add whale example, allow examples to get data registry files (#348)

dascore/data_registry.txt

@@ -17,3 +17,4 @@ brady_hs_DAS_DTS_coords.csv b2e766136aac6516ddbb757d7dc26a8df0d5de48af03c8be769c
 dispersion_event.h5 598c8baa2a5610c930e1c003f2ba02da13f8d8686e3ccf2a034e94bfc5e1990c https://github.com/dasdae/test_data/raw/master/das/dispersion_event.h5
 PoroTomo_iDAS_1.h5 967a2885e79937ac0426b2022a9c03d5f24790ecf3abbaa9a16eb28055566fc6 https://github.com/dasdae/test_data/raw/master/das/PoroTomo_iDAS_1.h5
 DASDMSShot00_20230328155653619.das 12ac53f78b32d8b0e32cc674c43ff5b4c79a6c8b19de2ad577fd481679b2b7b3 https://github.com/dasdae/test_data/raw/master/das/DASDMSShot00_20230328155653619.das
+whale_1.hdf5 a09922969e740307bf26dc6ffa7fb9fbb834dc7cd7d4ced02c66b159fb1ce0cd http://piweb.ooirsn.uw.edu/das/data/Optasense/NorthCable/TransmitFiber/North-C1-LR-P1kHz-GL50m-Sp2m-FS200Hz_2021-11-03T15_06_51-0700/North-C1-LR-P1kHz-GL50m-Sp2m-FS200Hz_2021-11-04T020002Z.h5

dascore/examples.py

@@ -3,6 +3,7 @@
 
 import tempfile
 from collections.abc import Sequence
+from contextlib import suppress
 from pathlib import Path
 
 import numpy as np
@@ -413,10 +414,20 @@ def get_example_patch(example_name="random_das", **kwargs) -> dc.Patch:
     print(df.to_markdown(index=False, stralign="center"))
     ```
 
+    Using an entry from the data_registry file is also supported.
+    If multiple patches are contained in the specified file, only the
+    first is returned. Data registry files are:
+    ```{python}
+    #| echo: false
+    #| output: asis
+    from dascore.utils.downloader import get_registry_df
+    print(get_registry_df()[['name']].to_markdown(index=False, stralign="center"))
+    ```
+
     Parameters
     ----------
     example_name
-        The name of the example to load. Options are:
+        The name of the example to load. Options are listed above.
     **kwargs
         Passed to the corresponding functions to generate data.
 
@@ -426,6 +437,9 @@ def get_example_patch(example_name="random_das", **kwargs) -> dc.Patch:
         unregistered patch is requested.
     """
     if example_name not in EXAMPLE_PATCHES:
+        # Allow the example name to be a data registry entry.
+        with suppress(ValueError):
+            return dc.spool(fetch(example_name))[0]
         msg = (
             f"No example patch registered with name {example_name} "
             f"Registered example patches are {list(EXAMPLE_PATCHES)}"
@@ -451,6 +465,15 @@ def get_example_spool(example_name="random_das", **kwargs) -> dc.BaseSpool:
     print(df.to_markdown(index=False, stralign="center"))
     ```
 
+    Using an entry from the data_registry file is also supported.
+    These include:
+    ```{python}
+    #| echo: false
+    #| output: asis
+    from dascore.utils.downloader import get_registry_df
+    print(get_registry_df()[['name']].to_markdown(index=False, stralign="center"))
+    ```
+
     Parameters
     ----------
     example_name
@@ -460,9 +483,13 @@ def get_example_spool(example_name="random_das", **kwargs) -> dc.BaseSpool:
 
     Raises
     ------
-        UnknownExample if unregistered patch is requested.
+    (`UnknownExampleError`)['dascore.examples.UnknownExampleError`] if
+        unregistered patch is requested.
     """
     if example_name not in EXAMPLE_SPOOLS:
+        # Allow the example spool to be a data registry file.
+        with suppress(ValueError):
+            return dc.spool(fetch(example_name))
         msg = (
             f"No example spool registered with name {example_name} "
             f"Registered example spools are {list(EXAMPLE_SPOOLS)}"

dascore/io/prodml/utils.py

@@ -115,7 +115,7 @@ def _get_prodml_attrs(fi, extras=None) -> list[dict]:
         t_coord = _get_time_coord(node)
         info.update(t_coord.get_attrs_dict("time"))
         info.update(_get_data_unit_and_type(node))
-        info["dims"] = ["time", "distance"]
+        info["dims"] = _get_dims(node)
         if extras is not None:
             info.update(extras)
         info["coords"] = {"time": t_coord, "distance": d_coord}

tests/test_examples.py

@@ -37,6 +37,11 @@ def test_sin_wav(self):
         out = dc.get_example_patch("sin_wav")
         assert isinstance(out, dc.Patch)
 
+    def test_data_file_name(self):
+        """Ensure get_example_spool works on a datafile."""
+        spool = dc.get_example_spool("dispersion_event.h5")
+        assert isinstance(spool, dc.BaseSpool)
+
 
 class TestGetExampleSpool:
     """Test suite for `get_example_spool`."""
@@ -51,6 +56,11 @@ def test_raises_on_bad_key(self):
         with pytest.raises(UnknownExampleError, match="No example spool"):
             dc.get_example_spool("NotAnExampleRight????")
 
+    def test_data_file_name(self):
+        """Ensure get_example_spool works on a datafile."""
+        spool = dc.get_example_spool("dispersion_event.h5")
+        assert isinstance(spool, dc.BaseSpool)
+
 
 class TestRickerMoveout:
     """Tests for Ricker moveout patch."""

tests/test_io/test_common_io.py

@@ -71,6 +71,9 @@
 # only flat patches can be written to WAV, don't put it here.
 COMMON_IO_WRITE_TESTS = (PickleIO(), DASDAEV1())
 
+# Specifies data registry entries which should not be tested.
+SKIP_DATA_FILES = {"whale_1.hdf5", "brady_hs_DAS_DTS_coords.csv"}
+
 
 @cache
 def _cached_read(path, io=None):
@@ -111,10 +114,10 @@ def io_path_tuple(request):
 @pytest.fixture(scope="session", params=get_registry_df()["name"])
 def data_file_path(request):
     """A fixture of all data files. Will download if needed."""
-    # TODO remove this segy skip once we support it.
     param = request.param
-    if param.endswith("csv"):
-        pytest.skip("Not a DAS file.")
+    # Some files should be skipped if not DAS or too big.
+    if str(param) in SKIP_DATA_FILES:
+        pytest.skip(f"Skipping {param}")
     return fetch(request.param)