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[[scipamato]] == SciPaMaTo
SciPaMaTo (Scientific Paper Management Tool) is a database centric application that was developed for and with the LUDOK team of the Swiss Tropical and Public Health Institute (https://www.swisstph.ch/[Swiss TPH]) located in Basel, Switzerland.
https://www.swisstph.ch/en/projects/ludok/[LUDOK] (in German: "Dokumentationsstelle Luftverschmutzung und Gesundheit") is a documentation office that has been collecting and cataloguing scientific literature regarding the effects of air pollution on human health for over 30 years. This is a service LUDOK provides on behalf of the Swiss Federal Office for the Environment (https://www.bafu.admin.ch/bafu/en/home.html[FOEN]).
SciPaMaTo was developed under the BSD-3 license to replace the former Filemaker Database that has been serving its purpose for many years.
SciPaMaTo consists of two main components:
SciPaMaTo is a Spring Boot web-application using Apache Wicket as front-end and stores the data in PostgreSQL-Databases. It offers simplified ways of importing relevant items of information from Pubmed. SciPaMaTo offers quite extensive search facilities that allow scrutinizing the database. Parts of the data managed within ScipMaTo-Core can be synchronized into SciPaMaTo-Public, which is accessible for the interested public over the internet.
=== C4-Diagrams
==== Context Diagram
flowchart TD
PM["PubMed<br/>[Software System]<br/><br/>National Library of Medicine"]
click PM href "https://pubmed.ncbi.nlm.nih.gov" _blank
PublicViewer["Public Viewer<br/>[Person]<br/><br/>Anonymous Reader<br/>on the Internet"]
subgraph dmz[DMZ]
SP["SciPaMaTo Public<br/>[Software System]<br/><br/>Public System,<br/>reachable anonymously<br/>from public internet"]
click SP href "https://www.swisstph.ch/en/projects/ludok/datenbanksuche" _blank
SPDB("fas:fa-database Public Database<br/>[System DB]")
end
subgraph internal[Internal Network]
Editor["Editor<br/>[Person]<br/><br/>Maintaining<br/>data in Core"]
Viewer["Read only user<br/>[Person]<br/><br/>Read only viewer<br/>in SciPaMaTo-Core"]
Admin["Admin user<br/>[Person]<br/><br/>User maintaining<br/>user accounts"]
SC["SciPaMaTo Core<br/>[Software System]<br/><br/>Core System,<br/>only reachable inside<br/>the private network"]
SCDB("fas:fa-database Core Database<br/>[System DB]")
end
Editor<==>|"Enters and<br/>maintains data"|SC
Viewer<-->|"Views Data"|SC
Admin<-->|"Maintains user<br/>accounts in"|SC
SC<--->|"imports from"|PM
SC<-.->|"read/write"|SCDB
SC-.->|"synchronizes"|SPDB
SP-.-|"read only"|SPDB
PublicViewer-->|"searches database,<br/>views newsletters"|SP
classDef focusSystem fill:#1168bd,stroke:#0b4884,color:#ffffff
classDef supportingSystem fill:#666,stroke:#0b4884,color:#ffffff
classDef person fill:#08427b,stroke:#052e56,color:#ffffff
classDef boundary fill:none,stroke:#CCC,stroke-width:2px,stroke-dasharray: 5 5
class Editor,Viewer,Admin,PublicViewer person
class SC,SP focusSystem
class PM supportingSystem
class dmz,internal boundary==== Container Diagram SciPaMaTo-Core
flowchart TD
PM["PubMed<br/>[Software System]<br/><br/>National Library of Medicine"]
subgraph dmz[DMZ]
subgraph dbserver2[DB Server]
SPDB("fas:fa-database Public Database<br/>[PostgreSQL]")
end
end
subgraph internal[Internal Network]
Editor["Editor<br/>[Person]<br/><br/>Maintaining<br/>data in Core"]
Viewer["Read only user<br/>[Person]<br/><br/>Read only viewer<br/>in SciPaMaTo-Core"]
Admin["Admin user<br/>[Person]<br/><br/>User maintaining<br/>user accounts"]
subgraph webserver[Web Server]
RP["Reverse Proxy<br/>[Apache HTTPD]"]
SC["Web Application<br/>[Spring Boot Application]"]
end
subgraph dbserver1[DB Server]
SCDB("fas:fa-database Core Database<br/>[PostgreSQL]")
end
Editor<==>|"enters and<br/>maintains data<br/>[HTTPS]"|RP
Editor<-->|"triggers<br/>sync to public<br/>[HTTPS]"|RP
Editor<-->|"triggers<br/>import from PubMed<br/>[HTTPS]"|RP
Viewer<-->|"Views Data<br/>[HTTPS]"|RP
Admin<-->|"Maintains user<br/>accounts in<br/>[HTTPS]"|RP
end
RP<-->|"relays<br/>[HTTP]"|SC
SC-.-|"reads/writes<br/>[JDBC]"|SCDB
SC-.->|"synchronizes<br/>[JDBC]"|SPDB
SC<--->|"imports<br/>from<br/>[HTTPS]"|PM
classDef container fill:#1168bd,stroke:#0b4884,color:#ffffff
classDef supportingSystem fill:#666,stroke:#0b4884,color:#ffffff
classDef person fill:#08427b,stroke:#052e56,color:#ffffff
class Editor,Viewer,Admin person
class SC,RP,SCDB container
class PM,SPDB supportingSystem
classDef boundary fill:none,stroke:#CCC,stroke-width:2px,stroke-dasharray: 5 5
class dmz,internal boundary
classDef server fill:none,stroke:#CCC,stroke-width:2px,stroke-dasharray: 5 5
class dbserver1,dbserver2,webserver server==== Container Diagram SciPaMaTo-Public
flowchart TD
Searcher["Database Searcher<br/>[Person]<br/><br/>Anonymous Reader<br/>on the Internet"]
Viewer["Newsletter Viewer<br/>[Person]<br/><br/>Anonymous Reader<br/>on the Internet"]
subgraph dmz[DMZ]
subgraph webserverp[Web Server]
RP["Reverse Proxy<br/>[Apache HTTPD]"]
SP["Web Application<br/>[Spring Boot Application]"]
click SP href "https://www.swisstph.ch/en/projects/ludok/datenbanksuche" _blank
end
subgraph dbserverp[DB Server]
SPDB("fas:fa-database Public Database<br/>[PostgreSQL]")
end
end
subgraph internal[Internal Network]
subgraph webserverc[Web Server]
SC["Web Application<br/>[Spring Boot Application]"]
end
subgraph dbserverc[DB Server]
SCDB("fas:fa-database Core Database<br/>[PostgreSQL]")
end
SC<-.->|"[JDBC]"|SCDB
end
Searcher<-->|"searches database<br/>[HTTPS]"|RP
Viewer<-->|"views newsletters<br/>[HTTPS]"|RP
RP<-->|"relays<br/>[HTTP]"|SP
SP-.-|"read only<br/>[JDBC]"|SPDB
SC-.->|"synchronizes<br/>[JDBC]"|SPDB
classDef container fill:#1168bd,stroke:#0b4884,color:#ffffff
classDef supportingSystem fill:#666,stroke:#0b4884,color:#ffffff
classDef person fill:#08427b,stroke:#052e56,color:#ffffff
class Searcher,Viewer,CoreUser person
class SP,RP,SPDB container
class SC,SCDB supportingSystem
classDef boundary fill:none,stroke:#CCC,stroke-width:2px,stroke-dasharray: 5 5
class dmz,internal boundary
classDef server fill:none,stroke:#CCC,stroke-width:2px,stroke-dasharray: 5 5
class dbserverp,dbserverc,webserverp,webserverc server[[technology-stack]] == Technology Stack
[[architecture-documentation]] == Architecture Documentation
I started using https://structure101.com/[Structure101] to assess and track the architecture of SciPaMaTo. Many thanks to the friendly people of Structure101 to provide a free license for SciPaMaTo as an open source project!
image:https://structure101.com/images/s101_170.png[Structure101]
[[user-documentation]] == User Documentation
[[user-docu-scipamato-core]] === SciPaMaTo-Core Documentation
[[user-docu-scipamato-public]] === SciPaMaTo-Public Documentation
[[information-for-developers]] == Information for Developers
Refer to the https://github.com/ursjoss/scipamato/wiki/QuickStart[Quick-Start Guide] to get the project up and running as quickly as possible.
See https://github.com/ursjoss/scipamato/wiki/Developer-Information[Developer Wiki]
[[information-for-operations]] == Information for Operations
See https://github.com/ursjoss/scipamato/wiki/Operations[Operations Wiki]