias sweep table file from pipeline.event_log table data.
+
+    For more information about the Bias sweeping, see section 'BIAS sweeping' of
+    the RPW DAS User Manual (RPW-SYS-MEB-DPS-NTT-000859-LES)
+
+    """
+
+    plugin_name = "roc.film"
+    name = "db_to_anc_bia_sweep_table"
+
+    csv_fieldnames = [
+        "TC_EXE_UTC_TIME",
+        "BIA_SWEEP_TABLE_CUR",
+        "EEPROM_LOADING",
+        "TC_NAME",
+        "TC_EXE_STATE",
+    ]
+
+    def add_targets(self):
+        self.add_output(target_class=FileTarget, identifier="anc_bia_sweep_table")
+
+    def setup_inputs(self):
+        # get a database session, table model and table columns (except primary key)
+        self.session = Connector.manager[PIPELINE_DATABASE].session
+        self.model = EventLog
+        self.columns = get_columns(self.model, remove=["id"])
+
+        # Get tryouts from pipeline properties
+        self.tryouts = self.pipeline.get("tryouts", default=[TRYOUTS], create=True)[0]
+
+        # Get wait from pipeline properties
+        self.wait = self.pipeline.get("wait", default=[TIME_WAIT_SEC], create=True)[0]
+
+        # Retrieve --limit keyword value
+        self.limit = self.pipeline.get(
+            "limit",
+            default=[SQL_LIMIT],
+        )[0]
+
+        # Get products directory (folder where final output files will be
+        # moved)
+        self.products_dir = self.pipeline.get(
+            "products_dir", default=[None], args=True
+        )[0]
+
+        # Get output dir
+        self.output_dir = get_output_dir(self.pipeline)
+        if not is_output_dir(self.output_dir, products_dir=self.products_dir):
+            logger.info(f"Making {self.output_dir}")
+            os.makedirs(self.output_dir)
+        else:
+            logger.debug(f"Output files will be saved into folder {self.output_dir}")
+
+        # Get or create failed_files list from pipeline properties
+        self.failed_files = self.pipeline.get("failed_files", default=[], create=True)
+
+        # Get or create processed_files list from pipeline properties
+        self.processed_files = self.pipeline.get(
+            "processed_files", default=[], create=True
+        )
+
+        # Get or create ignored_target list from pipeline properties
+        self.ignored_target = self.pipeline.get(
+            "ignored_target", default=[], create=True
+        )
+
+        # Get overwrite argument
+        self.overwrite = self.pipeline.get("overwrite", default=False, args=True)
+
+        # Get force optional keyword
+        self.force = self.pipeline.get("force", default=False, args=True)
+
+        # Retrieve output dataset to produce for the task (it should be one)
+        self.dataset = get_datasets(self, self.name)[0]
+        logger.debug(
+            f"Produce file(s) for the following dataset: {self.dataset['name']}"
+        )
+
+        # Get start_time input value
+        self.start_time = valid_time(
+            self.pipeline.get("start_time", default=[None])[0],
+            format=TIME_DAILY_STRFORMAT,
+        )
+
+        # Get end_time input value
+        self.end_time = valid_time(
+            self.pipeline.get("end_time", default=[None])[0],
+            format=TIME_DAILY_STRFORMAT,
+        )
+
+        # Define query filters for existing data in database
+        self.filters = []
+        if self.start_time:
+            self.filters.append(self.model.start_time >= str(self.start_time))
+        if self.end_time:
+            self.filters.append(self.model.end_time < str(self.end_time))
+
+        return True
+
+    @CachedProperty
+    def output_filepath(self):
+        # Build output filename using metadata
+        filename_items = {}
+        filename_items["File_naming_convention"] = (
+            "<Source_name>_<LEVEL>_<Descriptor>_<Datetime>_V<Data_version>"
+        )
+        filename_items["Source_name"] = "SOLO>Solar Orbiter"
+        filename_items["Descriptor"] = "RPW-BIA-SWEEP-TABLE>RPW Bias sweep table report"
+        filename_items["LEVEL"] = "ANC>Ancillary data"
+        filename_items["Data_version"] = self.dataset["version"]
+
+        filename_items["Datetime"] = (
+            self.start_time.strftime(TIME_DAILY_STRFORMAT)
+            + "-"
+            + self.end_time.strftime(TIME_DAILY_STRFORMAT)
+        )
+        filename_items["Logical_file_id"] = set_logical_file_id(filename_items)
+        return generate_filepath(
+            self,
+            filename_items,
+            "csv",
+            output_dir=self.output_dir,
+            overwrite=self.overwrite,
+        )
+
+    def run(self):
+        # Define task job ID (long and short)
+        self.job_uuid = str(uuid.uuid4())
+        self.job_id = f"{self.job_uuid[:8]}"
+        logger.info(f"Task {self.job_id} is starting")
+        try:
+            self.setup_inputs()
+        except Exception:
+            logger.exception(f"Initializing inputs has failed for {self.job_id}!")
+            try:
+                os.makedirs(os.path.join(self.output_dir, "failed"))
+            except Exception:
+                logger.error("output_dir argument is not defined!")
+            self.pipeline.exit()
+            return
+
+        # First retrieve sweep table data from pipeline.event_log table
+        self.filters.append(self.model.label.in_(BIA_SWEEP_TABLE_PACKETS))
+        logger.debug(
+            f"Getting existing event_log data between {self.start_time} and {self.end_time}"
+        )
+        # Return existing data as a pandas.DataFrame object
+        table_data = query_db(
+            self.session,
+            self.model,
+            filters=and_(*self.filters),
+            tryouts=self.tryouts,
+            wait=self.wait,
+            limit=self.limit,
+        )
+        n_data = table_data.shape[0]
+        if n_data == 0:
+            logger.warning("No sweep table TC found in the database")
+            return
+        else:
+            logger.info(f"{n_data} sweep table TCs found in the database")
+            # Prepare table data to be saved in the CSV file
+            table_data = DbToAncBiaSweepTable.prep_sweep_table(table_data)
+
+            # Convert current list to string values separated by ;
+            table_data["BIA_SWEEP_TABLE_CUR"] = table_data["BIA_SWEEP_TABLE_CUR"].apply(
+                lambda x: na_to_str(x)
+            )
+
+        if not self.start_time:
+            self.start_time = table_data["TC_EXE_UTC_TIME"].min()
+            self.end_time = table_data["TC_EXE_UTC_TIME"].max()
+
+        # Write output CSV file
+        output_filepath = self.output_filepath
+        logger.info(f"Writing {output_filepath}...")
+        try:
+            with open(output_filepath, "w", newline="") as csvfile:
+                table_data.to_csv(csvfile, sep=",")
+        except Exception:
+            if output_filepath not in self.failed_files:
+                self.failed_files.append(output_filepath)
+            raise TargetFileNotSaved(
+                "Anc Bias sweep table csv file production has failed!"
+            )
+
+        if not os.path.isfile(output_filepath):
+            if output_filepath not in self.failed_files:
+                self.failed_files.append(output_filepath)
+            raise FileNotFoundError(f"{output_filepath} not found")
+        else:
+            logger.info(f"{output_filepath} saved")
+            if output_filepath not in self.processed_files:
+                self.processed_files.append(output_filepath)
+
+        self.outputs["anc_bia_sweep_table"] = output_filepath
+
+    @staticmethod
+    def parse_bia_sweep_table_file(sweep_table_file):
+        """
+        Parse an input bia sweep table CSV file
+
+        :param sweep_table_file: File to parse
+        :return: list of sweep tables
+        """
+
+        # Initialize output list
+        sweep_table_list = []
+
+        if not os.path.isfile(sweep_table_file):
+            logger.error(f"{sweep_table_file} not found!")
+        else:
+            # Read file and store in output list
+            with open(sweep_table_file, "r", newline="") as csv_file:
+                reader = csv.DictReader(csv_file)
+
+                # Loop over rows
+                for row in reader:
+                    row["TC_EXE_UTC_TIME"] = datetime.strptime(
+                        row["TC_EXE_UTC_TIME"], TIME_ISO_STRFORMAT
+                    )
+                    row["BIA_SWEEP_TABLE_CUR"] = row["BIA_SWEEP_TABLE_CUR"].split(";")
+                    sweep_table_list.append(row)
+
+        return sweep_table_list
+
+    @staticmethod
+    def get_latest_sweep_table(current_time, sweep_table_list):
+        """
+        Get the latest sweep table for a given datetime
+
+        :param current_time: Time for which sweep table must be returned (datetime object)
+        :param sweep_table_list: list of sweep tables (pandas.DataFrame)
+        :return: row of the sweep table list
+        """
+
+        w = (sweep_table_list["TC_EXE_STATE"] == "PASSED") & (
+            sweep_table_list["TC_EXE_UTC_TIME"] <= current_time
+        )
+        output_table = sweep_table_list[w]
+
+        if output_table.shape[0] > 0:
+            output_table = output_table.iloc[-1]
+
+        return output_table
+
+    @staticmethod
+    def prep_sweep_table(table_data):
+        """
+        Preprocess sweep table data coming from pipeline.event_log
+        to be compatible with output CSV content
+
+        :param table_data:  Sweep table data
+                            extracted from event_log table
+                            (Pandas.DataFrame object as returned by query_db())
+        :return: modified table_data
+        """
+        n_data = table_data.shape[0]
+        # First, sort by ascending start_time
+        table_data.sort_values(by=["start_time"], inplace=True, ignore_index=True)
+
+        # rename some columns
+        table_data.rename(
+            columns={
+                "start_time": "TC_EXE_UTC_TIME",
+                "label": "TC_NAME",
+            },
+            inplace=True,
+        )
+
+        # add columns for TC_EXE_STATE, EEPROM_LOADING and BIA_SWEEP_TABLE_CUR
+        new_data = {
+            "TC_EXE_STATE": ["PASSED"] * n_data,
+            "EEPROM_LOADING": [
+                int(row["sweep_eeprom"] is True) for row in table_data["description"]
+            ],
+            "BIA_SWEEP_TABLE_CUR": [
+                row["sweep_step_na"] for row in table_data["description"]
+            ],
+        }
+        table_data = pd.concat([table_data, pd.DataFrame.from_dict(new_data)], axis=1)
+
+        # delete unwanted columns
+        for table_col in [
+            "id",
+            "end_time",
+            "is_predictive",
+            "description",
+            "insert_time",
+        ]:
+            del table_data[table_col]
+
+        # Convert current values from string to float
+        table_data["BIA_SWEEP_TABLE_CUR"] = table_data["BIA_SWEEP_TABLE_CUR"].apply(
+            str_to_float
+        )
+
+        return table_data
+
+
+def na_to_str(bia_current):
+    """
+
+    :param bia_current:
+    :return:
+    """
+    if not bia_current:
+        return ""
+    else:
+        return ";".join([str(current) for current in bia_current])
+
+
+def str_to_float(str_values):
+    """
+    Convert string(s) to float(s)
+    (with some extra rules)
+
+    :param str_values: string value(s) to convert
+    :return: converted float value(s)
+    """
+    if not str_values:
+        return None
+
+    is_list = isinstance(str_values, list)
+    if not is_list:
+        out_values = [str_values]
+    else:
+        out_values = str_values
+
+    for i, out_value in enumerate(out_values):
+        if out_value:
+            if out_value == "nan":
+                out_values[i] = None
+            else:
+                out_values[i] = float(out_value)
+        else:
+            out_values[i] = None
+
+    if not is_list:
+        out_values = out_values[0]
+
+    return out_values