Звіт у форматі JSON машиночитний
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{
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{
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{
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{
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"status": "partial",
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"max_points": 10
}
]
},
{
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"note": null,
"notes": [],
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"issue_closed_ratio": 0.318,
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"code": "issues_closed_share",
"params": {
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}
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{
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"detail": "1/1 decided PRs merged",
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{
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{
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]
},
{
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"notes": [
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"code": "excluded_no_data",
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"components": [
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{
"code": "weights_renormalized",
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"inputs": {
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}
],
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{
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"code": "not_applicable_to_user_accounts",
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{
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"details": [
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"login": "edgardomortiz"
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],
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{
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"status": "partial",
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{
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}
],
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},
{
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"name": "Engineering Quality",
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"weight": 0.2,
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"notes": [
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"code": "excluded_no_data",
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},
{
"code": "weights_renormalized",
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{
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{
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{
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{
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]
},
{
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"notes": [],
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"inputs": {
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}
],
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{
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{
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"points": 0,
"status": "missed",
"details": [],
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{
"key": "fuzzing",
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"status": "missed",
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},
{
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"details": [],
"max_points": 2.5
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{
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{
"key": "packaging",
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"status": "excluded",
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"code": "no_data",
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{
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"status": "excluded",
"details": [
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"code": "no_data",
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],
"max_points": 5
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{
"key": "sast",
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{
"key": "security_policy",
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"status": "missed",
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{
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{
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],
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{
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},
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"notes": [
{
"code": "jurisdiction_evidence_limits",
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],
"value": 100,
"inputs": {
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"components": [
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"status": "met",
"details": [
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"code": "jurisdiction_no_match",
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}
],
"max_points": 100
}
]
}
],
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},
{
"key": "ai_readiness",
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"weight": 0,
"metrics": [
{
"key": "ai_agent_context",
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"notes": [],
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"inputs": {
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"components": [
{
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],
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{
"key": "machine_readable_docs_llms_txt",
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{
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],
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]
},
{
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"code": "excluded_no_data",
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},
{
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],
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"inputs": {
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"toolchain_manifests": [],
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"components": [
{
"key": "one_command_bootstrap",
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"status": "missed",
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},
{
"key": "automated_tests",
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