validationscript.py

#!/usr/bin/env python3
 
 
 
import re
import os
from typing import Optional, List
import logging
from pathlib import Path
 
# Import XML Parser. Use C-Version, if available
try:
    import xml.etree.cElementTree as XMLTree
except ImportError:
    import xml.etree.ElementTree as XMLTree
 
import json_objects
 
 
# todo [code quality, low prio, easy]: This should be an enum
class ScriptStatus:
 
    """!
    Enumeration of the states a script can be during its execution
    cycle
    """
 
    # script is waiting for execution
    class waiting:
        pass
 
    # script is running atm
    class running:
        pass
 
    # script execution has been successfully finished
    class finished:
        pass
 
    # script execution has failed
    class failed:
        pass
 
    # script has been marked to be skipped
    class skipped:
        pass
 
    # script output is already cached, do not execute script
    class cached:
        pass
 
 
class Script:
 
    """!
    The object representation of a steering file.
 
    @var path: The path to the steering file
    @var name: The name of the file, but without special chars or spaces
    @var package: The package to which the steering file belongs to
    @var header: The contents of the XML file header
    @var dependencies: On which scripts does the steering file depend
    @var status: The current status, e.g. 'running' or 'finished'
    @var control: Execute locally or on the cluster?
    @var returncode: The returncode of the steering file
    @var _object: Pointer to the object itself. Is this even necessary?
    """
 
    def __init__(
        self, path: str, package: str, log: Optional[logging.Logger] = None
    ):
        """!
        The default constructor.
        """
 
        # Pointer to the script object itself
        # Is this necessary?
        self._object = self
 
        # stores the reference to the logging object used in this validation
        # run
        if log is None:
            log = logging.Logger("script")
        self.log: logging.Logger = log
 
        # The (absolute) path of the steering file
        self.path = path
 
        # The runtime of the script
        self.runtime: Optional[int] = None
        self.start_time: Optional[int] = None
 
        # The name of the steering file. Basically the file name of the
        # steering file, but everything that is not a letter is replaced
        # by an underscore. Useful e.g. for cluster controls.
        self.name = self.sanitize_file_name(str(os.path.basename(self.path)))
        # useful when displaying the filename to the user
        self.name_not_sanitized = str(os.path.basename(self.path))
 
        # The package to which the steering file belongs
        self.package = package
 
        
        self._header = dict()
        
        self.header_parsing_errors = False
        
        self._header_parsing_attempted = False
 
        # A list of script objects, on which this script depends
        self.dependencies = []
 
        # Current status of the script.
        # Possible values: waiting, running, finished, failed, skipped
        self.status = ScriptStatus.waiting
 
        # Which control is used for executing the script, i.e. cluster or
        # local. Useful when using different script level, e.g. data creation
        # scripts are being run on the cluster, but plotting scripts are
        # executed locally
        self.control = None
 
        # The returncode of the script. Should be 0 if all went well.
        self.returncode: Optional[int] = None
 
        
        self.job_id: Optional[str] = None
 
    @staticmethod
    def sanitize_file_name(file_name):
        """!
        Replaces the . between the file name and extension with an underscore _
        """
        return re.sub(r"[\W_]+", "_", file_name)
 
    def to_json(self, current_tag):
 
        string_status = ""
 
        if self.status == ScriptStatus.failed:
            string_status = "failed"
        elif self.status == ScriptStatus.finished:
            string_status = "finished"
        elif self.status == ScriptStatus.running:
            string_status = "running"
        elif self.status == ScriptStatus.skipped:
            string_status = "skipped"
        elif self.status == ScriptStatus.waiting:
            string_status = "waiting"
        elif self.status == ScriptStatus.cached:
            string_status = "cached"
 
        # filter for simulated files
        input_file_names = [ip.split('/')[-1] for ip in self.input_files if '../' in ip]
        output_file_names = [op.split('/')[-1] for op in self.output_files if '../' in op]
 
        return json_objects.Script(
            self.name_not_sanitized,
            self.path,
            string_status,
            log_url=os.path.join(self.package, self.name_not_sanitized)
            + ".log",
            return_code=self.returncode,
            input=input_file_names,
            output=output_file_names,
        )
 
    def get_recursive_dependencies(self, scripts, level=0):
        """!
        Loops over all dependencies of this script and recursively retrieves
        their sub-dependencies
        """
 
        if level > 50:
            self.log.error(
                f"Recurisve dependency lookup reached level {level} and will "
                f"quit now. Possibly circular dependcencies in the validation "
                f"scripts ? "
            )
 
        all_deps = set()
        for dep in self.dependencies:
            # only add, if not already in the dependencies list
            all_deps.add(dep.name)
 
            next_level = level + 1
 
            # find script object
            dep_script = [x for x in scripts if x.name == dep.name]
            rec_deps = []
            if len(dep_script) == 1:
                rec_deps = dep_script[0].get_recursive_dependencies(
                    scripts, next_level
                )
            else:
                self.log.error(
                    f"Depending script with the name {dep.name} could not be "
                    f"found in the list of registered scripts. "
                )
 
            # only add, if not already in the dependencies list
            for rc in rec_deps:
                all_deps.add(rc)
 
        return all_deps
 
    def unique_name(self):
        """
        Generates a unique name from the package and name of the script
        which only occurs once in th whole validation suite
        """
        return f"script_unique_name_{self.package}_{self.name}"
 
    def compute_dependencies(self, scripts):
        """!
        Loops over the input files given in the header and tries to find the
        corresponding Script objects, which will then be stored in the
        script.dependencies-list
        @return: None
        """
        # Loop over all the dependencies given in the header information
        for root_file in self.input_files:
 
            # Find the script which is responsible for the creation of
            # the input file (in the same package or in validation folder)
            creator = find_creator(root_file, self.package, scripts, self.log)
 
            # If no creator could be found, raise an error!
            if creator is None:
                self.log.error(
                    f"Unmatched dependency for {self.path}: {root_file} "
                    f"has no creator! This means that we will have to skip "
                    f"this script."
                )
                self.status = ScriptStatus.skipped
 
            # If creator(s) could be found, add those scripts to the
            # list of scripts on which self depends
            else:
                self.dependencies += creator
 
        # remove double entries
        self.dependencies = list(set(self.dependencies))
 
    def load_header(self):
        """!
        This method opens the file given in self.path, tries to extract the
        XML-header of it and then parse it.
        It then fills the self.header variable with a dict containing the
        values that were read from the XML header.
        @return: None
        """
        if self._header_parsing_attempted:
            return
 
        self._header_parsing_attempted = True
 
        # Read the file as a whole
        # We specify encoding and errors here to avoid exceptions for people
        # with strange preferred encoding settings in their OS
        with open(self.path, encoding="utf-8", errors="replace") as data:
            steering_file_content = data.read()
 
        # Define the regex to extract everything between the <header>-tags
        pat = re.compile("(<header>.*?</header>)", re.DOTALL | re.M)
 
        # Apply the regex, i.e. filter out the <header>...</header> part of
        # each steering file.
        try:
            xml = pat.findall(steering_file_content)[0].strip()
        except IndexError:
            self.log.error("No file header found: " + self.path)
            self.header_parsing_errors = True
            return
 
        # Create an XML tree from the plain XML code.
        try:
            xml_tree = XMLTree.ElementTree(XMLTree.fromstring(xml)).getroot()
        except XMLTree.ParseError:
            self.log.error("Invalid XML in header: " + self.path)
            self.header_parsing_errors = True
            return
 
        # we have a header
        self._header = {}
 
        # Loop over that tree
        for branch in xml_tree:
 
            # The keywords that should be parsed into a list
            list_tags = ["input", "output", "contact"]
 
            # If the tag is empty branch.text is None. Replacing None with an
            # empty string in this case.
            branch_text = branch.text or ""
 
            # Format the values of each branch
            if branch.tag.strip() in list_tags:
                branch_value = [__.strip() for __ in branch_text.split(",")]
                if branch_value == [""]:
                    branch_value = []
            else:
                branch_value = re.sub(" +", " ", branch_text.replace("\n", ""))
                branch_value = branch_value.strip()
 
            # Append the branch and its values to the header-dict. This
            # implementation technically allows multiple occurrences of the
            # same <tag></tag>-pair, which will be bundled to the same key in
            # the key in the returned dictionary
            if branch.tag.strip() in self._header:
                self._header[branch.tag.strip()] += branch_value
            else:
                self._header[branch.tag.strip()] = branch_value
 
    # Below are all of the getter methods for accessing data from the header
    # If the header isn't loaded at the time they are called, we do that.
 
    @property
    def input_files(self):
        """
        return a list of input files which this script will read.
        This information is only available, if load_header has been called
        """
        self.load_header()
        return self._header.get("input", [])
 
    @property
    def output_files(self):
        """
        return a list of output files this script will create.
        This information is only available, if load_header has been called
        """
        self.load_header()
        return self._header.get("output", [])
 
    @property
    def is_cacheable(self):
        """
        Returns true, if the script must not be executed if its output
        files are already present.
        This information is only available, if load_header has been called
        """
        self.load_header()
        return "cacheable" in self._header
 
    @property
    def noexecute(self) -> bool:
        """ A flag set in the header that tells us to simply ignore this
        script for the purpose of running the validation.
        """
        self.load_header()
        return "noexecute" in self._header
 
    @property
    def description(self) -> str:
        """ Description of script as set in header """
        self.load_header()
        return self._header.get("description", "")
 
    @property
    def contact(self) -> str:
        """ Contact of script as set in header """
        self.load_header()
        return self._header.get("contact", "")
 
    @property
    def interval(self) -> str:
        """ Interval of script executation as set in header """
        self.load_header()
        return self._header.get("interval", "nightly")
 
    def remove_output_files(self) -> None:
        """Remove all output files. This is used to clean up files after a
        script is marked as failed. Leaving the output files in a possible
        corrupted state and risk having them found by the validation framework
        later for crashes isn't sensible.
        """
        for f in map(Path, self.output_files):
            self.log.warning(
                f"Removing output file {f} (if exists) because script failed"
            )
            f.unlink(missing_ok=True)
 
 
def find_creator(
    outputfile: str, package: str, scripts: List[Script], log: logging.Logger
) -> Optional[List[Script]]:
    """!
    This function receives the name of a file and tries to find the file
    in the given package which produces this file, i.e. find the file in
    whose header 'outputfile' is listed under <output></output>.
    It then returns a list of all Scripts who claim to be creating 'outputfile'
 
    @param outputfile: The file of which we want to know by which script is
        created
    @param package: The package in which we want to search for the creator
    @param scripts: List of all script objects/candidates
    @param log: Logger
    """
 
    # Get a list of all Script objects for scripts in the given package as well
    # as from the validation-folder
    candidates = [
        script
        for script in scripts
        if script.package in [package, "validation"]
    ]
 
    # Reserve some space for the results we will return
    results = []
 
    # Loop over all candidates and check if they have 'outputfile' listed
    # under their outputs
    for candidate in candidates:
        if outputfile in candidate.output_files:
            results.append(candidate)
 
    # Return our results and warn if there is more than one creator
    if len(results) == 0:
        return None
    if len(results) > 1:
        log.warning("Found multiple creators for" + outputfile)
    return results