Release v 1.3#211
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… are assigned to the selected timeline
…e cross-site scripting' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
…e cross-site scripting' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
…e cross-site scripting' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
… remote source' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
…cript without escaping
…t,epoch.type,epoch.epoch_uid; rollback deletes entities in coirrect order; made safe for legacy db deployments
…ne matrix so the user can schedule it
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Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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| f"<div class='error' style='color:#c62828;'>" | ||
| f"Amendment creation failed: {err}</div>", |
| primary_reason_other: str = Form(""), | ||
| ): | ||
| if not soa_exists(soa_id): | ||
| raise HTTPException(404, "SOA not found") |
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| def _require_other_reason(self): | ||
| if self.primary_reason_code == "C17649" and not self.primary_reason_other: | ||
| raise ValueError( | ||
| "otherReason is required when primary reason code is C17649" | ||
| ) |
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| class StudyAmendmentCreate(BaseModel): | ||
| name: str | ||
| number: str | ||
| summary: str | ||
| label: Optional[str] = None | ||
| description: Optional[str] = None | ||
| primary_reason_code: str | ||
| primary_reason_other: Optional[str] = None | ||
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| @model_validator(mode="after") | ||
| def _require_other_reason(self): | ||
| if self.primary_reason_code == "C17649" and not self.primary_reason_other: | ||
| raise ValueError( | ||
| "otherReason is required when primary reason code is C17649" | ||
| ) | ||
| return self | ||
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| class StudyAmendmentUpdate(BaseModel): | ||
| name: Optional[str] = None | ||
| number: Optional[str] = None | ||
| summary: Optional[str] = None | ||
| label: Optional[str] = None | ||
| description: Optional[str] = None | ||
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| class StudyAmendmentReasonCreate(BaseModel): | ||
| code: str | ||
| other_reason: Optional[str] = None | ||
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| @model_validator(mode="after") | ||
| def _require_other(self): | ||
| if self.code == "C17649" and not self.other_reason: | ||
| raise ValueError("otherReason is required when reason code is C17649") | ||
| return self |
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| <label class="am-field-label">Primary Reason <span class="am-required">*</span></label> | ||
| <select name="primary_reason_code" required class="am-select" | ||
| onchange="var o=this.options[this.selectedIndex];document.getElementById('primary-other-row').style.display=o.getAttribute('data-code')==='C17649'?'flex':'none';"> | ||
| <option value="" disabled selected>— select reason —</option> | ||
| {% for code, sv in reason_terms.items()|sort(attribute='1') %} | ||
| <option value="{{ sv }}" data-code="{{ code }}">{{ sv }}</option> | ||
| {% endfor %} | ||
| </select> |
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| <select name="code" required class="am-select" | ||
| onchange="var o=this.options[this.selectedIndex];this.closest('form').querySelector('.other-reason-box').style.display=o.getAttribute('data-code')==='C17649'?'flex':'none';"> | ||
| <option value="" disabled selected>— select reason —</option> | ||
| {% for code, sv in reason_terms.items()|sort(attribute='1') %} | ||
| <option value="{{ sv }}" data-code="{{ code }}">{{ sv }}</option> | ||
| {% endfor %} | ||
| </select> | ||
| <div class="other-reason-box am-field" style="display:none"> | ||
| <input name="other_reason" class="am-input" placeholder="Specify other reason" /> | ||
| </div> |
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| if not code_uid: | ||
| return { | ||
| "id": f"Code_{kind}Level_unknown", | ||
| "extensionAttributes": [], | ||
| "code": "", | ||
| "codeSystem": "", | ||
| "codeSystemVersion": "", | ||
| "decode": "", | ||
| "instanceType": "Code", | ||
| } |
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| def get_next_biomedical_concept_property_uid(cur: Any, soa_id: int) -> str: | ||
| """Compute next unique BiomedicalConceptProperty_N for the given SOA. | ||
|
|
||
| Assumes `cur` is a sqlite cursor within an open transaction. | ||
| """ | ||
| cur.execute( | ||
| "SELECT biomedical_concept_property_uid FROM" | ||
| " biomedical_concept_property WHERE soa_id=?" | ||
| " AND biomedical_concept_property_uid LIKE" | ||
| " 'BiomedicalConceptProperty_%'", | ||
| (soa_id,), | ||
| ) | ||
| existing = [x[0] for x in cur.fetchall() if x[0]] | ||
| n = 1 | ||
| if existing: | ||
| try: | ||
| n = max(int(x.split("_")[1]) for x in existing) + 1 | ||
| except Exception: | ||
| n = len(existing) + 1 | ||
| return f"BiomedicalConceptProperty_{n}" | ||
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| def get_next_extension_attribute_uid(cur: Any, soa_id: int) -> str: | ||
| """Compute next unique ExtensionAttribute_N for the given SOA. | ||
|
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| Assumes `cur` is a sqlite cursor within an open transaction. | ||
| """ | ||
| cur.execute( | ||
| "SELECT extension_attribute_uid FROM activity_concept_dss" | ||
| " WHERE soa_id=?" | ||
| " AND extension_attribute_uid LIKE 'ExtensionAttribute_%'", | ||
| (soa_id,), | ||
| ) | ||
| existing = [x[0] for x in cur.fetchall() if x[0]] | ||
| n = 1 | ||
| if existing: | ||
| try: | ||
| n = max(int(x.split("_")[1]) for x in existing) + 1 | ||
| except Exception: | ||
| n = len(existing) + 1 | ||
| return f"ExtensionAttribute_{n}" | ||
|
|
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| echo "Retrieving storage account key..." | ||
| STORAGE_KEY=$(az storage account keys list \ | ||
| --resource-group "$RESOURCE_GROUP" \ | ||
| --account-name "$STORAGE_ACCOUNT" \ | ||
| --query '[0].value' \ | ||
| --output tsv 2>&1) | ||
|
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| if [ $? -ne 0 ]; then | ||
| echo -e "${RED}Error: Failed to retrieve storage account key${NC}" | ||
| echo "Please verify:" | ||
| echo " 1. Resource group '$RESOURCE_GROUP' exists" | ||
| echo " 2. Storage account '$STORAGE_ACCOUNT' exists" | ||
| echo " 3. You have permission to access the storage account" | ||
| exit 1 | ||
| fi |
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| # Run database migrations (handled by app lifespan) | ||
| # Start gunicorn with uvicorn worker | ||
| gunicorn soa_builder.web.app:app \ | ||
| --bind 0.0.0.0:8000 \ | ||
| --workers 1 \ | ||
| --worker-class uvicorn.workers.UvicornWorker \ | ||
| --timeout 120 \ | ||
| --access-logfile - \ | ||
| --error-logfile - No newline at end of file |
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| # Configuration - UPDATE THESE VALUES | ||
| RESOURCE_GROUP="rg-soa-workbench-prod" | ||
| STORAGE_ACCOUNT="soaworkbenchsa" # Replace <uniqueid> with your storage account suffix | ||
| FILE_SHARE="soa-workbench-data" | ||
| LOCAL_DB="soa_builder_web.db" |
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| # Get storage account key | ||
| echo "Retrieving storage account key..." | ||
| STORAGE_KEY=$(az storage account keys list \ | ||
| --resource-group "$RESOURCE_GROUP" \ | ||
| --account-name "$STORAGE_ACCOUNT" \ | ||
| --query '[0].value' \ | ||
| --output tsv 2>&1) | ||
|
|
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| if [ $? -ne 0 ]; then | ||
| echo -e "${RED}Error: Failed to retrieve storage account key${NC}" | ||
| echo "Please verify:" | ||
| echo " 1. Resource group '$RESOURCE_GROUP' exists" | ||
| echo " 2. Storage account '$STORAGE_ACCOUNT' exists" | ||
| echo " 3. You have permission to access the storage account" | ||
| exit 1 | ||
| fi |
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| cur.execute( | ||
| "SELECT codelist_table, codelist_code, code " | ||
| "FROM code_association WHERE soa_id=? AND code_uid=? LIMIT 1", | ||
| (soa_id, code_uid), | ||
| ) | ||
| row = cur.fetchone() | ||
| conn.close() | ||
| if not row: |
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| LICENSE | ||
| README.md | ||
| pyproject.toml | ||
| src/sdtm/generate_ta.py | ||
| src/sdtm/generate_te.py | ||
| src/sdtm/generate_tv.py | ||
| src/soa_builder/__init__.py |
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