bugfixes and cleanup

matthiasprobst · Sep 26, 2023 · f74b385 · f74b385
1 parent b812be2
commit f74b385
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Showing 7 changed files with 50 additions and 77 deletions.
diff --git a/docs/conventions/examples/EngMeta.ipynb b/docs/conventions/examples/EngMeta.ipynb
@@ -322,8 +322,8 @@
        "\n",
        "              <ul style=\"list-style-type: none;\" class=\"h5grp-sections\">\n",
        "                    <li>\n",
-       "                        <input id=\"group-ds--5757953000\" type=\"checkbox\" checked>\n",
-       "                        <label style=\"font-weight: bold\" for=\"group-ds--5757953000\">\n",
+       "                        <input id=\"group-ds--9176614900\" type=\"checkbox\" checked>\n",
+       "                        <label style=\"font-weight: bold\" for=\"group-ds--9176614900\">\n",
        "                        /<span>(0)</span></label>\n",
        "                  \n",
        "\n",

diff --git a/docs/conventions/examples/EngMeta.yaml b/docs/conventions/examples/EngMeta.yaml
@@ -89,7 +89,7 @@ description:
 keywords:
   description: List of describing keywords.
   target_method: __init__
-  validator: $list_of_str
+  validator: List[str]
   default_value: $NONE
 
 $subject:

diff --git a/docs/howto/ht004.ipynb b/docs/howto/ht004.ipynb
@@ -6,7 +6,7 @@
    "metadata": {},
    "source": [
     "# ... add an affix-function to a standard name table during runtime?\n",
-    "If you are using the [standard name convention](../conventions/standard_name_convention.ipynb) you are familiar with transformation functions like \"derivative_of_\\<SN1\\>_wrt_\\<SN2\\>\" or \"square_of_\\<SN\\>\".\n",
+    "If you are using the [standard name convention](../conventions/standard_attributes_and_conventions.ipynb) you are familiar with transformation functions like \"derivative_of_\\<SN1\\>_wrt_\\<SN2\\>\" or \"square_of_\\<SN\\>\".\n",
     "\n",
     "Now, you want to add your custom transformation function without changing the package code. Say, you want to add the transformation \"maximum_of_<StdName>\", referring to the maximum value of your data.\n",
     "\n",
@@ -15,7 +15,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "id": "791af21d-0c99-4d0b-bb0b-b5f59ecb1c8c",
    "metadata": {},
    "outputs": [
@@ -59,7 +59,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "id": "dc0db89c-c3b9-4c41-87dc-6a5ae91fc356",
    "metadata": {},
    "outputs": [],
@@ -83,7 +83,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "id": "e10d2b65-b6ea-42ce-909d-a375a0ba71ed",
    "metadata": {},
    "outputs": [],
@@ -101,7 +101,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "id": "9f9d5fa2-9dfa-46ff-bc9b-8b9db8f5870a",
    "metadata": {},
    "outputs": [
@@ -111,7 +111,7 @@
        "True"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -122,7 +122,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "id": "f54490f6-0272-4483-86f2-71fba12207c0",
    "metadata": {},
    "outputs": [
@@ -132,7 +132,7 @@
        "False"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -151,7 +151,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "id": "a5ae8c3a-3115-400f-bd02-3d75578c707a",
    "metadata": {},
    "outputs": [],
@@ -161,7 +161,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "id": "835d7ccb-afca-429a-a5f1-38b8a18e4230",
    "metadata": {},
    "outputs": [
@@ -170,8 +170,8 @@
       "text/html": [
        "<ul style=\"list-style-type: none;\" class=\"h5grp-sections\">\n",
        "    <li>\n",
-       "        <input id=\"group-maximum_of_static_pressure22629808100\" type=\"checkbox\" checked>\n",
-       "        <label style=\"font-weight: bold\" for=\"group-maximum_of_static_pressure22629808100\">\n",
+       "        <input id=\"group-maximum_of_static_pressure6668567300\" type=\"checkbox\" checked>\n",
+       "        <label style=\"font-weight: bold\" for=\"group-maximum_of_static_pressure6668567300\">\n",
        "        maximum_of_static_pressure</label>\n",
        "        <ul class=\"h5tb-attr-list\">\n",
        "           <li style=\"list-style-type: none; font-style: italic\">units : Pa</li>           <li style=\"list-style-type: none; font-style: italic\">description : Maximum of static_pressure. Static pressure refers to the force per unit area exerted by a fluid. Pressure is a scalar quantity.</li>      </il>\n",
@@ -182,7 +182,7 @@
        "<StandardName: \"maximum_of_static_pressure\" [Pa] Maximum of static_pressure. Static pressure refers to the force per unit area exerted by a fluid. Pressure is a scalar quantity.>"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -193,7 +193,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "id": "ccc894ff-2748-4e1b-9677-5b37d0b7d792",
    "metadata": {},
    "outputs": [
@@ -203,7 +203,7 @@
        "True"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -237,7 +237,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.17"
+   "version": "3.8.18"
   }
  },
  "nbformat": 4,

diff --git a/h5rdmtoolbox/conventions/references.py b/h5rdmtoolbox/conventions/references.py
@@ -1,15 +1,4 @@
-import json
 import requests
-import warnings
-from typing import Union
-
-BIBTEX_ENTRY_TYPES = ('article',
-                      'book',
-                      'booklet',
-                      'conference',
-                      'inbook',
-                      'incollection',
-                      'inproceedings',)
 
 
 def validate_url(url: str) -> bool:
@@ -32,35 +21,3 @@ def validate_url(url: str) -> bool:
     if response.status_code == 200:
         return True
     return False
-
-
-def validate_bibtex(bibtex: Union[str, dict]) -> bool:
-    """Validate BibTeX entry based on the mandatory keys.
-
-    Example entry:
-    bibtex = {'article': {'title': 'Title',
-                            'author': 'Author',
-                            'year': '2020',
-                            ...}
-                            }
-    """
-    if isinstance(bibtex, str):
-        bibtex = json.loads(bibtex)
-    mandatory_keys = ['title', 'author', 'year']
-    for entry_type, fields in bibtex.items():
-        if entry_type[0] == '@':
-            entry_type = entry_type[1:]
-        if entry_type.lower() not in BIBTEX_ENTRY_TYPES:
-            warnings.warn(f'Invalid BibTeX entry type: {entry_type}. Expected types: {BIBTEX_ENTRY_TYPES}')
-            return False
-        if not all(k in fields for k in mandatory_keys):
-            return False
-    return True
-
-
-def validate_reference(reference: str) -> bool:
-    if isinstance(reference, dict):
-        return validate_bibtex(reference)
-    if isinstance(reference, str) and reference[0] == '{':
-        return validate_bibtex(json.loads(reference))
-    return validate_url(reference)
diff --git a/h5rdmtoolbox/conventions/toolbox_validators.py b/h5rdmtoolbox/conventions/toolbox_validators.py
@@ -11,15 +11,6 @@
 from h5rdmtoolbox import get_ureg, errors
 
 
-def __validate_list_of_str(value, handler, info):
-    if not isinstance(value, list):
-        raise TypeError(f'Expected a list but got {type(value)}')
-    for v in value:
-        if not isinstance(v, str):
-            raise TypeError(f'Value {v} is not a string: {type(v)}')
-    return value
-
-
 def __validate_orcid(value, handler, info):
     from h5rdmtoolbox import orcid
     if not isinstance(value, str):
@@ -190,7 +181,6 @@ class IntValidator(BaseModel):
     value: Annotated[str, WrapValidator(_get_validate_type(int))]
 
 
-list_of_str = Annotated[str, WrapValidator(__validate_list_of_str)]
 units = Annotated[str, WrapValidator(__validate_units)]
 dateFormat = Annotated[str, WrapValidator(__validate_date_format)]
 quantity = Annotated[str, WrapValidator(__validate_quantity)]

diff --git a/tests/conventions/test_references.py b/tests/conventions/test_references.py
@@ -0,0 +1,22 @@
+"""Testing the standard attributes"""
+import pathlib
+import unittest
+
+from h5rdmtoolbox.conventions import references
+
+__this_dir__ = pathlib.Path(__file__).parent
+
+bibtext = """@ONLINE{hdf5group,
+    author = {{The HDF Group}},
+    title = "{Hierarchical Data Format, version 5}",
+    year = {1997-NNNN},
+    note = {https://www.hdfgroup.org/HDF5/},
+    addendum = "(accessed: 25.09.2023)",
+}"""
+
+
+class TestReferences(unittest.TestCase):
+
+    def test_url(self):
+        self.assertFalse(references.validate_url(123))
+
diff --git a/tests/conventions/test_toolbox_validators.py b/tests/conventions/test_toolbox_validators.py
@@ -4,6 +4,8 @@
 import pint
 import unittest
 from pydantic import BaseModel
+from pydantic import ValidationError
+from typing import List, Union
 
 import h5rdmtoolbox as h5tbx
 from h5rdmtoolbox.conventions import toolbox_validators
@@ -15,14 +17,16 @@ class TestTbxValidators(unittest.TestCase):
 
     def test_validate_list_of_str(self):
         class MyStr(BaseModel):
-            los: toolbox_validators.list_of_str
+            los: Union[str, List[str]]
 
-        with self.assertRaises(TypeError):
+        with self.assertRaises(ValidationError):
             MyStr(los=3.4)
-        with self.assertRaises(TypeError):
-            MyStr(los='3.4')
+
+        MyStr(los='3.4')
+
         MyStr(los=['3.4', 'str'])
-        with self.assertRaises(TypeError):
+
+        with self.assertRaises(ValidationError):
             MyStr(los=['3.4', 3.4])
 
         cv = h5tbx.conventions.from_yaml(__this_dir__ / 'ListOfStr.yaml', overwrite=True)