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breck7 · May 15, 2024 · ebc30cc · ebc30cc
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diff --git a/404.scroll b/404.scroll
@@ -1,7 +1,8 @@
 permalink 404.html
+title Page not found
 
 import rootHeader.scroll
-title Page not found
+printTitle
 thinColumns 1
 
 Sorry, the url you requested was not found.

diff --git a/concepts/acd-au.scroll b/concepts/acd-au.scroll
@@ -2,7 +2,7 @@ import ../measures/conceptPage.scroll
 id ACD
 type registry
 appeared 1982
-standsFor Australian Cancer Database 
+standsFor Australian Cancer Database
 conceptDescription The Australian Cancer Database (ACD) contains data about all new cases of cancer diagnosed in Australia since 1 January 1982, excluding basal and squamous cell carcinomas of the skin.Cancer is a notifiable disease in all Australian states and territories. The relevant legislation requires certain individuals and organisations to notify all new cases of cancer to the jurisdiction's central cancer registry. These registries supply data annually to the AIHW, which cleans and standardises the data, notifies the registries of inter-state duplicates and produces the Australian Cancer Database.The Australian Cancer Database (ACD) contains data about all new cases of cancer diagnosed in Australia since 1 January 1982, excluding basal and squamous cell carcinomas of the skin. Geographical coverage is both National and State.
 
 website https://www.aihw.gov.au/about-our-data/our-data-collections/australian-cancer-database

diff --git a/concepts/actcr-au.scroll b/concepts/actcr-au.scroll
@@ -2,7 +2,7 @@ import ../measures/conceptPage.scroll
 id ACTCR
 type registry
 appeared 1982
-standsFor  
+standsFor
 conceptDescription The ACT Cancer Registry (ACTCR) registers all new cases of cancer diagnosed in ACT residents (excluding non-melanoma skin cancer) and all deaths of people with cancer to gain a comprehensive picture of the burden of cancer across the population. It is managed by the ACT Health Directorate. The ACT CR is a case-based registry in which all notifications relating to a particular case of cancer are linked to form a single record. A case of cancer is the occurrence of a malignant neoplasm in a particular person. Therefore a case of malignant melanoma in a particular person counts as one case. If the same person subsequently develops leukaemia, the leukaemia counts as a second case. The CHeReL has incorporated ACT CR data from 1994 into the Master Linkage Key. It is possible to obtain ACT CR data back to 1982, but the CHeReL and ACT CR data custodian recommend using data from 1994 for linkage studies.  From 1982 to 1994 the quality of the linkage is likely to be compromised by missing or estimated dates of birth, and incomplete pathology reports.  Researchers should therefore exercise caution if interpreting results including pre 1994 data.
 
 website https://www.aihw.gov.au/reports-data/health-conditions-disability-deaths/cancer/overview

diff --git a/concepts/bbcr-ar.scroll b/concepts/bbcr-ar.scroll
@@ -2,7 +2,7 @@ import ../measures/conceptPage.scroll
 id BBCR
 type registry
 appeared 1993
-standsFor Bahía Blanca Cancer Registry 
+standsFor Bahía Blanca Cancer Registry
 conceptDescription The Regional Tumor Registry of the South of the Province of Buenos Aires covers the political area of Bahía Blanca, with a population of 290 000 at the 2005 census.Although the registry was recognized by a provincial law and a municipal resolution in 1993, it does not have a speciĺc budget. The Argentine Association for Cancer Prevention and Education (AAPEC), a non-profit organization founded in 19 to improve cancer control, maintains the registry and other high-priority projects, such as the tobacco control programme. Although resources are limited, the registry employs two registrars and a registry coordinator. Most of the registry’s resources are provided by the municipal government of Bahía Blanca.
 
 reference https://publications.iarc.fr/_publications/media/download/3756/9a1a372c6a6f112d48d63e82f2fee9a6dc1c3844.pdf

diff --git a/concepts/cocr-ar.scroll b/concepts/cocr-ar.scroll
@@ -1,8 +1,8 @@
 import ../measures/conceptPage.scroll
-id COCR 
+id COCR
 type registry
 appeared 2003
-standsFor Córdoba Cancer Registry Argentina 
+standsFor Córdoba Cancer Registry Argentina
 conceptDescription One registry covering a whole province of the country exists:the Córdoba Cancer Registry. Córdoba Cancer Registry is a provincial population-based registry which started in 2003 and covers approximately 9% of the Argentinean population. Seems to be located in the University of Córdoba.
 
 reference https://accamargo.phlnet.com.br/applied/ACR201030p.245-52.pdf

diff --git a/concepts/crptdf-ar.scroll b/concepts/crptdf-ar.scroll
@@ -1,7 +1,7 @@
 import ../measures/conceptPage.scroll
-id CRPTDF 
+id CRPTDF
 type registry
-standsFor Cancer Registry of the Province of Tierra del Fuego 
+standsFor Cancer Registry of the Province of Tierra del Fuego
 conceptDescription Population-based Cancer Registry of the Province of Tierra del Fuego.
 
 reference https://gco.iarc.fr/includes/CSA_WorkingGroup.pdf

diff --git a/concepts/crsba-dz.scroll b/concepts/crsba-dz.scroll
@@ -1,5 +1,5 @@
 import ../measures/conceptPage.scroll
-id CRSBA 
+id CRSBA
 type registry
 standsFor Cancer Registry of Sidi-Bel-Abbès
 conceptDescription The hospital is a specialized center in the fight against cancer. Made up of : Block A: Hospital admissions service Block B: Nuclear medicine service and laboratories. Block C: Service of the central operating theater and resuscitation, medical imaging, pharmacy, catering services and teaching service. Block D: Radiotherapy and brachytherapy department, blood collection and analysis unit.

diff --git a/concepts/ercr-ar.scroll b/concepts/ercr-ar.scroll
@@ -2,7 +2,7 @@ import ../measures/conceptPage.scroll
 id ERCR
 type registry
 standsFor Entre Ríos Cancer Registry
-conceptDescription Entre Ríos State Population-Based Cancer Registry, also seems to be called Registro Poblacional de Tumores de Concordia (Cancer Registry of Concordia) 
+conceptDescription Entre Ríos State Population-Based Cancer Registry, also seems to be called Registro Poblacional de Tumores de Concordia (Cancer Registry of Concordia)
 
 reference https://www.paho.org/hq/dmdocuments/2009/Registries%20in%20Latin%20America%20and%20the%20Caribbean%20and%20its%20relation%20to%20cancer%20programs_Laura_IARC.pdf
 reference https://publications.iarc.fr/_publications/media/download/3637/5216466e44d81ede51575b4886667b9cdc315043.pdf

diff --git a/concepts/iacc-ao.scroll b/concepts/iacc-ao.scroll
@@ -2,7 +2,7 @@ import ../measures/conceptPage.scroll
 id IACC
 type registry
 appeared 2007
-standsFor Instituto Angolano de Controlo do Cancer 
+standsFor Instituto Angolano de Controlo do Cancer
 conceptDescription The Instituto Angolano de Controlo do Cancer (IACC) Cancer Registry in Luanda, Angola is the most ancient and organized hospital-based cancer registry in Angola and provides data on cancer cases treated in several hospital facilities in Luanda.The Instituto Angolano de Controlo do Cancer (IACC) in Luanda (formerly the National Oncology Centre), is the oldest public centre for the treatment of cancer patients in Angola and hosts a hospital-based cancer registry. The registry employs passive methods of case finding and receives information from two semi-private institutions in Luanda. The primary data sources are the inpatient wards and oncology outpatient clinics of IACC. Additionally, records of specific cancer research studies are included. Information from the other public hospitals in Luanda, (Prenda Hospital, Central Military Hospital, Augusto Ngangula Maternity) is only included in the registry when the patient is transferred to the IACC for eventual treatment or multidisciplinary team discussion. Currently, there is no active case finding and minimal follow-up of cases performed by HBCR/IACC.
 
 reference https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839121/

diff --git a/concepts/ncr-ar.scroll b/concepts/ncr-ar.scroll
@@ -2,8 +2,8 @@ import ../measures/conceptPage.scroll
 id NCR-AR
 type registry
 appeared 2007
-standsFor Neuquén Cancer Registry Argentina 
-conceptDescription In 2007, the Neuquén Undersecretary of Health, by Provision No. 1727, created the Permanent Commission for the Provincial Registry of Tumors under the Department of Information and Planning, within the scope of the Undersecretary of Health. During 2008, the "Confidentiality Directives" were prepared for this registry, in accordance with Provincial Law No. 2399/03, to guarantee the right to honor and privacy of individuals and regulate access to the information that is registered. The Neuquén Registry will be of the Population type since it collects the data on new cases that occur in a resident population in a certain geographical area, an essential requirement to calculate the incidence. 
+standsFor Neuquén Cancer Registry Argentina
+conceptDescription In 2007, the Neuquén Undersecretary of Health, by Provision No. 1727, created the Permanent Commission for the Provincial Registry of Tumors under the Department of Information and Planning, within the scope of the Undersecretary of Health. During 2008, the "Confidentiality Directives" were prepared for this registry, in accordance with Provincial Law No. 2399/03, to guarantee the right to honor and privacy of individuals and regulate access to the information that is registered. The Neuquén Registry will be of the Population type since it collects the data on new cases that occur in a resident population in a certain geographical area, an essential requirement to calculate the incidence.
 
 reference https://hero.epa.gov/hero/index.cfm/reference/details/reference_id/9825163
 reference https://www.hospitalneuquen.org.ar/institucional/sistema-de-salud/registro-de-tumores-del-neuquen/

diff --git a/concepts/nswcr-au.scroll b/concepts/nswcr-au.scroll
@@ -3,7 +3,7 @@ id NSWCR
 type registry
 appeared 1972
 standsFor The New South Wales Cancer Registry
-conceptDescription The NSWCR is the first Australian population-based cancer registry to include data on cancer stage, treatment and quality of care. Treatment delivered in the majority of hospitals in the public sector is covered, with data from the remaining public hospitals and the private sector being included in the future.Notification of new cancer cases and cancer deaths is required under the Public Health Act 2010.The NSWCR contains demographic, incidence and death details for people diagnosed with cancer in NSW since 1972. It also includes these details for residents of NSW diagnosed with cancer in other Australian states and territories. 
+conceptDescription The NSWCR is the first Australian population-based cancer registry to include data on cancer stage, treatment and quality of care. Treatment delivered in the majority of hospitals in the public sector is covered, with data from the remaining public hospitals and the private sector being included in the future.Notification of new cancer cases and cancer deaths is required under the Public Health Act 2010.The NSWCR contains demographic, incidence and death details for people diagnosed with cancer in NSW since 1972. It also includes these details for residents of NSW diagnosed with cancer in other Australian states and territories.
 
 website https://www.cancer.nsw.gov.au/research-and-data/cancer-data-and-statistics/request-unlinked-unit-record-data-for-research/nsw-cancer-registry
 reference https://www.cancer.nsw.gov.au

diff --git a/concepts/sacr-au.scroll b/concepts/sacr-au.scroll
@@ -3,7 +3,7 @@ id SACR
 type registry
 appeared 1977
 standsFor South Australian Cancer Registry
-conceptDescription The South Australian Cancer Registry operates within Wellbeing SA’s Epidemiology Branch and supports surveillance of trends in cancer incidence, mortality and survival within South Australia, as well as insight into affected populations and risk factors for cancer. This database helps to inform cancer service planning and health policy, as well supports evaluation of prevention activities and local screening services such as the Cervix Screening Program and BreastScreen SA. The South Australian Cancer Registry has been collecting data about cancer since 1977. This continuous monitoring provides a rich database to support identification of changes in cancer incidence patterns over time, and allows for prompt response to public concerns about clusters of cancer or regional evaluations when required. 
+conceptDescription The South Australian Cancer Registry operates within Wellbeing SA’s Epidemiology Branch and supports surveillance of trends in cancer incidence, mortality and survival within South Australia, as well as insight into affected populations and risk factors for cancer. This database helps to inform cancer service planning and health policy, as well supports evaluation of prevention activities and local screening services such as the Cervix Screening Program and BreastScreen SA. The South Australian Cancer Registry has been collecting data about cancer since 1977. This continuous monitoring provides a rich database to support identification of changes in cancer incidence patterns over time, and allows for prompt response to public concerns about clusters of cancer or regional evaluations when required.
 
 website https://www.wellbeingsa.sa.gov.au/evidence-data/south-australian-cancer-registry
 

diff --git a/concepts/tcr-au.scroll b/concepts/tcr-au.scroll
@@ -2,7 +2,7 @@ import ../measures/conceptPage.scroll
 id TCR
 type registry
 appeared 1978
-standsFor Tasmanian Cancer Registry 
+standsFor Tasmanian Cancer Registry
 conceptDescription The Tasmanian Cancer registry is responsible for collecting, collating and reporting incidence of all malignant neoplasms in Tasmanian residents. By law, cancer registration is required in all Australian States and Territories to assist State and National efforts to understand the causes of cancer, to plan health services and assist prevention efforts and treatment decisions. The Tasmanian Cancer Registry is funded by the Department of Health Tasmania. The Director of the Registry is Dr Jessica Roydhouse, and the manager is Bruna Ragaini.The Registry produces annual reports with data on the number of cancer cases and deaths from cancer, and periodical reports on cancer survival and prevalence.
 
 website https://www.menzies.utas.edu.au/research/research-centres/tasmanian-cancer-registry

diff --git a/concepts/wacanreg.scroll b/concepts/wacanreg.scroll
@@ -2,7 +2,7 @@ import ../measures/conceptPage.scroll
 id WACANREG
 type registry
 appeared 1982
-standsFor Western Australian Cancer Registry 
+standsFor Western Australian Cancer Registry
 conceptDescription The Western Australian Cancer Registry collects information about cancer diagnoses across the State. This information is required to be collected by law from pathology reports and radiation oncology treatment records.A separate register records asbestos exposure and other history for all cases of malignant mesothelioma.
 
 website https://www.health.wa.gov.au/Articles/U_Z/Western-Australian-Cancer-Registry

diff --git a/download.scroll b/download.scroll
@@ -1,5 +1,10 @@
-import rootHeader.scroll
 title Download CancerDB
+writeConcepts cancerdb.csv cancerdb.json cancerdb.tsv
+ sortBy -measurements
+writeMeasures measures.tsv measures.csv measures.json
+
+import rootHeader.scroll
+printTitle
 
 css
  .scrollTable td {
@@ -15,15 +20,12 @@ Download the CancerDB concept dataset as: CSV | TSV | JSON
 
 import measures/cancerDBMeasures.scroll
 loadConcepts concepts
-writeConcepts cancerdb.csv cancerdb.json cancerdb.tsv
- sortBy -measurements
 
 Statistics on the measures (columns) are below and can be downloaded as: CSV | TSV | JSON
  link measures.csv CSV
  link measures.tsv TSV
  link measures.json JSON
-writeMeasures measures.tsv measures.csv measures.json
 printMeasures
 tableSearch
 
-import footer.scroll
+import footer.scroll
diff --git a/index.scroll b/index.scroll
@@ -1,8 +1,10 @@
-import rootHeader.scroll
-
 title CancerDB
  hidden
 
+import rootHeader.scroll
+
+printTitle
+
 # CancerDB: Datasets about Cancer
 
 <center>

diff --git a/list.scroll b/list.scroll
@@ -1,6 +1,8 @@
-import rootHeader.scroll
 title CancerDB - All Concepts
 
+import rootHeader.scroll
+printTitle
+
 snippets concepts/All
 
 import footer.scroll
diff --git a/measures/cancerDBMeasures.scroll b/measures/cancerDBMeasures.scroll
@@ -9,7 +9,6 @@ amazonParser
  extends abstractUrlMeasureParser
  description What is the Amazon product URL for this item?
 
-
 // annualDeathsReport
 annualDeathsReportParser
  cells measureNameCell stringCell urlCell
@@ -237,7 +236,7 @@ oldNameParser
 tradenamesParser
  description What are the tradenames for the drug?
  extends abstractStringMeasureParser
- listDelimiter  && 
+ listDelimiter  &&
 
 // nci
 // todo Add enum for: Comprehensive Cancer Center && Basic Laboratory Cancer Center && Cancer Center
@@ -499,4 +498,4 @@ youTubeChannelParser
  description What is the URL of this entity's YouTube channel?
  string sourceDomain youtube.com
  followersParser
-  extends abstractFollowersParser
+  extends abstractFollowersParser
diff --git a/measures/commonMeasures.scroll b/measures/commonMeasures.scroll
@@ -41,7 +41,6 @@ abstractConceptIdsMeasureParser
   }
   // todo: re-add the method to update these foreign keys if an ID changes.
 
-
 // Common blob parsers
 abstractStringBlobMeasureParser
  string typeForCsvDocs multilineString

diff --git a/measures/conceptPage.scroll b/measures/conceptPage.scroll
@@ -1,22 +1,20 @@
 importOnly
-replace BASE_URL ..
-import cancerDBMeasures.scroll
-
 groups All
-
-keyboardNav
-
-import ../header.scroll
-
-viewSourceBaseUrl https://github.com/breck7/CancerDB/blob/main/concepts/
-
+replace BASE_URL ..
 replaceJs TEMPLATE
  {
   const code = originalScrollCode.replace("import ../measures/conceptPage.scroll\n", "");
   const template = `title ${tree.get("id")}\ncode\n ${code.replace(/\n/g, "\n ")}`;
   template;
  }
+viewSourceBaseUrl https://github.com/breck7/CancerDB/blob/main/concepts/
+
+import cancerDBMeasures.scroll
+
+keyboardNav
+
+import ../header.scroll
+
 TEMPLATE
 
 import ../footer.scroll
-
diff --git a/package.json b/package.json
@@ -25,6 +25,6 @@
   "homepage": "https://cancerdb.com",
   "dependencies": {
     "lodash": "^4.17.21",
-    "scroll-cli": "^87.0.0"
+    "scroll-cli": "^89.0.0"
   }
 }
diff --git a/pages/about.scroll b/pages/about.scroll
@@ -1,8 +1,9 @@
 groups index
 replaceJs BUILT_ON_DAY dayjs().format("MM/DD/YYYY")
+title About
 
 import header.scroll
-title About
+printTitle
 
 thinColumns 2
 

diff --git a/pages/acknowledgements.scroll b/pages/acknowledgements.scroll
@@ -10,9 +10,10 @@ replaceNodejs
      .map(item => `- ${item.login}\n ${item.html_url}`)
      .join("\n")
  }
+title Acknowledgements
 
 import header.scroll
-title Acknowledgements
+printTitle
 // IMPORTS
 
 thinColumns 4

diff --git a/pages/explore.scroll b/pages/explore.scroll
@@ -1,11 +1,4 @@
-import header.scroll
 groups index
-
-<div class="singleColumn">
-title Explore CancerDB
-
-endSnippet
-
 replaceNodejs
  const lodash = require("lodash")
  const data = lodash.chain(require("../cancerdb.json"))
@@ -16,10 +9,18 @@ replaceNodejs
  const rows = lodash.map(data, row => lodash.values(row).join('\t'));
  const tsv = [header, ...rows].join('\n ');
  module.exports = {ALL : 'tabTable\n ' + tsv}
+title Explore CancerDB
+
+import header.scroll
+
+<div class="singleColumn">
+printTitle
+
+endSnippet
 
 ALL
 
 </div>
 
 import ../footer.scroll
-tableSearch
+tableSearch
diff --git a/posts/cancer-heatmaps.scroll b/posts/cancer-heatmaps.scroll
@@ -1,13 +1,14 @@
 author https://github.com/breck7 Breck Yunits
 date 03-15-2023
 groups All
+openGraphImage https://cancerdb.com/posts/cancerHeatmap.jpg
 replaceNodejs
  module.exports = require(`./heatmap.json`)
-openGraphImage https://cancerdb.com/posts/cancerHeatmap.jpg
+title Cancer in the United States
 
 import header.scroll
 
-title Cancer in the United States
+printTitle
 
 # Heatmap visualizations
 

diff --git a/posts/cat-food.scroll b/posts/cat-food.scroll
@@ -1,9 +1,10 @@
 date 11-29-2022
 groups Commercials
 openGraphImage https://cancerdb.com/posts/catfood.png
+title Cat food
 
 import header.scroll
-title Cat food
+printTitle
 
 youTube https://www.youtube.com/embed/e0fPvvDBY6s
 

diff --git a/posts/commercials.scroll b/posts/commercials.scroll
@@ -1,4 +1,6 @@
-import header.scroll
 title CancerDB Commercials
+
+import header.scroll
+printTitle
 snippets commercials
 import ../footer.scroll
diff --git a/posts/funQuiz.scroll b/posts/funQuiz.scroll
@@ -1,9 +1,10 @@
 date 12-09-2022
 groups Commercials
 openGraphImage https://cancerdb.com/posts/funQuiz.jpg
+title Fun quiz
 
 import header.scroll
-title Fun quiz
+printTitle
 
 youTube https://www.youtube.com/embed/b4VE9cx8bhQ