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Commit 0bfcc93f authored by Diogo Batista Lima's avatar Diogo Batista Lima
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Update README-Template.md

parent 40b62699
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## How to use
<!--
#### HTTP Request through Neo4j Browser
Blueprint Repository was implemented with a Neo4j database. This database management system includes the Neo4j Browser tool which allows
users to access a given database's contents through a web browser, without requiring programming knowledge. After connecting to Universidade
do Minho's VPN, go to the following [link](http://palsson.di.uminho.pt:7475/browser/) to access Neo4j Browser. In the main page enter the following
credentials:
* Connect URL - bolt://palsson.di.uminho.pt:7688
* Username - neo4j
* Password - admin
Click the left database logo to see the database's contents, including its nodes, relationships and properties. One may click any of the
aforementioned entities to automatically access a set of examples. Custom queries may be entered in the upper bar prompt. Neo4j Browser
does not give access to Blueprint's source code, data and tools but it enables accessing the database's contents without requiring additional dependencies.
#### Palsson server SSH access to a Docker with source code via Ubuntu command line
Open Ubuntu command line and enter:
`ssh dlima@palsson.di.uminho.pt`
Password - blueprint2019
To access Blueprint's source code enter:
`cd blueprint_docker/code`
To try Blueprint's Request system enter the following commands after accessing the Palsson server:
`cd blueprint_docker`
`docker run -v /home/dlima/blueprint_docker//:/home/ -it blueprint_code`
The menu interface allows access to the database and its contents. Enter 0 for a short explanation regarding each option.
#### Download source code, data and tools
To explore all the source code, downloaded/generated data and tools go to the following OneDrive [link](https://uminho365-my.sharepoint.com/personal/pg32938_uminho_pt/_layouts/15/onedrive.aspx?id=%2Fpersonal%2Fpg32938_uminho_pt%2FDocuments%2FBlueprint_repository%2FBlueprint_TRN_Repository.rar&parent=%2Fpersonal%2Fpg32938_uminho_pt%2FDocuments%2FBlueprint_repository&cid=a4e2f5a8-708e-4131-ac9b-f82d236deb35)
and download the rar file. To execute the downloaded code it is necessary to install the dependencies listed on the next section and to connect to
Universidade do Minho's VPN (to access Blueprint's database hosted in the Palsson server)-->
## Prerequisites
<!--
To access the database via web browser it is only necessary to have access to the Universidade do Minho's VPN and follow the previous instructions.
To access Blueprint's source code and Request system via SSH access to the Palsson server it is necessary to have access to the Universidade do Minho's VPN
and to a [Ubuntu](https://www.microsoft.com/en-us/p/ubuntu/9nblggh4msv6?activetab=pivot:overviewtab) command line. To explore all of Blueprint's content
after downloading the rar file from the OneDrive service, it is necessary to fulfill a few prerequisites. -->
All code was written in Python 3.6, thus it it is necessary to install [Python](https://www.python.org/downloads/). Any Python 3 version should work
......@@ -74,15 +34,6 @@ Visit [http://localhost:7474](http://localhost:7474) in your web browser of choi
* [seaborn](https://pypi.org/project/seaborn/) - Another option for publication quality graphics `pip install seaborn`
* [bioservices](https://pypi.org/project/bioservices/) - Biological Web Services used for Uniprot requests `pip install bioservices`
## Blueprint Repository source code and tools - what has been done and how to use it
The downloadable Blueprint Repository rar file is divided in four directories:
* data - all data downloaded/generated throughout the construction of the database
* neo4j_database - a local backup of the most recent version of the database
* topology - a document detailing the database's structure, its topology and the meaning behind the data and its relationships
* code - contains all code developed for the five repository systems; Data Retrieval, Knowledge Expansion, Integration, Report and Request. Additional tools, such as Automatic Integration of TRNs are also in this directory
#### Code - Structure
The database construction process included the integration of 10 external sources:
......
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