renalware-core 2.0.0.pre.beta8 → 2.0.0.pre.beta9

data/db/seeds/default/patients/patients_languages.rb

@@ -4,7 +4,7 @@ module Renalware
     file_path = File.join(File.dirname(__FILE__), "patients_languages.csv")
 
     CSV.foreach(file_path, headers: true) do |row|
-      Patients::Language.find_or_create_by!(name: row["name"])
+      Patients::Language.find_or_create_by!(code: row["code"], name: row["name"])
     end
   end
 end

data/db/seeds/default/patients/patients_religions.csv

@@ -22,3 +22,5 @@
 "Scientology"
 "Pantheism"
 "Heathenism"
+"Other"
+"Unknown"

data/db/seeds/default/reporting/audits.rb

@@ -1,15 +1,16 @@
 module Renalware
-  #log "Adding default audits" do
+  log "Adding default audits" do
     file_path = File.join(File.dirname(__FILE__), "audits.yml")
     yml_audits = YAML.load_file(file_path)
     yml_audits.each do |yml_audit|
       yml_audit.symbolize_keys!
       Reporting::Audit.find_or_create_by!(name: yml_audit[:name]) do |audit|
         audit.description = yml_audit[:description]
-        audit.materialized_view_name = yml_audit[:materialized_view_name]
+        audit.view_name = yml_audit[:view_name]
+        audit.materialized = yml_audit[:materialized]
         audit.refresh_schedule = yml_audit[:refresh_schedule]
         audit.display_configuration = yml_audit[:display_configuration]
       end
     end
-  #end
+  end
 end

data/db/seeds/default/reporting/audits.yml

@@ -1,7 +1,8 @@
 -
   name: Main Authors
   description: A list of authors with their letter statistics.
-  materialized_view_name: reporting_main_authors_audit
+  view_name: reporting_main_authors_audit
+  materialized: true
   refresh_schedule: "1 0 * * *"
   display_configuration: >
     { "columnDefs": [
@@ -14,7 +15,8 @@
 -
   name: HD Blood Pressures
   description:
-  materialized_view_name: reporting_hd_blood_pressures_audit
+  view_name: reporting_hd_blood_pressures_audit
+  materialized: true
   refresh_schedule: "1 0 * * *"
   display_configuration: >
     {
@@ -28,16 +30,57 @@
 -
   name: HD Overall
   description: An overview of HD activity in the current month across all HD units.
-  materialized_view_name: reporting_hd_overall_audit
+  view_name: reporting_hd_overall_audit
+  materialized: true
   refresh_schedule: "1 0 * * *"
   display_configuration: >
     { "columnDefs": [
       { "title": "Unit", "targets": 0, width: "300" },
       { "title": "No. patients", "targets": 1, width: "120" },
-      { "title": "% HB > 100", "targets": 2, width: "120" },
+      { "title": "% HGB > 100", "targets": 2, width: "120" },
       { "title": "% URR > 65", "targets": 3, width: "120" },
       { "title": "% Phosphate < 1.8", "targets": 4, width: "200" },
       { "title": "% w/fistula or graft", "targets": 5, width: "200" },
       { "title": "Avg. missed HD time", "targets": 6, width: "200" }
       { "title": "% missing >5% HD time", "targets": 7, width: "200" }
     ]}
+-
+  name: Bone
+  description: Bone audit
+  view_name: reporting_bone_audit
+  materialized: false
+  refresh_schedule:
+  display_configuration: >
+    { "columnDefs": [
+      { "title": "Modality", "targets": 0, width: "200" },
+      { "title": "No. patients", "targets": 1, width: "100" },
+      { "title": "Avg CCA", "targets": 2, width: "100" },
+      { "title": "% CCA 2.1-2.4", "targets": 4, width: "110" },
+      { "title": "% PTH > 300", "targets": 5, width: "100" },
+      { "title": "% PTH > 800", "targets": 6, width: "100" },
+      { "title": "Avg PHOS", "targets": 7, width: "100" },
+      { "title": "Max PHOS", "targets": 8, width: "100" },
+      { "title": "% PHOS < 1.8", "targets": 8, width: "110" }
+    ]}
+-
+  name: Anaemia
+  description: ESD/EPO audit
+  view_name: reporting_anaemia_audit
+  materialized: false
+  refresh_schedule:
+  display_configuration: >
+    { "columnDefs": [
+      { "title": "Modality", "targets": 0, width: "160" },
+      { "title": "Patients", "targets": 1, width: "80" },
+      { "title": "Avg HGB", "targets": 2, width: "90" },
+      { "title": "% HGB ≥ 10", "targets": 4, width: "100" },
+      { "title": "% HGB ≥ 11", "targets": 5, width: "100" },
+      { "title": "% HGB ≥ 13", "targets": 6, width: "100" },
+      { "title": "Avg FER", "targets": 7, width: "80" },
+      { "title": "% FER ≥ 150", "targets": 8, width: "100" },
+      { "title": "No on EPO", "targets": 9, width: "90" },
+      { "title": "Count Mircer*", "targets": 9, width: "100" },
+      { "title": "Count Neo*", "targets": 9, width: "90" },
+      { "title": "Count Ara*", "targets": 9, width: "90" }
+    ]}
+

data/db/seeds/default/system/countries.csv

@@ -0,0 +1,250 @@
+name,alpha2,alpha3
+United Kingdom,GB,GBR
+Afghanistan,AF,AFG
+Albania,AL,ALB
+Algeria,DZ,DZA
+American Samoa,AS,ASM
+Andorra,AD,AND
+Angola,AO,AGO
+Anguilla,AI,AIA
+Antarctica,AQ,ATA
+Antigua & Barbuda,AG,ATG
+Argentina,AR,ARG
+Armenia,AM,ARM
+Aruba,AW,ABW
+Australia,AU,AUS
+Austria,AT,AUT
+Azerbaijan,AZ,AZE
+Bahamas,BS,BHS
+Bahrain,BH,BHR
+Bangladesh,BD,BGD
+Barbados,BB,BRB
+Belarus,BY,BLR
+Belgium,BE,BEL
+Belize,BZ,BLZ
+Benin,BJ,BEN
+Bermuda,BM,BMU
+Bhutan,BT,BTN
+Bolivia,BO,BOL
+Bosnia,BA,BIH
+Botswana,BW,BWA
+Bouvet Island,BV,BVT
+Brazil,BR,BRA
+British Indian Ocean Territory,IO,IOT
+British Virgin Islands,VG,VGB
+Brunei,BN,BRN
+Bulgaria,BG,BGR
+Burkina Faso,BF,BFA
+Burundi,BI,BDI
+Cambodia,KH,KHM
+Cameroon,CM,CMR
+Canada,CA,CAN
+Cape Verde,CV,CPV
+Caribbean Netherlands,BQ,BES
+Cayman Islands,KY,CYM
+Central African Republic,CF,CAF
+Chad,TD,TCD
+Chile,CL,CHL
+China,CN,CHN
+Christmas Island,CX,CXR
+Cocos (Keeling) Islands,CC,CCK
+Colombia,CO,COL
+Comoros,KM,COM
+Congo - Brazzaville,CG,COG
+Congo - Kinshasa,CD,COD
+Cook Islands,CK,COK
+Costa Rica,CR,CRI
+Croatia,HR,HRV
+Cuba,CU,CUB
+Cura̤ao,CW,CUW
+Cyprus,CY,CYP
+Czech Republic,CZ,CZE
+Côte d'Ivoire,CI,CIV
+Denmark,DK,DNK
+Djibouti,DJ,DJI
+Dominica,DM,DMA
+Dominican Republic,DO,DOM
+Ecuador,EC,ECU
+Egypt,EG,EGY
+El Salvador,SV,SLV
+Equatorial Guinea,GQ,GNQ
+Eritrea,ER,ERI
+Estonia,EE,EST
+Ethiopia,ET,ETH
+Falkland Islands,FK,FLK
+Faroe Islands,FO,FRO
+Fiji,FJ,FJI
+Finland,FI,FIN
+France,FR,FRA
+French Guiana,GF,GUF
+French Polynesia,PF,PYF
+French Southern Territories,TF,ATF
+Gabon,GA,GAB
+Gambia,GM,GMB
+Georgia,GE,GEO
+Germany,DE,DEU
+Ghana,GH,GHA
+Gibraltar,GI,GIB
+Greece,GR,GRC
+Greenland,GL,GRL
+Grenada,GD,GRD
+Guadeloupe,GP,GLP
+Guam,GU,GUM
+Guatemala,GT,GTM
+Guernsey,GG,GGY
+Guinea,GN,GIN
+Guinea-Bissau,GW,GNB
+Guyana,GY,GUY
+Haiti,HT,HTI
+Heard & McDonald Islands,HM,HMD
+Honduras,HN,HND
+Hong Kong,HK,HKG
+Hungary,HU,HUN
+Iceland,IS,ISL
+India,IN,IND
+Indonesia,ID,IDN
+Iran,IR,IRN
+Iraq,IQ,IRQ
+Ireland,IE,IRL
+Isle of Man,IM,IMN
+Israel,IL,ISR
+Italy,IT,ITA
+Jamaica,JM,JAM
+Japan,JP,JPN
+Jersey,JE,JEY
+Jordan,JO,JOR
+Kazakhstan,KZ,KAZ
+Kenya,KE,KEN
+Kiribati,KI,KIR
+Kuwait,KW,KWT
+Kyrgyzstan,KG,KGZ
+Laos,LA,LAO
+Latvia,LV,LVA
+Lebanon,LB,LBN
+Lesotho,LS,LSO
+Liberia,LR,LBR
+Libya,LY,LBY
+Liechtenstein,LI,LIE
+Lithuania,LT,LTU
+Luxembourg,LU,LUX
+Macau,MO,MAC
+Macedonia,MK,MKD
+Madagascar,MG,MDG
+Malawi,MW,MWI
+Malaysia,MY,MYS
+Maldives,MV,MDV
+Mali,ML,MLI
+Malta,MT,MLT
+Marshall Islands,MH,MHL
+Martinique,MQ,MTQ
+Mauritania,MR,MRT
+Mauritius,MU,MUS
+Mayotte,YT,MYT
+Mexico,MX,MEX
+Micronesia,FM,FSM
+Moldova,MD,MDA
+Monaco,MC,MCO
+Mongolia,MN,MNG
+Montenegro,ME,MNE
+Montserrat,MS,MSR
+Morocco,MA,MAR
+Mozambique,MZ,MOZ
+Myanmar,MM,MMR
+Namibia,NA,NAM
+Nauru,NR,NRU
+Nepal,NP,NPL
+Netherlands,NL,NLD
+New Caledonia,NC,NCL
+New Zealand,NZ,NZL
+Nicaragua,NI,NIC
+Niger,NE,NER
+Nigeria,NG,NGA
+Niue,NU,NIU
+Norfolk Island,NF,NFK
+North Korea,KP,PRK
+Northern Mariana Islands,MP,MNP
+Norway,NO,NOR
+Oman,OM,OMN
+Pakistan,PK,PAK
+Palau,PW,PLW
+Palestine,PS,PSE
+Panama,PA,PAN
+Papua New Guinea,PG,PNG
+Paraguay,PY,PRY
+Peru,PE,PER
+Philippines,PH,PHL
+Pitcairn Islands,PN,PCN
+Poland,PL,POL
+Portugal,PT,PRT
+Puerto Rico,PR,PRI
+Qatar,QA,QAT
+Romania,RO,ROU
+Russia,RU,RUS
+Rwanda,RW,RWA
+R̩union,RE,REU
+Samoa,WS,WSM
+San Marino,SM,SMR
+Sao Tome and Principe,ST,STP
+Saudi Arabia,SA,SAU
+Senegal,SN,SEN
+Serbia,RS,SRB
+Seychelles,SC,SYC
+Sierra Leone,SL,SLE
+Singapore,SG,SGP
+Sint Maarten,SX,SXM
+Slovakia,SK,SVK
+Slovenia,SI,SVN
+Solomon Islands,SB,SLB
+Somalia,SO,SOM
+South Africa,ZA,ZAF
+South Georgia & South Sandwich Islands,GS,SGS
+South Korea,KR,KOR
+South Sudan,SS,SSD
+Spain,ES,ESP
+Sri Lanka,LK,LKA
+St. Barth̩lemy,BL,BLM
+St. Helena,SH,SHN
+St. Kitts & Nevis,KN,KNA
+St. Lucia,LC,LCA
+St. Martin,MF,MAF
+St. Pierre & Miquelon,PM,SPM
+St. Vincent & Grenadines,VC,VCT
+Sudan,SD,SDN
+Suriname,SR,SUR
+Svalbard & Jan Mayen,SJ,SJM
+Swaziland,SZ,SWZ
+Sweden,SE,SWE
+Switzerland,CH,CHE
+Syria,SY,SYR
+Taiwan,TW,TWN
+Tajikistan,TJ,TJK
+Tanzania,TZ,TZA
+Thailand,TH,THA
+Timor-Leste,TL,TLS
+Togo,TG,TGO
+Tokelau,TK,TKL
+Tonga,TO,TON
+Trinidad & Tobago,TT,TTO
+Tunisia,TN,TUN
+Turkey,TR,TUR
+Turkmenistan,TM,TKM
+Turks & Caicos Islands,TC,TCA
+Tuvalu,TV,TUV
+U.S. Outlying Islands,UM,UMI
+U.S. Virgin Islands,VI,VIR
+Uganda,UG,UGA
+Ukraine,UA,UKR
+United Arab Emirates,AE,ARE
+Uruguay,UY,URY
+US,US,USA
+Uzbekistan,UZ,UZB
+Vanuatu,VU,VUT
+Vatican City,VA,VAT
+Venezuela,VE,VEN
+Vietnam,VN,VNM
+Wallis & Futuna,WF,WLF
+Western Sahara,EH,ESH
+Yemen,YE,YEM
+Zambia,ZM,ZMB
+Zimbabwe,ZW,ZWE
+Åland Islands,AX,ALA

data/db/seeds/default/system/countries.rb

@@ -0,0 +1,12 @@
+module Renalware
+  log "Adding Countries" do
+    file_path = File.join(File.dirname(__FILE__), "countries.csv")
+      CSV.foreach(file_path, headers: true) do |row, index|
+        System::Country.find_or_create_by!(
+          name: row["name"],
+          alpha2: row["alpha2"],
+          alpha3: row["alpha3"]
+        ).tap{ |country| country.position = index }
+    end
+  end
+end

data/db/seeds/default/system/seeds.rb

@@ -1,2 +1,3 @@
+require_relative "./countries"
 require_relative "./roles"
 require_relative "./users"

data/db/seeds/default/transplants/transplant_registration_statuses.rb

@@ -1,29 +1,40 @@
 module Renalware
   log "Adding Transplant Registration Statuses" do
 
+    # HC on #1664: The only difficulty is for patients who receive a pre-emptive transplant so
+    # their ESRF date is the date of their transplant. The RR list does not
+    # accommodate that but I would put them as On Transplant List (3)
+    #
+    # RR ESR61 codes:
+    # 1 Unsuitable
+    # 2 Working Up or under discussion
+    # 3 On Transplant List
+    # 4 Suspended on Transplant List
+    # 5 Not Assessed by Start of Dialysis
     statuses = [
-      [:active, "Active"],
-      [:suspended, "Suspended"],
-      [:transplanted, "Transplanted"],
-      [:live_transplanted, "Live transplanted"],
-      [:off_by_patient, "Off by patient request"],
-      [:not_eligible, "Not eligible for NHS Tx"],
-      [:unfit_reconsider, "Unfit (not listed -- reconsider)"],
-      [:unfit_permanent, "Unfit (not listed -- permanent)"],
-      [:working_up, "X - working up"],
-      [:working_up_lrf, "X - working up LRF"],
-      [:not_for_work_up, "Not for work up - eGFR too high"],
-      [:workup_complete, "Workup complete - low creat"],
-      [:transfer_out, "Transfer Out"],
-      [:died, "Died"]
+      [:active, "Active", 3, "ESRF61: On Transplant List"],
+      [:suspended, "Suspended", 4, "ESRF61: Suspended on Transplant List"],
+      [:transplanted, "Transplanted", nil, "Not relevant for ESRF61"],
+      [:live_transplanted, "Live transplanted", nil, "Not relevant for ESRF61"],
+      [:off_by_patient, "Off by patient request", 1, "ERF61: Unsuitable"],
+      [:not_eligible, "Not eligible for NHS Tx", 1, "ERF61: Unsuitable"],
+      [:unfit_reconsider, "Unfit (not listed -- reconsider)", 1, "ERF61: Unsuitable"],
+      [:unfit_permanent, "Unfit (not listed -- permanent)", 1, "ERF61: Unsuitable"],
+      [:working_up, "X - working up", 2, "ERF61: Working Up or under discussion"],
+      [:working_up_lrf, "X - working up LRF", 2, "ERF61: Working Up or under discussion"],
+      [:not_for_work_up, "Not for work up - eGFR too high", 1, "ERF61: Unsuitable"],
+      [:workup_complete, "Workup complete - low creat", 2, "ERF61: Working Up or under discussion"],
+      [:transfer_out, "Transfer Out", nil, "Not relevant for ESRF61"],
+      [:died, "Died", nil, "Not relevant for ESRF61"]
     ]
 
     statuses.each_with_index do |status, index|
-      Transplants::RegistrationStatusDescription.create!(
-        code: status[0],
-        name: status[1],
-        position: index * 10
-      )
+      Transplants::RegistrationStatusDescription.find_or_create_by(code: status[0]) do |desc|
+        desc.name = status[1]
+        desc.rr_code = status[2]
+        desc.rr_comment = status[3]
+        desc.position = index * 10
+      end
     end
   end
 end

data/db/views/medication_current_prescriptions_v01.sql

@@ -0,0 +1,28 @@
+ SELECT mp.id,
+    mp.patient_id,
+    mp.drug_id,
+    mp.treatable_type,
+    mp.treatable_id,
+    mp.dose_amount,
+    mp.dose_unit,
+    mp.medication_route_id,
+    mp.route_description,
+    mp.frequency,
+    mp.notes,
+    mp.prescribed_on,
+    mp.provider,
+    mp.created_at,
+    mp.updated_at,
+    mp.created_by_id,
+    mp.updated_by_id,
+    mp.administer_on_hd,
+    mp.last_delivery_date,
+    drugs.name as drug_name,
+    drug_types.code AS drug_type_code,
+    drug_types.name AS drug_type_name
+   FROM medication_prescriptions mp
+     FULL JOIN medication_prescription_terminations mpt ON mpt.prescription_id = mp.id
+     JOIN drugs ON drugs.id = mp.drug_id
+     FULL JOIN drug_types_drugs ON drug_types_drugs.drug_id = drugs.id
+     FULL JOIN drug_types ON drug_types_drugs.drug_type_id = drug_types.id
+      AND (mpt.terminated_on IS NULL OR mpt.terminated_on > now());