bonnie_bundler 2.2.5 → 3.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 73fb66a28d5fd842de1a34b699f8c7f2a2bf0e73f384c69c72714b9aaecf608b
-  data.tar.gz: 40d84a8e2ebc92eb0cac9492fbf13a4c883d5275ca3f1a7f6f36e35af3979e90
+  metadata.gz: 327ca5f0f9c6e8b7d15aec442443fcf5cf74162967fc814a8edd80e2804dacf9
+  data.tar.gz: 0f8b190e0a145f8b188b1d0d707c17a5fdbcaefac8573c7244e825a5f2d80a51
 SHA512:
-  metadata.gz: 5be05ce7481e06afd9ca223b27ea4276823dc1fe05efea78820577d1743b886643eecfbf3baf4923637cdbdc2885d76d118545d0e1692a8d1a25573cdf549e9e
-  data.tar.gz: 90d9f1fe7edf0e397febdfcfa47cb99e9adca9ecc35c28d6ab560578fc5fa8e344a797fb7f1c2c7e417402d7579dfc1c3786b903f58570ba016dcb828791d9c7
+  metadata.gz: c94fc587d3a98914a9f9dd7cbb71025b9b56c1cd563f92f17b048f2e03286206890ff80609cdabd24a226d6086a63e6d4e849908f51a7d5afda8b8d5980cd3d3
+  data.tar.gz: 33ded10c16749888bb8658e6a4bdb5f8b30d48317f98779377d19a516a30c1aecfd02b6d4be4c9d8ef34ba1493bf76c21acf33d05f637645f5c75ed326c95863

data/.github/gitleaks.toml

@@ -0,0 +1,268 @@
+title = "gitleaks config"
+
+[[rules]]
+    description = "AWS Manager ID"
+    regex = '''(A3T[A-Z0-9]|AKIA|AGPA|AIDA|AROA|AIPA|ANPA|ANVA|ASIA)[A-Z0-9]{16}'''
+    tags = ["key", "AWS"]
+
+[[rules]]
+    description = "AWS cred file info"
+    regex = '''(?i)(aws_access_key_id|aws_secret_access_key)(.{0,20})?=.[0-9a-zA-Z\/+]{20,40}'''
+    tags = ["AWS"]
+
+[[rules]]
+    description = "AWS Secret Key"
+    regex = '''(?i)aws(.{0,20})?(?-i)['\"][0-9a-zA-Z\/+]{40}['\"]'''
+    tags = ["key", "AWS"]
+
+[[rules]]
+    description = "AWS MWS key"
+    regex = '''amzn\.mws\.[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}'''
+    tags = ["key", "AWS", "MWS"]
+
+[[rules]]
+    description = "Facebook Secret Key"
+    regex = '''(?i)(facebook|fb)(.{0,20})?(?-i)['\"][0-9a-f]{32}['\"]'''
+    tags = ["key", "Facebook"]
+
+[[rules]]
+    description = "Facebook Client ID"
+    regex = '''(?i)(facebook|fb)(.{0,20})?['\"][0-9]{13,17}['\"]'''
+    tags = ["key", "Facebook"]
+
+[[rules]]
+    description = "Twitter Secret Key"
+    regex = '''(?i)twitter(.{0,20})?['\"][0-9a-z]{35,44}['\"]'''
+    tags = ["key", "Twitter"]
+
+[[rules]]
+    description = "Twitter Client ID"
+    regex = '''(?i)twitter(.{0,20})?['\"][0-9a-z]{18,25}['\"]'''
+    tags = ["client", "Twitter"]
+
+[[rules]]
+    description = "Github"
+    regex = '''(?i)github(.{0,20})?(?-i)['\"][0-9a-zA-Z]{35,40}['\"]'''
+    tags = ["key", "Github"]
+
+[[rules]]
+    description = "LinkedIn Client ID"
+    regex = '''(?i)linkedin(.{0,20})?(?-i)['\"][0-9a-z]{12}['\"]'''
+    tags = ["client", "LinkedIn"]
+
+[[rules]]
+    description = "LinkedIn Secret Key"
+    regex = '''(?i)linkedin(.{0,20})?['\"][0-9a-z]{16}['\"]'''
+    tags = ["secret", "LinkedIn"]
+
+[[rules]]
+    description = "Slack"
+    regex = '''xox[baprs]-([0-9a-zA-Z]{10,48})?'''
+    tags = ["key", "Slack"]
+
+[[rules]]
+    description = "EC"
+    regex = '''-----BEGIN EC PRIVATE KEY-----'''
+    tags = ["key", "EC"]
+
+
+[[rules]]
+    description = "Google API key"
+    regex = '''AIza[0-9A-Za-z\\-_]{35}'''
+    tags = ["key", "Google"]
+
+
+[[rules]]
+    description = "Heroku API key"
+    regex = '''(?i)heroku(.{0,20})?['"][0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}['"]'''
+    tags = ["key", "Heroku"]
+
+[[rules]]
+    description = "MailChimp API key"
+    regex = '''(?i)(mailchimp|mc)(.{0,20})?['"][0-9a-f]{32}-us[0-9]{1,2}['"]'''
+    tags = ["key", "Mailchimp"]
+
+[[rules]]
+    description = "Mailgun API key"
+    regex = '''(?i)(mailgun|mg)(.{0,20})?['"][0-9a-z]{32}['"]'''
+    tags = ["key", "Mailgun"]
+
+[[rules]]
+    description = "PayPal Braintree access token"
+    regex = '''access_token\$production\$[0-9a-z]{16}\$[0-9a-f]{32}'''
+    tags = ["key", "Paypal"]
+
+[[rules]]
+    description = "Picatic API key"
+    regex = '''sk_live_[0-9a-z]{32}'''
+    tags = ["key", "Picatic"]
+
+[[rules]]
+    description = "Slack Webhook"
+    regex = '''https://hooks.slack.com/services/T[a-zA-Z0-9_]{8}/B[a-zA-Z0-9_]{8}/[a-zA-Z0-9_]{24}'''
+    tags = ["key", "slack"]
+
+[[rules]]
+    description = "Stripe API key"
+    regex = '''(?i)stripe(.{0,20})?['\"][sk|rk]_live_[0-9a-zA-Z]{24}'''
+    tags = ["key", "Stripe"]
+
+[[rules]]
+    description = "Square access token"
+    regex = '''sq0atp-[0-9A-Za-z\-_]{22}'''
+    tags = ["key", "square"]
+
+[[rules]]
+    description = "Square OAuth secret"
+    regex = '''sq0csp-[0-9A-Za-z\\-_]{43}'''
+    tags = ["key", "square"]
+
+[[rules]]
+    description = "Twilio API key"
+    regex = '''(?i)twilio(.{0,20})?['\"][0-9a-f]{32}['\"]'''
+    tags = ["key", "twilio"]
+
+[[rules]]
+    description = "Env Var"
+    regex = '''(?i)(apikey|secret|key|api|password|pass|pw|host)=[0-9a-zA-Z-_.{}]{4,120}'''
+
+    [[rules.whitelist]]
+        regex='''Key\='''
+        description = "Reference to repo for sonarqube"
+        file = '''(?i)jenkinsfile'''
+
+    [[rules.whitelist]]
+        regex='''config.s3.aws_secret_access_key'''
+        description = "variable placeholder"
+        file = '''s3_connector.py'''
+
+    [[rules.whitelist]]
+        regex='''key=os\.path\.dirname'''
+        description = "env var whitelist"
+
+    [[rules.whitelist]]
+        regex='''.*os\.getenv.*|.*key=os\.environ\.get'''
+
+    
+    [[rules.whitelist]]
+        regex='''.*(?i)(s3secretkey|ENV_VAR|test_token|test\/key|testkey|Bearer|key.pem|key-specification|hadoop.*|Key=None|HOST=minio|KEY=S3AccessKey|api_url(),data.*|key=_file_mmset_sort_key)'''
+#[[rules]]
+#   description = "Port"
+#   regex = '''(?i)port(.{0,4})?[0-9]{1,10}'''
+#   [[rules.whitelist]]
+#       regex = '''(?i)port '''
+#       description = "ignore export "
+
+
+
+#[[rules]]
+#    description = "Email"
+#    regex = '''[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\.[a-zA-Z]{2,4}'''
+#    tags = ["email"]
+#    [[rules.whitelist]]
+#        file = '''(?i)bashrc'''
+#        description = "ignore bashrc emails"
+
+
+[[rules]]
+    description = "Generic Credential"
+    regex = '''(?i)(dbpasswd|dbuser|dbname|dbhost|api_key|apikey|secret|key|api|password|user|guid|hostname|pw|auth)(.{0,20})?['|"]([0-9a-zA-Z-_\/+!{}/=]{4,120})['|"]'''
+    tags = ["key", "API", "generic"]
+    # ignore leaks with specific identifiers like slack and aws
+    [[rules.whitelist]]
+        regex = '''xox[baprs]-([0-9a-zA-Z]{10,48})'''
+        description = "ignore slack"
+    [[rules.whitelist]]
+        description = "MailChimp API key"
+        regex = '''(?i)(.{0,20})?['"][0-9a-f]{32}-us[0-9]{1,2}['"]'''
+    [[rules.whitelist]]
+        description = "AWS Manager ID"
+        regex = '''(A3T[A-Z0-9]|AKIA|AGPA|AIDA|AROA|AIPA|ANPA|ANVA|ASIA)[A-Z0-9]{16}'''
+    [[rules.whitelist]]
+        regex='''(dns_secret_key|dns_access_key)'''
+        description = "Ignore credstash secrets in Terraform files"        
+
+    [[rules.whitelist]]
+        regex='''(linkKey)'''
+        description = "Ignore references to linkkey in scala files"
+        file = '''(?i)\.scala'''
+
+    [[rules.whitelist]]
+        regex='''(linkNum)'''
+        description = "Ignore references to linknum is input.json. Not sensitive"
+        file = '''(?i)input\.json'''
+
+    [[rules.whitelist]]
+        regex='''(link_key)'''
+        description = "Ignore references to this in json files. Not sensitive"
+        file = '''(?i)\.json'''
+
+    [[rules.whitelist]]
+        regex='''keys \"position\", \"category\"'''
+        description = "Config information, not sensitive"
+        file = '''(cost_attribution_rules_from_xlsx.pyi|codes_to_config.py)'''
+
+    [[rules.whitelist]]
+        regex='''(json_name)'''
+        description = "google protoobuf descriptor"
+        file = '''(protos/google/protobuf/descriptor.proto)'''
+    [[rules.whitelist]]
+        regex='''KEY \=.*'''
+        description = "Delta deleter script, can ignore"
+        file = '''(claims-api-submitter/deletion/delta_deleter.py)'''
+       
+    [[rules.whitelist]]
+        regex = '''secret=os.getenv\(\"AWS_SECRET_ACCESS_KEY\"'''
+        description = "claims deleter key reference"
+        file = '''claims-api-submitter/tests/integration_tests/test_claims_api_deleter.py'''
+
+   [[rules.whitelist]]
+        regex = '''key\": \"testkey\"'''
+        
+    [[rules.whitelist]]
+       regex='''.*os\.getenv.*'''
+
+    [[rules.whitelist]]
+        regex='''.*(?i)(s3secretkey|ENV_VAR|test_token|test_cookie|test\/key|testkey|Bearer|helper|max_user_ip|keywords|randomly|sslcert|disable|none|\"api_token\"|dry_run_url|API_TOKEN = \"submissions?_api_token\"|KEY_ID = \"AWS_ACCESS_KEY_ID\".*|key=None|api\(\"test\"|api_url()|key prefix|GET response|bad_format|key=_file_mmset_sort_key|KEYS = \[.*|no_submission_key|)'''
+
+    [[rules.whitelist]]
+        regex='''.*(?i)(user=\"hadoop\"|key=None)'''
+
+
+   [[rules]]
+    description = "High Entropy"
+    regex = '''[0-9a-zA-Z-_!{}/=]{4,120}'''
+    fileNameRegex = '''(?i)(dump.sql|high-entropy-misc.txt)$'''
+    tags = ["entropy"]
+        [[rules.Entropies]]
+            Min = "4.3"
+            Max = "7.0"
+        [[rules.whitelist]]
+            description = "ignore public ssh key and pems"
+            file = '''(pem|ppk|env)$'''
+            path = '''(.*)?ssh'''
+   
+
+[[rules]]
+    description = "Potential bash var"
+    regex='''(?i)(=)([0-9a-zA-Z-_!{}=]{4,120})'''
+    tags = ["key", "bash", "API", "generic"]
+        [[rules.Entropies]]
+            Min = "3.5"
+            Max = "4.5"
+            Group = "1"
+
+[[rules]]
+    description = "WP-Config"
+    regex='''define(.{0,20})?(DB_CHARSET|NONCE_SALT|LOGGED_IN_SALT|AUTH_SALT|NONCE_KEY|DB_HOST|DB_PASSWORD|AUTH_KEY|SECURE_AUTH_KEY|LOGGED_IN_KEY|DB_NAME|DB_USER)(.{0,20})?['|"].{10,120}['|"]'''
+    tags = ["key", "API", "generic"]
+
+[[rules]]
+    description = "Files with keys and credentials"
+    fileNameRegex = '''(?i)(id_rsa|passwd|id_rsa.pub|pgpass|pem|key|shadow)'''
+
+[whitelist]
+    description = "image whitelists"
+    files = ['''(.*?)(jpg|gif|doc|pdf|bin|CMS31v4_SimpleXML.xml|CMS31v4.xml|vsac_auth_bad_credentials.yml|swagger_generator.rb|sonar.properties|sonar-project.properties|build.sbt|sonar-project-benelevel-eligibility-filter.properties)$''']
+
+

data/.github/workflows/main.yml

@@ -0,0 +1,31 @@
+name: Github Secret Scanner
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    env:
+      REPO: https://github.com/projecttacoma/bonnie_bundler
+      REMOTE_EXCLUDES_URL: https://raw.githubusercontent.com/projecttacoma/bonnie_bundler/master/.github/gitleaks.toml
+      GITLEAKS_VERSION: v4.3.0
+    steps:
+    - name: Execute Gitleaks
+      run: |
+        #wget ${REMOTE_EXCLUDES_URL} -O gitleaks.toml
+        curl -H 'Authorization: token ${{ secrets.ACCESS_TOKEN_GITLEAKS }}' ${REMOTE_EXCLUDES_URL} -o gitleaks.toml
+        wget https://github.com/zricethezav/gitleaks/releases/download/${GITLEAKS_VERSION}/gitleaks-linux-amd64 -O gitleaks
+        chmod +x gitleaks
+        echo ${GITHUB_SHA}
+        echo "gitleaks --repo=${REPO} -v --pretty --redact --commit=${GITHUB_SHA} --config=gitleaks.toml"
+        ./gitleaks --repo=${REPO} -v --pretty --redact --commit=${GITHUB_SHA} --config=gitleaks.toml --access-token=${{ secrets.ACCESS_TOKEN_GITLEAKS }}
+    - name: Slack notification
+      if: failure()
+      env:
+        SLACK_WEBHOOK_GITLEAKS: ${{ secrets.SLACK_WEBHOOK_GITLEAKS }}
+      uses: Ilshidur/action-slack@master
+      with:
+        args: 'Potential Secrets found in: https://github.com/{{ GITHUB_REPOSITORY }}/commit/{{ GITHUB_SHA }} Link to build with full gitleaks output: https://github.com/{{ GITHUB_REPOSITORY }}/commit/{{ GITHUB_SHA }}/checks'
+

data/.travis.yml

@@ -1,9 +1,9 @@
 language: ruby
 rvm:
-  - "2.3.7"
+  - "2.3.8"
 services: mongodb
 script:
-  - bundle exec bundle-audit check --update
+  - bundle exec bundle-audit check --update --ignore CVE-2020-5267 CVE-2020-8166 CVE-2020-8164 CVE-2020-15169 CVE-2020-8163 CVE-2020-8167 CVE-2020-8165 CVE-2020-8184 CVE-2020-8161 CVE-2020-10663 CVE-2019-15587 CVE-2020-7595 CVE-2019-13117 CVE-2019-16782 CVE-2020-8130 CVE-2019-16892
   - bundle exec rake
 notifications:
   email:

data/Gemfile

@@ -1,7 +1,7 @@
 source "https://rubygems.org"
 gemspec
 
- gem 'health-data-standards', :git => 'https://github.com/projectcypress/health-data-standards.git', :branch => 'master_bonnie'
+# gem 'health-data-standards', :git => 'https://github.com/projectcypress/health-data-standards.git', :branch => 'master_bonnie'
 # gem 'quality-measure-engine', :git => 'https://github.com/projectcypress/quality-measure-engine.git', :branch => 'master'
 # gem 'hqmf2js', :git => 'https://github.com/projecttacoma/hqmf2js.git', :branch => 'master'
 # gem 'hquery-patient-api', :git => 'https://github.com/projecttacoma/patientapi.git', :branch => 'master'

data/Gemfile.lock

@@ -1,29 +1,7 @@
-GIT
-  remote: https://github.com/projectcypress/health-data-standards.git
-  revision: 58975d21251e60050b66c5c8ed3acb146d909392
-  branch: master_bonnie
-  specs:
-    health-data-standards (4.3.5)
-      activesupport (~> 4.2.11)
-      builder (~> 3.1)
-      erubis (~> 2.7.0)
-      highline (~> 1.7.0)
-      log4r (~> 1.1.10)
-      memoist (~> 0.9.1)
-      mongo (~> 2.4.3)
-      mongoid (~> 5.0.0)
-      mongoid-tree (~> 2.0.0)
-      nokogiri (~> 1.10.3)
-      protected_attributes (~> 1.0.5)
-      rest-client (~> 2.0.1)
-      rubyzip (~> 1.2.1)
-      uuid (~> 2.3.7)
-      zip-zip (~> 0.3)
-
 PATH
   remote: .
   specs:
-    bonnie_bundler (2.2.5)
+    bonnie_bundler (3.0.0)
       diffy (~> 3.0.0)
       health-data-standards (~> 4.3.2)
       hqmf2js (~> 1.4)
@@ -31,7 +9,7 @@ PATH
       mongoid (~> 5.0)
       quality-measure-engine (~> 3.2)
       rails (>= 4.2, < 6.0)
-      roo (~> 1.13)
+      roo (~> 2.7)
       rubyzip (~> 1.2, >= 1.2.1)
       simplexml_parser (~> 1.0)
       zip-zip (~> 0.3)
@@ -73,16 +51,16 @@ GEM
       minitest (~> 5.1)
       thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
-    addressable (2.6.0)
+    addressable (2.5.2)
       public_suffix (>= 2.0.2, < 4.0)
     arel (6.0.4)
-    awesome_print (1.8.0)
+    awesome_print (1.2.0)
     bson (4.4.2)
     builder (3.2.3)
-    bundler-audit (0.6.1)
-      bundler (>= 1.2.0, < 3)
+    bundler-audit (0.6.0)
+      bundler (~> 1.2)
       thor (~> 0.18)
-    coderay (1.1.2)
+    coderay (1.1.0)
     coffee-script (2.4.1)
       coffee-script-source
       execjs
@@ -93,19 +71,35 @@ GEM
     crass (1.0.4)
     delayed_job (4.1.5)
       activesupport (>= 3.0, < 5.3)
-    delayed_job_mongoid (2.3.1)
+    delayed_job_mongoid (2.3.0)
       delayed_job (>= 3.0, < 5)
-      mongoid (>= 3.0, < 8)
+      mongoid (>= 3.0, < 7)
       mongoid-compatibility (>= 0.4.0)
     diffy (3.0.7)
-    docile (1.3.1)
+    docile (1.1.3)
     domain_name (0.5.20180417)
       unf (>= 0.0.5, < 1.0.0)
     erubis (2.7.0)
     execjs (2.7.0)
     globalid (0.4.2)
       activesupport (>= 4.2.0)
-    hashdiff (0.3.9)
+    hashdiff (0.3.6)
+    health-data-standards (4.3.5)
+      activesupport (~> 4.2.11)
+      builder (~> 3.1)
+      erubis (~> 2.7.0)
+      highline (~> 1.7.0)
+      log4r (~> 1.1.10)
+      memoist (~> 0.9.1)
+      mongo (~> 2.4.3)
+      mongoid (~> 5.0.0)
+      mongoid-tree (~> 2.0.0)
+      nokogiri (~> 1.10.3)
+      protected_attributes (~> 1.0.5)
+      rest-client (~> 2.0.1)
+      rubyzip (~> 1.2.1)
+      uuid (~> 2.3.7)
+      zip-zip (~> 0.3)
     highline (1.7.10)
     hike (1.2.3)
     hqmf2js (1.4.0)
@@ -123,7 +117,7 @@ GEM
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.2.0)
+    json (2.1.0)
     libv8 (3.16.14.19)
     log4r (1.1.10)
     loofah (2.2.3)
@@ -134,7 +128,7 @@ GEM
     mail (2.7.1)
       mini_mime (>= 0.1.1)
     memoist (0.9.3)
-    method_source (0.9.2)
+    method_source (0.8.2)
     mime-types (3.2.2)
       mime-types-data (~> 3.2015)
     mime-types-data (3.2019.0331)
@@ -143,10 +137,10 @@ GEM
     minitest (5.11.3)
     mongo (2.4.3)
       bson (>= 4.2.1, < 5.0.0)
-    mongoid (5.2.1)
+    mongoid (5.0.2)
       activemodel (~> 4.0)
-      mongo (>= 2.4.1, < 3.0.0)
-      origin (~> 2.3)
+      mongo (~> 2.1)
+      origin (~> 2.1)
       tzinfo (>= 0.3.37)
     mongoid-compatibility (0.5.1)
       activesupport
@@ -155,17 +149,18 @@ GEM
       mongoid (>= 4.0, < 6.0)
     multi_json (1.13.1)
     netrc (0.11.0)
-    nokogiri (1.10.3)
+    nokogiri (1.10.4)
       mini_portile2 (~> 2.4.0)
     origin (2.3.1)
     protected_attributes (1.0.9)
       activemodel (>= 4.0.1, < 5.0)
-    pry (0.12.2)
-      coderay (~> 1.1.0)
-      method_source (~> 0.9.0)
-    pry-nav (0.3.0)
-      pry (>= 0.9.10, < 0.13.0)
-    public_suffix (3.0.3)
+    pry (0.9.12.6)
+      coderay (~> 1.0)
+      method_source (~> 0.8)
+      slop (~> 3.4)
+    pry-nav (0.2.3)
+      pry (~> 0.9.10)
+    public_suffix (3.0.0)
     quality-measure-engine (3.2.0)
       delayed_job_mongoid (~> 2.2)
       mongoid (~> 5.0)
@@ -198,29 +193,26 @@ GEM
       activesupport (= 4.2.11.1)
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
-    rake (12.3.2)
+    rake (12.0.0)
     ref (2.0.0)
     rest-client (2.0.2)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    roo (1.13.2)
-      nokogiri
-      rubyzip
-      spreadsheet (> 0.6.4)
-    ruby-ole (1.2.12.2)
+    roo (2.8.2)
+      nokogiri (~> 1)
+      rubyzip (>= 1.2.1, < 2.0.0)
     rubyzip (1.2.2)
-    safe_yaml (1.0.5)
-    simplecov (0.16.1)
-      docile (~> 1.1)
-      json (>= 1.8, < 3)
-      simplecov-html (~> 0.10.0)
-    simplecov-html (0.10.2)
+    safe_yaml (1.0.4)
+    simplecov (0.8.2)
+      docile (~> 1.1.0)
+      multi_json
+      simplecov-html (~> 0.8.0)
+    simplecov-html (0.8.0)
     simplexml_parser (1.0.1)
       health-data-standards (~> 4.0)
       tilt (~> 1.4)
-    spreadsheet (1.2.3)
-      ruby-ole (>= 1.0)
+    slop (3.5.0)
     sprockets (2.12.5)
       hike (~> 1.2)
       multi_json (~> 1.0)
@@ -247,8 +239,8 @@ GEM
     unf_ext (0.0.7.6)
     uuid (2.3.9)
       macaddr (~> 1.0)
-    vcr (4.0.0)
-    webmock (3.5.1)
+    vcr (3.0.3)
+    webmock (3.0.1)
       addressable (>= 2.3.6)
       crack (>= 0.3.2)
       hashdiff
@@ -262,7 +254,6 @@ DEPENDENCIES
   awesome_print
   bonnie_bundler!
   bundler-audit
-  health-data-standards!
   minitest (~> 5.0)
   pry
   pry-nav
@@ -272,4 +263,4 @@ DEPENDENCIES
   webmock
 
 BUNDLED WITH
-   1.17.3
+   1.17.1

data/LICENSE.txt

@@ -0,0 +1,201 @@
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+                        http://www.apache.org/licenses/
+
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+   Copyright [yyyy] [name of copyright owner]
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+
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data/README.md

@@ -2,3 +2,15 @@ bonnie_bundler
 ==============
 
 Gem for creating and managing bonnie bundles
+
+## License
+
+Copyright 2014 The MITRE Corporation
+
+Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
+
+```
+http://www.apache.org/licenses/LICENSE-2.0
+```
+
+Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

data/bonnie-bundler.gemspec

@@ -7,7 +7,7 @@ Gem::Specification.new do |s|
   s.email = "pophealth-talk@googlegroups.com"
   s.homepage = "http://github.com/projecttacoma/bonnie_bundler"
   s.authors = ["The MITRE Corporation"]
-  s.version = '2.2.5'
+  s.version = '3.0.0'
   s.license = 'Apache-2.0'
 
   s.add_dependency 'health-data-standards', '~> 4.3.2'
@@ -23,7 +23,7 @@ Gem::Specification.new do |s|
   s.add_dependency 'diffy', '~> 3.0.0'
 
   # needed for parsing value sets (we need to use roo rather than rubyxl because the value sets are in xls rather than xlsx)
-  s.add_dependency 'roo', '~> 1.13'
+  s.add_dependency 'roo', '~> 2.7'
 
   s.files = s.files = `git ls-files`.split("\n")
 end

data/lib/measures/loading/exceptions.rb

@@ -1,8 +1,8 @@
 module Measures
-  class ValueSetException < Exception
+  class ValueSetException < StandardError
   end
-  class HQMFException < Exception
+  class HQMFException < StandardError
   end
-  class MeasureLoadingException < Exception
+  class MeasureLoadingException < StandardError
   end
-end 
+end

data/lib/util/vsac_api.rb

@@ -8,7 +8,7 @@ module Util
     class VSACError < StandardError
     end
 
-    # Error represnting a not found response from the API. Includes OID for reporting to user.
+    # Error representing a not found response from the API. Includes OID for reporting to user.
     class VSNotFoundError < VSACError
       attr_reader :oid
       def initialize(oid)
@@ -17,7 +17,7 @@ module Util
       end
     end
 
-    # Error represnting a program not found response from the API.
+    # Error representing a program not found response from the API.
     class VSACProgramNotFoundError < VSACError
       attr_reader :oid
       def initialize(program)
@@ -25,7 +25,7 @@ module Util
       end
     end
 
-    # Error represnting a response from the API that had no concepts.
+    # Error representing a response from the API that had no concepts.
     class VSEmptyError < VSACError
       attr_reader :oid
       def initialize(oid)
@@ -44,14 +44,14 @@ module Util
     # Raised when the user credentials were invalid.
     class VSACInvalidCredentialsError < VSACError
       def initialize
-        super('VSAC ULMS credentials are invalid.')
+        super('VSAC UMLS credentials are invalid.')
       end
     end
 
     # Raised when a call requiring auth is attempted when no ticket_granting_ticket or credentials were provided.
     class VSACNoCredentialsError < VSACError
       def initialize
-        super('VSAC ULMS credentials were not provided.')
+        super('VSAC UMLS credentials were not provided.')
       end
     end
 
@@ -92,7 +92,7 @@ module Util
         end
 
         # if a ticket_granting_ticket was passed in, check it and raise errors if found
-        # username and password will be ignored
+        # VSAC API Key will be ignored
         if !options[:ticket_granting_ticket].nil?
           provided_ticket_granting_ticket = options[:ticket_granting_ticket]
           if provided_ticket_granting_ticket[:ticket].nil? || provided_ticket_granting_ticket[:expires].nil?
@@ -108,9 +108,9 @@ module Util
           @ticket_granting_ticket = { ticket: provided_ticket_granting_ticket[:ticket],
             expires: provided_ticket_granting_ticket[:expires] }
 
-        # if username and password were provided use them to get a ticket granting ticket
-        elsif !options[:username].nil? && !options[:password].nil?
-          @ticket_granting_ticket = get_ticket_granting_ticket(options[:username], options[:password])
+        # if api key was provided use it to get a ticket granting ticket
+        elsif !options[:api_key].nil?
+          @ticket_granting_ticket = get_ticket_granting_ticket(options[:api_key])
         end
       end
 
@@ -153,7 +153,7 @@ module Util
       # Gets the details for a program. This may be used without credentials.
       #
       # Optional parameter program is the program to request from the API. If it is not provided it will look for
-      # a :program in the config passed in during construction. If there is no :program in the config it will use 
+      # a :program in the config passed in during construction. If there is no :program in the config it will use
       # the DEFAULT_PROGRAM constant for the program.
       #
       # Returns the JSON parsed response for program details.
@@ -180,7 +180,7 @@ module Util
       #   }
       #
       # Optional parameter program is the program to request from the API. If it is not provided it will look for
-      # a :program in the config passed in during construction. If there is no :program in the config it will use 
+      # a :program in the config passed in during construction. If there is no :program in the config it will use
       # the DEFAULT_PROGRAM constant for the program.
       #
       # Returns the name of the latest profile for the given program.
@@ -288,9 +288,9 @@ module Util
         end
       end
 
-      def get_ticket_granting_ticket(username, password)
+      def get_ticket_granting_ticket(api_key)
         begin
-          ticket = RestClient.post("#{@config[:auth_url]}/Ticket", username: username, password: password)
+          ticket = RestClient.post("#{@config[:auth_url]}/Ticket", apikey: api_key)
           return { ticket: String.new(ticket), expires: Time.now + 8.hours }
         rescue RestClient::Unauthorized
           raise VSACInvalidCredentialsError.new

data/notice.md

@@ -0,0 +1,9 @@
+NOTICE
+======
+This (software/technical data) was produced for the U. S. Government under Contract Number HHSM-500-2012-00008I, and is subject to Federal Acquisition Regulation Clause 52.227-14, Rights in Data-General.  
+
+No other use other than that granted to the U. S. Government, or to those acting on behalf of the U. S. Government under that Clause is authorized without the express written permission of The MITRE Corporation.
+
+To the extent necessary MITRE hereby grants express written permission to use, reproduce, distribute, modify, and otherwise leverage this software to the extent permitted by the Apache 2.0 license.
+
+For further information, please contact The MITRE Corporation, Contracts Management Office, 7515 Colshire Drive, McLean, VA  22102-7539, (703) 983-6000.

data/test/test_helper.rb

@@ -23,7 +23,7 @@ def dump_db
 end
 
 def get_ticket_granting_ticket
-  api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+  api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
   return api.ticket_granting_ticket
 end
 

data/test/unit/vsac_api_auth_test.rb

@@ -4,10 +4,10 @@ require 'vcr_setup.rb'
 # Tests that ensure VSAC authentication related situations are handled
 class VSACAPIAuthTest < ActiveSupport::TestCase
 
-  test 'valid username and password provided' do
+  test 'valid api_key provided' do
     VCR.use_cassette("vsac_auth_good_credentials") do
       assert_nothing_raised do
-        api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+        api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
         assert_not_nil api.ticket_granting_ticket
         assert_not_nil api.ticket_granting_ticket[:ticket]
         assert_not_nil api.ticket_granting_ticket[:expires]
@@ -15,42 +15,18 @@ class VSACAPIAuthTest < ActiveSupport::TestCase
     end
   end
 
-  test 'invalid username and password provided' do
+  test 'invalid api_key provided' do
     VCR.use_cassette("vsac_auth_bad_credentials") do
       assert_raise Util::VSAC::VSACInvalidCredentialsError do
-        api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: 'baduser', password: 'badpass')
+        api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: 'badapikey')
       end
     end
   end
 
-  test 'empty username and password provided' do
+  test 'empty api_key provided' do
     api = nil
     assert_nothing_raised do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: nil, password: nil)
-    end
-
-    # now attempt to get a valueset
-    assert_raise Util::VSAC::VSACNoCredentialsError do
-      api.get_valueset('2.16.840.1.113762.1.4.1')
-    end
-  end
-
-  test 'provided username but no password' do
-    api = nil
-    assert_nothing_raised do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: "vsacuser")
-    end
-
-    # now attempt to get a valueset
-    assert_raise Util::VSAC::VSACNoCredentialsError do
-      api.get_valueset('2.16.840.1.113762.1.4.1')
-    end
-  end
-
-  test 'provided password but no username' do
-    api = nil
-    assert_nothing_raised do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: "vsacuser")
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: nil)
     end
 
     # now attempt to get a valueset
@@ -62,7 +38,7 @@ class VSACAPIAuthTest < ActiveSupport::TestCase
   test 'valid ticket_granting_ticket provided and used' do
     VCR.use_cassette("vsac_auth_good_credentials_and_simple_call") do
       # first get a ticket_granting_ticket
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       assert_not_nil api.ticket_granting_ticket
 
       reused_ticket_granting_ticket = {

data/test/unit/vsac_api_test.rb

@@ -18,7 +18,7 @@ class VSACApiTest < ActiveSupport::TestCase
 
   test 'get_valueset with version' do
     VCR.use_cassette("vsac_vs_version") do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       vs = api.get_valueset("2.16.840.1.113883.3.600.1.1834", version: "MU2 EP Update 2014-07-01")
       assert_not_nil vs
       doc = Nokogiri::XML(vs)
@@ -28,7 +28,7 @@ class VSACApiTest < ActiveSupport::TestCase
 
   test 'get_valuest with include_draft no profile' do
     VCR.use_cassette("vsac_vs_include_draft_no_profile") do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       assert_raise Util::VSAC::VSACArgumentError do
         api.get_valueset("2.16.840.1.113883.3.600.1.1834", include_draft: true)
       end
@@ -37,7 +37,7 @@ class VSACApiTest < ActiveSupport::TestCase
 
   test 'get_valueset with include_draft specified profile' do
     VCR.use_cassette("vsac_vs_include_draft_with_profile") do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       vs = api.get_valueset("2.16.840.1.113762.1.4.1", include_draft: true, profile: "eCQM Update 2018-05-04")
       assert_not_nil vs
       doc = Nokogiri::XML(vs)
@@ -47,7 +47,7 @@ class VSACApiTest < ActiveSupport::TestCase
 
   test 'get_valueset no options' do
     VCR.use_cassette("vsac_vs_no_options") do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       vs = api.get_valueset("2.16.840.1.113762.1.4.1")
       assert_not_nil vs
       doc = Nokogiri::XML(vs)
@@ -57,7 +57,7 @@ class VSACApiTest < ActiveSupport::TestCase
 
   test 'get_valueset not found' do
     VCR.use_cassette("vsac_vs_not_found") do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       assert_raise Util::VSAC::VSNotFoundError do
         api.get_valueset("bad.oid")
       end
@@ -66,7 +66,7 @@ class VSACApiTest < ActiveSupport::TestCase
 
   test 'get_valueset with release' do
     VCR.use_cassette("vsac_vs_release") do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       vs = api.get_valueset("2.16.840.1.113762.1.4.1", release: "MU2 EP Update 2014-05-30")
       assert_not_nil vs
       doc = Nokogiri::XML(vs)

data/test/vcr_setup.rb

@@ -5,16 +5,14 @@ VCR.configure do |c|
   # This is where the various cassettes will be recorded to
   c.cassette_library_dir = 'test/fixtures/vcr_cassettes'
   c.hook_into :webmock
-  
+
   # To avoid storing plain text VSAC credentials or requiring the VSAC credentials
-  # be provided at every run of the rake tests, provide the VSAC_USERNAME and VSAC_PASSWORD
+  # be provided at every run of the rake tests, provide the VSAC_API_KEY
   # whenever you need to record a cassette that requires valid credentials
-  ENV['VSAC_USERNAME'] = "vcrtest" unless ENV['VSAC_USERNAME']
-  ENV['VSAC_PASSWORD'] = "vcrpass" unless ENV['VSAC_PASSWORD']
+  ENV['VSAC_API_KEY'] = "vcrpass" unless ENV['VSAC_API_KEY']
 
   # Ensure plain text passwords do not show up during logging
-  c.filter_sensitive_data('<VSAC_USERNAME>') {ENV['VSAC_USERNAME']}
-  c.filter_sensitive_data('<VSAC_PASSWORD>') {URI.escape(ENV['VSAC_PASSWORD'])}
+  c.filter_sensitive_data('<VSAC_API_KEY>') {URI.escape(ENV['VSAC_API_KEY'])}
   c.default_cassette_options = {record: :once }
 
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bonnie_bundler
 version: !ruby/object:Gem::Version
-  version: 2.2.5
+  version: 3.0.0
 platform: ruby
 authors:
 - The MITRE Corporation
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2019-05-15 00:00:00.000000000 Z
+date: 2020-10-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: health-data-standards
@@ -168,14 +168,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.13'
+        version: '2.7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.13'
+        version: '2.7'
 description: A Gem for creating and managing bonnie bundles
 email: pophealth-talk@googlegroups.com
 executables: []
@@ -184,10 +184,13 @@ extra_rdoc_files: []
 files:
 - ".github/CONTRIBUTING.md"
 - ".github/PULL_REQUEST_TEMPLATE.md"
+- ".github/gitleaks.toml"
+- ".github/workflows/main.yml"
 - ".gitignore"
 - ".travis.yml"
 - Gemfile
 - Gemfile.lock
+- LICENSE.txt
 - README.md
 - Rakefile
 - bonnie-bundler.gemspec
@@ -209,6 +212,7 @@ files:
 - lib/models/cql_measure.rb
 - lib/models/measure.rb
 - lib/util/vsac_api.rb
+- notice.md
 - test/fixtures/BCS_v5_0_Artifacts.zip
 - test/fixtures/CMS134v6.zip
 - test/fixtures/CMS158_v5_4_Artifacts.zip
@@ -286,7 +290,7 @@ homepage: http://github.com/projecttacoma/bonnie_bundler
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -301,9 +305,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.8
-signing_key: 
+rubygems_version: 3.0.8
+signing_key:
 specification_version: 4
 summary: A Gem for creating and managing bonnie bundles
 test_files: []