Merge pull request #155 from biosimulators/combined_ids_for_multi_id_…

…xpaths

Allow the return of combined IDs for multi-id xpaths.

.github/workflows/ci.yml

@@ -38,10 +38,10 @@ jobs:
           fetch-depth: 1
 
       - name: Install Java # for pyNeuroML
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
-          distribution: 'adopt'
-          java-version: '15'
+          distribution: 'temurin'
+          java-version: '21'
 
       - name: Install Perl # for BioNetGen
         run: |
@@ -53,7 +53,7 @@ jobs:
           sudo apt-get install -y --no-install-recommends wget make gcc libx11-dev libc6-dev xppaut
 
       - name: Install Singularity # to validate that the Docker image can be converted into a Singularity image
-        uses: eWaterCycle/setup-singularity@v5
+        uses: eWaterCycle/setup-singularity@v7
         with:
           singularity-version: 3.7.1
 
@@ -67,15 +67,15 @@ jobs:
         run: poetry run python -m flake8
 
       - name: Run the tests
-        uses: GabrielBB/xvfb-action@v1
+        uses: coactions/setup-xvfb@v1
         env:
           MPLBACKEND: PDF
           # BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/  # uncomment to execute tests with the dev deployment
         with:
           run: poetry run python -m pytest tests/ --cov=./biosimulators_utils --cov-report=xml
 
       - name: Upload the coverage report to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           flags: unittests

biosimulators_utils/_version.py

@@ -1 +1 @@
-__version__ = '0.2.2'
+__version__ = '0.2.3'

biosimulators_utils/sedml/validation.py

@@ -1715,14 +1715,16 @@ def validate_target(target, namespaces, context, language, model_id, model_etree
     return errors, warnings
 
 
-def validate_target_xpaths(targets, model_etree, attr='id'):
+def validate_target_xpaths(targets, model_etree, attr='id', separator=None):
     """ Validate that the target of each model change or variable matches one object in
-    an XML-encoded model and, optionally, return the value of one of its attributes
+    an XML-encoded model and, optionally, return the value of one of its attributes.
 
     Args:
         targets (:obj:`list` of :obj:`TargetGroupMixin`): model changes or variables
         model_source (:obj:`lxml.etree._ElementTree`): element tree for the XML model document
         attr (:obj:`str`, optional): attribute to get values of
+        separator (:obj:`str`, optional): string to use when combining attributes into a single id
+          (i.e. 'J0.n' from 'J0' and 'n'.)  If None, don't combine and just use final id.
 
     Returns:
         :obj:`dict` of :obj:`str` to :obj:`str`: dictionary that maps each XPath to the
@@ -1736,6 +1738,17 @@ def validate_target_xpaths(targets, model_etree, attr='id'):
                 x_path, _, _ = x_path.rpartition('/@')
             x_path_attrs[target.target] = validate_xpaths_ref_to_unique_objects(
                 model_etree, [x_path], target.target_namespaces, attr=attr)[x_path]
+    if separator is None:
+        return x_path_attrs
+    for xpath in x_path_attrs:
+        xpath_list = xpath.split("@" + attr + "=")
+        if len(xpath_list) < 3:
+            continue
+        combined_id = ""
+        for i in range(1, len(xpath_list)-1):
+            combined_id = combined_id + xpath_list[i].split(']')[0][1:-1] + separator
+        x_path_attrs[xpath] = combined_id + x_path_attrs[xpath]
+
     return x_path_attrs
 
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biosimulators-utils"
-version = "0.2.2"
+version = "0.2.3"
 description = "description"
 license = "MIT"
 authors = ["Center for Reproducible Biomedical Modeling <[email protected]>"]