Merge pull request #21688 from bernt-matthias/conditional-requirements-templates

[26.0] Check file source template config files for determining conditional dependencies + add constraint for zero-ice

Author: bgruening

lib/galaxy/dependencies/__init__.py

@@ -20,6 +20,7 @@
     parse_xml,
     which,
 )
+from galaxy.util.config_templates import apply_syntactic_sugar
 from galaxy.util.properties import (
     find_config_file,
     load_app_properties,
@@ -151,14 +152,21 @@ def collect_types(from_dict):
 
         # Parse file sources config
         file_sources_conf_yml = self.config_object.file_sources_config_file
-
         if exists(file_sources_conf_yml):
             with open(file_sources_conf_yml) as f:
                 file_sources_conf = yaml.safe_load(f)
         else:
             file_sources_conf = []
         self.file_sources = [c.get("type", None) for c in file_sources_conf]
 
+        # Parse file source templates config
+        file_source_templates_conf_yml = self.config_object.file_source_templates_config_file
+        if exists(file_source_templates_conf_yml):
+            with open(file_source_templates_conf_yml) as f:
+                file_source_templates_conf = apply_syntactic_sugar(yaml.safe_load(f))
+            for file_source_template in file_source_templates_conf:
+                self.file_sources.append(file_source_template["configuration"].get("type"))
+
         # Parse vault config
         vault_conf_yml = self.config_object.vault_config_file
         if exists(vault_conf_yml):

lib/galaxy/dependencies/conditional-constraints.txt

@@ -0,0 +1,6 @@
+zeroc-ice @ https://github.com/ome/zeroc-ice-py-github-ci/releases/download/0.2.0/zeroc_ice-3.6.5-cp310-cp310-linux_x86_64.whl ; platform_system=="Linux" and python_version=="3.10" #type: omero
+zeroc-ice @ https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl ; platform_system=="Linux" and python_version=="3.11" #type: omero
+zeroc-ice @ https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp312-cp312-manylinux_2_28_x86_64.whl ; platform_system=="Linux" and python_version=="3.12" #type: omero
+zeroc-ice @ https://github.com/glencoesoftware/zeroc-ice-py-macos-universal2/releases/download/20240131/zeroc_ice-3.6.5-cp310-cp310-macosx_11_0_universal2.whl ; platform_system!="Windows" and platform_system!="Linux" and python_version=="3.10" #type: omero
+zeroc-ice @ https://github.com/glencoesoftware/zeroc-ice-py-macos-universal2/releases/download/20240131/zeroc_ice-3.6.5-cp311-cp311-macosx_11_0_universal2.whl ; platform_system!="Windows" and platform_system!="Linux" and python_version=="3.11" #type: omero
+zeroc-ice @ https://github.com/glencoesoftware/zeroc-ice-py-macos-universal2/releases/download/20240131/zeroc_ice-3.6.5-cp312-cp312-macosx_11_0_universal2.whl ; platform_system!="Windows" and platform_system!="Linux" and python_version=="3.12" #type: omero

lib/galaxy/dependencies/conditional-requirements.txt

@@ -33,7 +33,7 @@ fs-azureblob # type: azure
 rspace-client>=2.6.1,<3  # type: rspace
 adlfs
 huggingface_hub
-omero-py #type: omero # Requires manual installation of additional dependencies, see https://omero.readthedocs.io/en/stable/developers/Python.html#omero-python-language-bindings
+omero-py #type: omero
 
 # Vault backend
 hvac

scripts/common_startup.sh

@@ -210,7 +210,7 @@ if [ $FETCH_WHEELS -eq 1 ]; then
             echo "An older version of psycopg2 (non-binary, version 2.7.3) has been detected.  Galaxy now uses psycopg2-binary, which will be installed after removing psycopg2."
             ${PIP_CMD} uninstall ${UNINSTALL_OPTIONS} psycopg2 psycopg2-binary
         fi
-        echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | ${PIP_CMD} install -r /dev/stdin --extra-index-url "${GALAXY_WHEELS_INDEX_URL}"
+        echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | ${PIP_CMD} install -r /dev/stdin --extra-index-url "${GALAXY_WHEELS_INDEX_URL}" --constraint lib/galaxy/dependencies/conditional-constraints.txt
     fi
 fi