Merge v0.2.2 to develop branch

las_geoh5/__init__.py

@@ -6,12 +6,11 @@
 #  (see LICENSE file at the root of this source code package).
 #
 
-# flake8: noqa
-
 from __future__ import annotations
 
 from pathlib import Path
 
+
 __version__ = "0.3.0-alpha.1"
 
 
@@ -25,3 +24,9 @@ def assets_path() -> Path:
         raise RuntimeError(f"Assets folder not found: {assets_folder}")
 
     return assets_folder
+
+
+__all__ = [
+    "__version__",
+    "assets_path",
+]

las_geoh5/import_files/driver.py

@@ -17,14 +17,13 @@
 from pathlib import Path
 from shutil import move
 
-import lasio
 from geoh5py import Workspace
 from geoh5py.shared.utils import fetch_active_workspace
 from geoh5py.ui_json import InputFile
 from tqdm import tqdm
 
 from las_geoh5.import_files.params import ImportOptions, NameOptions
-from las_geoh5.import_las import las_to_drillhole
+from las_geoh5.import_las import las_to_drillhole, lasio_read
 
 
 _logger = logging.getLogger(__name__)
@@ -113,11 +112,7 @@ def run(params_json: Path, output_geoh5: Path | None = None):
                     for file in tqdm(
                         ifile.data["files"].split(";"), desc="Reading LAS files"
                     ):
-                        futures.append(
-                            pool.apply_async(
-                                lasio.read, (file,), {"mnemonic_case": "preserve"}
-                            )
-                        )
+                        futures.append(pool.apply_async(lasio_read, (file,)))
 
                     lasfiles = [future.get() for future in futures]
 

las_geoh5/import_las.py

@@ -9,6 +9,7 @@
 from __future__ import annotations
 
 import logging
+import re
 from pathlib import Path
 from typing import Any
 
@@ -24,6 +25,9 @@
 from las_geoh5.import_files.params import ImportOptions, NameOptions
 
 
+_logger = logging.getLogger(__name__)
+
+
 class LASTranslator:
     """Translator for the weakly standardized LAS file standard."""
 
@@ -182,7 +186,7 @@
         survey = Path(survey)
 
     if survey.suffix == ".las":
-        file = lasio.read(survey, mnemonic_case="preserve")
+        file = lasio_read(survey)
         try:
             surveys = np.c_[get_depths(file)["depth"], file["DIP"], file["AZIM"]]
             if len(drillhole.surveys) == 1:
@@ -309,6 +313,8 @@
         translator = LASTranslator(NameOptions())
 
     name = translator.retrieve("well_name", lasfile)
+    if not isinstance(name, str):
+        name = str(name)
     if not name and logger is not None:
         logger.warning(
             "No well name provided for LAS file. "
@@ -414,3 +420,116 @@
             new_row = drillhole.surveys[0, :]
             new_row[0] = np.max(depths)
             drillhole.surveys = np.vstack([drillhole.surveys, new_row])
+
+
+def _patch_lasio_reader():
+    """Patch lasio.reader.configure_metadata_patterns to handle edge cases."""
+
+    # patch only once
+    if getattr(lasio.reader, "patched_configure_metadata_patterns", False):
+        return
+
+    _logger.debug("Patching lasio.reader.configure_metadata_patterns")
+
+    # TODO: Propose change on lasio to fix possible version issue
+
+    def configure_metadata_patterns(line, section_name):  # pylint: disable=too-many-locals
+        """Configure regular-expression patterns to parse section meta-data lines.
+
+        # OVERLOAD lasio.reader.configure_metadata_patterns
+
+        Arguments:
+            line (str): line from LAS header section
+            section_name (str): Name of the section the 'line' is from.
+
+        Returns:
+            An array of regular-expression strings (patterns).
+        """
+
+        # Default return value
+        patterns = []
+
+        # Default regular expressions for name, value and desc fields
+        name_re = r"\.?(?P<name>[^.]*)\."
+        value_re = r"(?P<value>.*):"
+        desc_re = r"(?P<descr>.*)"
+
+        # Default regular expression for unit field. Note that we
+        # attempt to match "1000 psi" as a special case which allows
+        # a single whitespace character, in contradiction to the LAS specification
+        # See GitHub issue #363 for details.
+        if "VERS" in line:
+            unit_re = r"(?P<unit>\D*)"
+        else:
+            unit_re = r"(?P<unit>([0-9]+\s)?[^\s]*)"
+
+        # Alternate regular expressions for special cases
+        name_missing_period_re = r"(?P<name>[^:]*):"
+        value_missing_period_re = r"(?P<value>.*)"
+        value_without_colon_delimiter_re = r"(?P<value>[^:]*)"
+        value_with_time_colon_re = (
+            r"(?P<value>.*?)(?:(?<!( [0-2][0-3]| hh| HH)):(?!([0-5][0-9]|mm|MM)))"
+        )
+        name_with_dots_re = r"\.?(?P<name>[^.].*[.])\."
+        no_desc_re = ""
+        no_unit_re = ""
+
+        # Configure special cases
+        # 1. missing period (assume that only name and value are present)
+        # 2. missing colon delimiter and description field
+        # 3. double_dots '..' caused by mnemonic abbreviation (with period)
+        #    next to the dot delimiter.
+        if ":" in line:
+            if "." not in line[: line.find(":")]:
+                # If there is no period, then we assume that the colon exists and
+                # everything on the left is the name, and everything on the right
+                # is the value - therefore no unit or description field.
+                name_re = name_missing_period_re
+                value_re = value_missing_period_re
+                desc_re = no_desc_re
+                unit_re = no_unit_re
+                value_with_time_colon_re = value_missing_period_re
+
+        if ":" not in line:
+            # If there isn't a colon delimiter then there isn't
+            # a description field either.
+            value_re = value_without_colon_delimiter_re
+            desc_re = no_desc_re
+
+            if ".." in line and section_name == "Curves":
+                name_re = name_with_dots_re
+        else:
+            if re.search(r"[^ ]\.\.", line) and section_name == "Curves":
+                double_dot = line.find("..")
+                desc_colon = line.rfind(":")
+
+                # Check that a double_dot is not in the
+                # description string.
+                if double_dot < desc_colon:
+                    name_re = name_with_dots_re
+
+        if section_name == "Parameter":
+            # Search for a value entry with a time-value first.
+            pattern = name_re + unit_re + value_with_time_colon_re + desc_re
+            patterns.append(pattern)
+
+        # Add the regular pattern for all section_names
+        # for the Parameter section this will run after time-value pattern
+        pattern = name_re + unit_re + value_re + desc_re
+        patterns.append(pattern)
+
+        return patterns
+
+    lasio.reader.configure_metadata_patterns = configure_metadata_patterns
+    lasio.reader.patched_configure_metadata_patterns = True
+
+
+def lasio_read(file):
+    """Read a LAS file using lasio.
+
+    Wrapper around lasio.read that patches the reader to handle some
+    edge cases in LAS files.
+    """
+
+    _patch_lasio_reader()
+    return lasio.read(file, mnemonic_case="preserve")

tests/import_las_test.py

@@ -415,3 +415,35 @@ def test_warning_no_well_name(tmp_path: Path, caplog):
         )
 
         assert match in caplog.text
+
+
+def test_handle_numeric_well_name(tmp_path: Path):
+    with Workspace.create(tmp_path / "test.geoh5") as workspace:
+        dh_group = DrillholeGroup.create(workspace, name="dh_group")
+
+    lasfile = generate_lasfile(
+        "123",
+        {"UTMX": 0.0, "UTMY": 0.0, "ELEV": 10.0},
+        np.arange(0, 11, 1),
+        {"my_property": np.zeros(11)},
+    )
+    lasfile = write_lasfile(tmp_path, lasfile)
+
+    filepath = write_import_params_file(
+        tmp_path / "import_las_files.ui.json",
+        dh_group,
+        "my_property_group",
+        [lasfile],
+        (
+            "UTMX",
+            "UTMY",
+            "ELEV",
+        ),
+    )
+
+    module = importlib.import_module("las_geoh5.import_files.driver")
+    module.run(filepath)
+
+    with workspace.open():
+        dh_group = workspace.get_entity("dh_group")[0]
+        assert "123" in [k.name for k in dh_group.children]

tests/script_las_to_geoh5_test.py

@@ -19,6 +19,7 @@
 from .helpers import generate_lasfile, write_import_params_file, write_lasfile
 
 
+# pylint: disable=duplicate-code
 @pytest.fixture(scope="module", name="lasfile")
 def lasfile_fixture(tmp_path_factory) -> Path:
     input_dir = tmp_path_factory.mktemp("input")
@@ -75,6 +76,7 @@ def test_las_to_geoh5_without_output_name(
     """Test the las_to_geoh5 script."""
 
     workspace_file = input_workspace.h5file
+    assert isinstance(workspace_file, Path)
     modified_date = workspace_file.stat().st_mtime
 
     with patch("sys.argv", ["las_to_geoh5", str(params_filepath)]):
@@ -93,6 +95,7 @@ def test_las_to_geoh5_with_monitoring_folder(
     """Test the las_to_geoh5 script."""
 
     workspace_file = input_workspace.h5file
+    assert isinstance(workspace_file, Path)
     modified_date = workspace_file.stat().st_mtime
 
     monitoring_folder = tmp_path / "monitored here"
@@ -124,6 +127,7 @@ def test_las_to_geoh5_with_output_name(
     """Test the las_to_geoh5 script."""
 
     workspace_file = input_workspace.h5file
+    assert isinstance(workspace_file, Path)
     modified_date = workspace_file.stat().st_mtime
 
     working_dir = tmp_path / "working"
@@ -150,6 +154,7 @@ def test_las_to_geoh5_with_absolute_output_path(
     """Test the las_to_geoh5 script."""
 
     workspace_file = input_workspace.h5file
+    assert isinstance(workspace_file, Path)
     modified_date = workspace_file.stat().st_mtime
 
     output_dir = tmp_path / "output"