Feature/adds slash to r and dialogue#40
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…tions cleanly until later updated [R/OHDSIAssistant/R/strategus_cohort_methods_shell.R](/ai-agent/HadesProject/OHDSI-Study-Agent/R/OHDSIAssistant/R/strategus_cohort_methods_shell.R:2014) so the shell now: - distinguishes recommendation identifiers cleanly, - treats only numeric IDs and `ohdsi:<id>` as directly computable in this workflow, - shows non-computable recommendations with their original identifier instead of just `?`, - stops with a clear message if a user selects an unsupported descriptive phenotype such as `cipher:<id>`. I also added a narrow regression test in [tests/test_cohort_methods_shell_recommendation_support.py](/ai-agent/HadesProject/OHDSI-Study-Agent/tests/test_cohort_methods_shell_recommendation_support.py:1) to lock in that behavior.
The shell was correctly selecting OHDSI cohort `1039`, but the source-definition lookup still assumed `definitions/1039.json`. I updated [R/OHDSIAssistant/R/strategus_cohort_methods_shell.R](/ai-agent/HadesProject/OHDSI-Study-Agent/R/OHDSIAssistant/R/strategus_cohort_methods_shell.R:2399) so it now resolves source files using the current index naming scheme: - numeric OHDSI IDs can resolve to `ohdsi__<id>.json` - namespaced IDs can resolve via `:` → `__` conversion, such as `ohdsi:1039` → `ohdsi__1039.json`
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This PR hardens the cohort method ACP/MCP support fixes some bugs due to the replacement of the phenotype indexing methods with one that scales to include CIPHER (mostly non-computable), and brings in the new |
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