vortex-nwp 2.0.0__py3-none-any.whl

vortex/data/contents.py

@@ -0,0 +1,622 @@
+"""
+A handful of abstract and generic :class:`DataContent` classes designed to access
+and modify data of a given "Resource".
+
+These classes are not meant to be used directly. To retrieve a
+:class:`DataContent` object on a given "Resource", please use the
+:data:`vortex.data.handlers.Handler.contents` property.
+"""
+
+import collections
+from string import Template
+
+from bronx.fancies import loggers
+from bronx.stdtypes.dictionaries import ReadOnlyDict
+from bronx.stdtypes.xtemplates import DefaultTemplate
+from bronx.syntax.decorators import secure_getattr
+import footprints
+
+from vortex import sessions
+
+#: No automatic export
+__all__ = []
+
+logger = loggers.getLogger(__name__)
+
+
+class DataContentError(ValueError):
+    """General content error."""
+
+    pass
+
+
+class DataContent:
+    """Root class for data contents used by resources."""
+
+    _diffable = False
+
+    def __init__(self, **kw):
+        self._datafmt = None
+        self._data = None
+        self._metadata = ReadOnlyDict()
+        self._size = 0
+        for k, v in kw.items():
+            self.__dict__["_" + k] = v
+
+    @secure_getattr
+    def __getattr__(self, attr):
+        """Forward get attribute request to internal data object."""
+        if attr not in ("__getstate__", "__deepcopy__"):
+            return getattr(self.data, attr)
+        else:
+            raise AttributeError(attr)
+
+    def __enter__(self):
+        """Enter a :keyword:`with` context."""
+        pass
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        """Exit from :keyword:`with` context."""
+        pass
+
+    @property
+    def data(self):
+        """The internal data encapsulated."""
+        return self._data
+
+    @property
+    def size(self):
+        """The actual size of the contents."""
+        return self._size
+
+    @property
+    def metadata(self):
+        """Return the metadata of the ressource in the container (maybe empty)."""
+        return self._metadata
+
+    def metadata_check(self, resource, delta=None):
+        """Check that the metadata of the resource in the container matches
+        the attributes of the resource given as an argument.
+
+        Prior to the comparison, the delta argument will be added to the
+        attribute read in the container. For example, if delta=dict(date='-PT1H'),
+        we will in fact check that the date of the resource in the container is
+        one hour before the date specified in the resource's footprint.
+        """
+        if not len(self.metadata):
+            logger.error(
+                "Metadata check is not implemented for this format. "
+                + "The check will always succeed..."
+            )
+        delta = delta or {}
+        outcome = True
+        for mkey, mval in self.metadata.items():
+            if hasattr(resource, mkey):
+                cval = getattr(resource, mkey)
+                if mkey in delta:
+                    cval += delta[mkey]
+                outcome = outcome and cval == mval
+        if not outcome:
+            logger.warning(
+                "The ressource in the container doesn't match the resource footprint: %s",
+                str(self.metadata),
+            )
+        return outcome
+
+    @property
+    def datafmt(self):
+        """The initial format of the contents."""
+        return self._datafmt
+
+    @classmethod
+    def export_dict(cls):
+        """Return current class name for shell or pure dict export mechanism."""
+        return (cls.__module__, cls.__name__)
+
+    @property
+    def updated(self):
+        return False
+
+    def slurp(self, container):
+        """Should be overwritten. Basically get the totalsize of the actual container."""
+        self._size = container.totalsize
+
+    def _merge_checkclass(self, *kargs):
+        """Utility method to check that all the kargs objects are compatible self."""
+        if not all([isinstance(obj, self.__class__) for obj in kargs]):
+            raise DataContentError(
+                "The object's types are not compatible with self"
+            )
+
+    def merge(self, *kargs):
+        """Merge several DataContents into one.
+
+        This method have to be implemented and _merge_checkclass should be called
+        to ensure that the object's types are compatible with self.
+        """
+        raise NotImplementedError("Merge is not implemented for this content.")
+
+    @classmethod
+    def is_diffable(cls):
+        """Is the diff operation implemented for this content class ?"""
+        return cls._diffable
+
+    def diff(self, ref):
+        """Compare the present content with the ``ref`` content."""
+        if not self.is_diffable():
+            raise NotImplementedError(
+                "Diff is not implemented for this content"
+            )
+        else:
+            return self._actual_diff(ref)
+
+    def _actual_diff(self, ref):
+        """A very simple kind of comparison... but it might work !"""
+        return self.data == ref.data
+
+    def rewrite(self, container):
+        """Abstract method."""
+        pass
+
+
+class UnknownContent(DataContent):
+    """Fake DataContent subclass."""
+
+    pass
+
+
+class AlmostDictContent(DataContent):
+    """Implement some dictionary-like functions."""
+
+    # The very simple diff method form DataContent should do the job.
+    _diffable = True
+
+    def __init__(self, **kw):
+        super().__init__(**kw)
+        if self._data is None:
+            self._data = dict()
+
+    def fmtkey(self, key):
+        """Reshape entry keys of the internal dictionary."""
+        return key
+
+    def __getitem__(self, idx):
+        return self._data[self.fmtkey(idx)]
+
+    def __setitem__(self, idx, value):
+        self._data[self.fmtkey(idx)] = value
+
+    def __delitem__(self, idx):
+        del self._data[self.fmtkey(idx)]
+
+    def __len__(self):
+        return len(self._data)
+
+    def __iter__(self):
+        yield from self._data.keys()
+
+    def __contains__(self, item):
+        return self.fmtkey(item) in self._data
+
+    def has_key(self, item):
+        """Dict-like behavior looking for the formatted ``item`` in internal data."""
+        return item in self
+
+    def merge(self, *kargs):
+        """Merge several data contents into one."""
+        self._merge_checkclass(*kargs)
+        for obj in kargs:
+            self._data.update(obj.data)
+            self._size += obj.size
+
+
+class IndexedTable(AlmostDictContent):
+    """
+    Multi-columns table indexed by first column.
+    Behaves mostly as a dictionary.
+    """
+
+    def append(self, item):
+        """Insert data according to index position given as the first element of the ``item`` list."""
+        if len(item) > 0:
+            i = item.pop(0)
+            self._data[self.fmtkey(i)] = item
+
+    def extend(self, addlist):
+        """Insert data according to index position given as the first item of ``addlist``."""
+        for idxinput in addlist:
+            self.append(idxinput)
+
+    def slurp(self, container):
+        """Get data from the ``container``."""
+        with container.preferred_decoding(byte=False):
+            container.rewind()
+            self.extend(
+                [
+                    x.split()
+                    for x in container.readlines()
+                    if not x.startswith("#")
+                ]
+            )
+            self._size = container.totalsize
+
+
+class JsonDictContent(AlmostDictContent):
+    """
+    The internal data is supposed to be read from a json file.
+    """
+
+    def __init__(self, **kw):
+        self._bronx_tpl = None
+        super().__init__(**kw)
+
+    def slurp(self, container):
+        """Get data from the ``container``."""
+        t = sessions.current()
+        with container.preferred_decoding(byte=False):
+            container.rewind()
+            self._data = t.sh.json_load(container.iotarget())
+            self._size = container.totalsize
+
+    def bronx_tpl_render(self, **kwargs):
+        """Use :mod:`bronx.stdtypes.xtemplates` to render a JSON template."""
+        if self._bronx_tpl is None:
+            # Freeze the original data
+            self._bronx_tpl = self._data
+        # Start rendering and overwrite data
+        dt = DefaultTemplate(self._bronx_tpl)
+        self._data = dt.render(**kwargs)
+
+    def rewrite(self, container):
+        """Write the list contents in the specified container."""
+        t = sessions.current()
+        container.close()
+        # In Python 2, json.dumps returns 'str', not unicode...
+        with container.iod_context():
+            with container.preferred_decoding(byte=False):
+                with container.preferred_write():
+                    iod = container.iodesc()
+                    t.sh.json_dump(self.data, iod, indent=4)
+        container.updfill(True)
+
+
+class AlmostListContent(DataContent):
+    """
+    Implement some list-like functions.
+    The argument maxprint is used for the maximum number of lines
+    to display through the str function.
+    """
+
+    # The very simple diff method form DataContent should do the job.
+    _diffable = True
+
+    def __init__(self, **kw):
+        self._maxprint = kw.pop("maxprint", 20)
+        super().__init__(**kw)
+        if self._data is None:
+            self._data = list()
+
+    def __delitem__(self, idx):
+        del self.data[idx]
+
+    def __delslice__(self, istart, iend):
+        del self.data[istart:iend]
+
+    def __setitem__(self, idx, value):
+        self.data[idx] = value
+
+    def __setslice__(self, istart, iend, value):
+        self.data[istart:iend] = value
+
+    def __getitem__(self, idx):
+        return self.data[idx]
+
+    def __getslice__(self, istart, iend):
+        return self.data[istart:iend]
+
+    def __sizeof__(self):
+        return self.data.__sizeof__()
+
+    def __len__(self):
+        return len(self.data)
+
+    def __iter__(self):
+        yield from self.data
+
+    def __call__(self):
+        return self.data
+
+    def _get_maxprint(self):
+        return self._maxprint
+
+    def _set_maxprint(self, value):
+        try:
+            self._maxprint = abs(int(value))
+        except (ValueError, TypeError):
+            pass
+        self._maxprint = max(10, self._maxprint)
+
+    maxprint = property(_get_maxprint, _set_maxprint, None)
+
+    def clear(self):
+        """Clear all internal data contents."""
+        self._data[:] = []
+
+    def slurp(self, container):
+        """Get data from the ``container``."""
+        with container.preferred_decoding(byte=False):
+            self._data.extend(container.readlines())
+            self._size = container.totalsize
+
+    def rewrite(self, container):
+        """Write the list contents in the specified container."""
+        container.close()
+        with container.iod_context():
+            with container.preferred_decoding(byte=False):
+                for xline in self:
+                    container.write(xline)
+
+    def sort(self, **sort_opts):
+        """Sort the current object."""
+        self._data.sort(**sort_opts)
+
+    def merge(self, *kargs, **kwargs):
+        """Merge several data contents into one."""
+        unique = kwargs.get("unique", False)
+        self._merge_checkclass(*kargs)
+        for obj in kargs:
+            self.data.extend(obj.data)
+            self._size += obj.size
+        # Check if the item are unique, raise an error if not (option unique = True)
+        if unique:
+            arg_elements = collections.Counter(self.data)
+            repeated_elements = [
+                element for element, count in arg_elements.items() if count > 1
+            ]
+            if len(repeated_elements) > 0:
+                logger.exception(
+                    "Repeated argument are present. It should not. Stop."
+                    + "The list of the repeated elements follows: %s",
+                    str(sorted(repeated_elements)),
+                )
+                raise DataContentError(
+                    "Repeated argument are present. It should not."
+                )
+
+
+class TextContent(AlmostListContent):
+    """
+    Multi-lines input text data split through blank seperator.
+    Behaves mostly as a list.
+    """
+
+    def __init__(self, **kw):
+        kw.setdefault("fmt", None)
+        super().__init__(**kw)
+
+    def __str__(self):
+        if len(self) > self.maxprint:
+            catlist = self[0:3] + ["..."] + self[-3:]
+        else:
+            catlist = self[:]
+        return "\n".join([str(x) for x in catlist])
+
+    def slurp(self, container):
+        with container.preferred_decoding(byte=False):
+            self._data.extend(
+                [x.split() for x in container if not x.startswith("#")]
+            )
+            self._size = container.totalsize
+
+    def formatted_data(self, item):
+        """Return a formatted string according to optional internal fmt."""
+        if self._fmt is None:
+            return " ".join([str(x) for x in item])
+        else:
+            return self._fmt.format(*item)
+
+    def rewrite(self, container):
+        """Write the text contents in the specified container."""
+        container.close()
+        with container.iod_context():
+            with container.preferred_decoding(byte=False):
+                for item in self:
+                    container.write(self.formatted_data(item) + "\n")
+
+
+class DataRaw(AlmostListContent):
+    """
+    Multi-lines raw data (no format assumed).
+    Behaves mostly as a list.
+    """
+
+    def __init__(self, data=None, window=0, datafmt=None):
+        if not data and window:
+            data = collections.deque(maxlen=window)
+        super().__init__(data=data, window=window, datafmt=datafmt)
+
+    def slurp(self, container):
+        with container.preferred_decoding(byte=False):
+            container.rewind()
+            end = False
+            while not end:
+                data, end = container.dataread()
+                self._data.append(data)
+                if self._window and len(self._data) >= self._window:
+                    end = True
+
+
+class DataTemplate(DataContent):
+    """
+    Multi-lines data which fits to a template.
+    Behave mostly as a list.
+    """
+
+    def slurp(self, container):
+        """Actually read a container."""
+        with container.preferred_decoding(byte=False):
+            container.rewind()
+            self._data = container.read()
+            super().slurp(container)
+
+    def setitems(self, keyvaluedict):
+        """
+        Substitute the different keys contained in a dictionary into
+        the data content using a template.
+
+        :param dict keyvaluedict: things to be substituted.
+        """
+        data_tmp = Template(self._data)
+        self._data = data_tmp.substitute(keyvaluedict)
+
+    def rewrite(self, container):
+        """Write the list contents in the specified container."""
+        container.close()
+        with container.iod_context():
+            with container.preferred_decoding(byte=False):
+                container.write(self.data)
+
+
+class FormatAdapter(DataContent):
+    """Adapter to objects that could manage a dedicated format."""
+
+    def __init__(self, **kw):
+        super().__init__(**kw)
+        if self._data is None and footprints.proxy.dataformats is None:
+            logger.warning("No collector for data formats")
+            self._datafmt = None
+
+    def __enter__(self):
+        """
+        Enter a :keyword:`with` context, setting some FORTRAN variables
+        in order to switch off parallelism (in case of execution).
+        """
+        t = sessions.current()
+        t.env.delta(
+            LFI_HNDL_SPEC=":1",
+            DR_HOOK_SILENT=1,
+            DR_HOOK_NOT_MPI=1,
+            OMP_NUM_THREADS=1,
+        )
+        return self
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        """Exit from :keyword:`with` context."""
+        t = sessions.current()
+        t.env.rewind()
+
+    def slurp(self, container):
+        """Load a dataformat object."""
+        if self.datafmt:
+            with self:
+                self._data = footprints.proxy.dataformat(
+                    filename=container.abspath,
+                    openmode="r",
+                    fmtdelayedopen=True,
+                    format=container.actualfmt.upper(),
+                )
+                # Look for a metadatareader object
+                if (
+                    self._data is not None
+                    and footprints.proxy.metadatareaders is not None
+                ):
+                    mreader = footprints.proxy.metadatareader(
+                        format=container.actualfmt.upper(),
+                        _emptywarning=False,
+                    )
+                    if mreader is not None:
+                        mreader.content_init(self._data)
+                        self._metadata = mreader
+
+
+class MetaDataReader(footprints.FootprintBase):
+    """
+    Abstract class for any MetaDataReader.
+
+    Note: _do_delayed_init have to be subclassed. That's where the content of the
+    container is actually read.
+    """
+
+    _abstract = True
+    _collector = ("metadatareader",)
+    _footprint = dict(
+        info="Abstract MetaDataReader",
+        attr=dict(
+            format=dict(
+                type=str,
+            )
+        ),
+    )
+
+    def __init__(self, *kargs, **kwargs):
+        self._content_in = None
+        self._datahide = None
+        super().__init__(*kargs, **kwargs)
+
+    @property
+    def _data(self):
+        """Internal: check if one needs to intialise the _datahide dict."""
+        if self._datahide is None and self._content_in is not None:
+            self._do_delayed_init()
+        return self._datahide
+
+    def content_init(self, thecontent):
+        """Set the data content that will be used to read the metadata"""
+        self._content_in = thecontent
+
+    def _do_delayed_init(self):
+        """Internal: actually initialise the _data array. Have to be subclassed !"""
+        raise NotImplementedError
+
+    def __getitem__(self, key):
+        return self._data[key]
+
+    def __len__(self):
+        return len(self._data)
+
+    def __iter__(self):
+        return iter(self._data)
+
+    def items(self):
+        """Iterate over the metadata."""
+        for k in self:
+            yield k, self[k]
+
+    def __repr__(self):
+        if self._datahide is None:
+            return "{}: Not yet initialised".format(self.__class__)
+        else:
+            return repr(self._data)
+
+    def __str__(self):
+        return str(self._data)
+
+
+class FormatAdapterAbstractImplementation(footprints.FootprintBase):
+    """
+    The minimal set of attributes needed to create a class that is compatible
+    with the :class:`FormatAdapter` content.
+    """
+
+    _abstract = True
+    _collector = ("dataformat",)
+    _footprint = dict(
+        attr=dict(
+            filename=dict(
+                info="Path to the target data.",
+            ),
+            openmode=dict(
+                info="File open-mode.",
+                values=["r", "rw"],
+                default="r",
+                optional=True,
+            ),
+            fmtdelayedopen=dict(
+                info="Delay the opening of the listing file.",
+                type=bool,
+                default=True,
+                optional=True,
+            ),
+            format=dict(),
+        )
+    )