Add TRY skills

.claude-plugin/marketplace.json

@@ -6,7 +6,7 @@
   },
   "metadata": {
     "description": "Skills for grounding environmental and biological research terms to ontologies and extracting variables from ESS-DIVE",
-    "version": "0.2.3"
+    "version": "0.2.4"
   },
   "plugins": [
     {
@@ -35,6 +35,15 @@
       "skills": [
         "./skills/essdive-search"
       ]
+    },
+    {
+      "name": "try-skills",
+      "description": "Skills for discovering datasets, traits, and species information from the TRY plant trait database",
+      "source": "./",
+      "strict": false,
+      "skills": [
+        "./skills/try-skills"
+      ]
     }
   ]
 }

bioepic_skills/test/test_try_parser.py

@@ -0,0 +1,22 @@
+from bioepic_skills.try_parser import parse_try_species_text
+
+
+def test_parse_try_species_text():
+    sample = (
+        "AccSpeciesID\tAccSpeciesName\tObsNum\tObsGRNum\tMeasNum\tMeasGRNum\tTraitNum\n"
+        "271060\tAa achalensis\t5\t\t5\t\t3\n"
+        "200002\tAa argyrolepis\t7\t\t9\t\t3\n"
+    )
+
+    records = parse_try_species_text(sample)
+
+    assert len(records) == 2
+    assert records[0].acc_species_id == 271060
+    assert records[0].acc_species_name == "Aa achalensis"
+    assert records[0].obs_num == 5
+    assert records[0].obs_gr_num is None
+    assert records[0].meas_num == 5
+    assert records[0].meas_gr_num is None
+    assert records[0].trait_num == 3
+    assert records[0].pub_num is None
+    assert records[0].acc_spec_num is None

bioepic_skills/test/test_try_parser_datasets.py

@@ -0,0 +1,18 @@
+from bioepic_skills.try_parser import parse_try_datasets_html_with_header
+
+
+def test_parse_try_datasets_html_with_header():
+    html = """
+    <table>
+      <tr><th>DatasetID</th><th>Dataset</th><th>Description</th></tr>
+      <tr><td>1</td><td>Example</td><td>Example dataset</td></tr>
+      <tr><td>2</td><td>Second</td><td>Another dataset</td></tr>
+    </table>
+    """
+
+    header, records = parse_try_datasets_html_with_header(html)
+
+    assert header == ["DatasetID", "Dataset", "Description"]
+    assert len(records) == 2
+    assert records[0]["DatasetID"] == "1"
+    assert records[0]["Dataset"] == "Example"

bioepic_skills/test/test_try_parser_datasets_entries.py

@@ -0,0 +1,34 @@
+from bioepic_skills.try_parser import parse_try_dataset_entries_html
+
+
+def test_parse_try_dataset_entries_html():
+    html = """
+    <table>
+      <tr><td><b>Title: </b></td><td>TRY - Categorical Traits Dataset</td></tr>
+      <tr><td><b>TRY File Archive ID: </b></td><td>3</td></tr>
+      <tr><td><b>Rights of use: </b></td><td>Public, CC.BY.3.0</td></tr>
+      <tr><td><b>Publication Date: </b></td><td>2012-03-19</td></tr>
+      <tr><td><b>Version: </b></td><td>1.0</td></tr>
+      <tr><td><b>Author: </b></td><td>Jens Kattge</td></tr>
+      <tr><td><b>Contributors: </b></td><td>TRY Consortium</td></tr>
+      <tr><td><b>Reference to publication: </b></td><td>TRY - a global database</td></tr>
+      <tr><td><b>Reference to data package: </b></td><td>TRY File Archive</td></tr>
+      <tr><td><b>DOI: </b></td><td>10.17871/TRY.3</td></tr>
+      <tr><td><b>Format: </b></td><td>Zipped archive</td></tr>
+      <tr><td><b>File name: </b></td><td>TRY_Categorical_Traits.zip</td></tr>
+      <tr><td><b>Description: </b></td><td>Categorical traits</td></tr>
+      <tr><td><b>Geolocation: </b></td><td>Global</td></tr>
+      <tr><td><b>Temporal coverage: </b></td><td>Holocene</td></tr>
+      <tr><td><b>Taxonomic coverage: </b></td><td>terrestrial vascular plants</td></tr>
+      <tr><td><b>Field list: </b></td><td>AccSpeciesID, AccSpeciesName, Genus</td></tr>
+    </table>
+    """
+
+    entries = parse_try_dataset_entries_html(html)
+
+    assert len(entries) == 1
+    entry = entries[0]
+    assert entry.title == "TRY - Categorical Traits Dataset"
+    assert entry.try_file_archive_id == "3"
+    assert entry.doi == "10.17871/TRY.3"
+    assert entry.field_list == ["AccSpeciesID", "AccSpeciesName", "Genus"]

bioepic_skills/test/test_try_parser_species_list.py

@@ -0,0 +1,8 @@
+from bioepic_skills.try_parser import parse_try_species_list_text
+
+
+def test_parse_try_species_list_text():
+    sample = "\nAa achalensis\n\nAa argyrolepis\n"
+    species = parse_try_species_list_text(sample)
+
+    assert species == ["Aa achalensis", "Aa argyrolepis"]

bioepic_skills/test/test_try_parser_traits.py

@@ -0,0 +1,29 @@
+from bioepic_skills.try_parser import parse_try_traits_html
+
+
+def test_parse_try_traits_html():
+    html = """
+    <table>
+      <tr>
+        <th>TraitID</th><th>Trait</th><th>ObsNum</th><th>ObsGRNum</th><th>PubNum</th><th>AccSpecNum</th>
+      </tr>
+      <tr>
+        <td>2957</td><td>Bark calcium (Ca) content per bark dry mass</td>
+        <td>30</td><td>30</td><td>30</td><td>5</td>
+      </tr>
+      <tr>
+        <td>617</td><td>Bark carbon (C) content per bark dry mass</td>
+        <td>772</td><td>534</td><td>772</td><td>274</td>
+      </tr>
+    </table>
+    """
+
+    records = parse_try_traits_html(html)
+
+    assert len(records) == 2
+    assert records[0].trait_id == 2957
+    assert records[0].trait.startswith("Bark calcium")
+    assert records[0].obs_num == 30
+    assert records[0].obs_gr_num == 30
+    assert records[0].pub_num == 30
+    assert records[0].acc_spec_num == 5