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Copy file name to clipboardexpand all lines: docs/customization.md
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## Gene information and GO terms
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By default, RDP will retrieve the latest gene information from NCBI, and GO terms
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from [Ontobee](http://www.ontobee.org/ontology/OBI). Users genes and GO terms will be updated after a
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successful update.
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from [Ontobee](http://www.ontobee.org/ontology/OBI). Users genes and GO terms will be updated after a successful update.
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Gene information are obtained from [NCBI Gene FTP server](https://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/)
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with URLs stored in the database. You can retrieve these with the following query:
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```sql
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select taxon_id, scientific_name, gene_url from taxon;
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```
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For example, the `gene_url` column for *Homo sapiens* would contain `ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz`
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For example, the `gene_url` column for *Homo sapiens* would
The taxon table is pre-populated during the very first installation of the software, at which time only Human taxon is activated. To enable other taxons, set their `active` column to `1` in the database.
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The taxon table is pre-populated during the very first installation of the software, at which time only Human taxon is
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activated. To enable other taxon, set their `active` column to `1` in the database.
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For example, the following will activate the mouse taxon:
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```sql
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update taxon set active =1where taxon_id =10090;
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```
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Every time the new model organisams are added to the application, they will have to be activated in this manner.
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Every time the new model organisms are added to the application, they will have to be activated in this manner.
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## Ortholog mapping
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There is an ortholog mapping file that is included with the application and will automatically
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populate the database on startup. The ortholog mappings are based
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There is an ortholog mapping file that is included with the application and will automatically populate the database on
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startup. The ortholog mappings are based
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on [DIOPT](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-357).
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The default value points to a classpath resource included within RDP archive:
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It's also possible to store all the above mentioned info locally, instead of fetching it remotely. The following settings will retrieve all the necessary files relative to the
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working directory of the Web application:
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It's also possible to store all the above mentioned info locally, instead of fetching it remotely. The following
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settings will retrieve all the necessary files relative to the working directory of the Web application:
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```ini
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#this setting relates only to gene info files. Files for all taxons will be stord under gene/
A secure communication between different instances is achieved using a special search token which gets appended to remote queries. Currently there is one
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token that is used by all partner registries.
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A secure communication between different instances is achieved using a special search token which gets appended to
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remote queries. Currently, there is one token that is used by all partner registries.
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The token can be generated using OpenSSL: `openssl rand -base64 24` and it would look something like this: `hrol3Y4z2OE0ayK227i8oHTLDjPtRfb4` (this is just an example). Once generated, this token is shared securely with partner registries.
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The token can be generated using OpenSSL: `openssl rand -base64 24` and it would look something like
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this: `hrol3Y4z2OE0ayK227i8oHTLDjPtRfb4` (this is just an example). Once generated, this token is shared securely with
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partner registries.
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The token is added to the `application.properties` file in the following way:
This allows you to query private data from the partner registry when logged in as an administrator on your own
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registry.
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This allows you to query private data from the partner registry when logged in as an administrator on your own registry.
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## Gene Tiers
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Users' genes are categorized in tiers based on their familiarity and experience with the gene. This is explained in detail in the users' documentation and FAQs. Users add TIER1 and TIER2 genes directly, while TIER3 genes are inferred from GO term associations.
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Users' genes are categorized in tiers based on their familiarity and experience with the gene. This is explained in
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detail in the users' documentation and FAQs. Users add TIER1 and TIER2 genes directly, while TIER3 genes are inferred
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from GO term associations.
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To enable only TIER1 and TIER2, and thus disabling GO terms-related features, add the following to your configuration:
Some text displayed in RDP can be customized and/or internationalized. To do so, copy a provided `messages.properties` file in the working directory of the Web application and edit it. The file is found in
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Some text displayed in RDP can be customized and/or internationalized. To do so, copy a provided `messages.properties`
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file in the working directory of the Web application and edit it. The file is found in
For custom cloud deployments see [Spring Boot: Deploying to the Cloud](https://docs.spring.io/spring-boot/docs/current/reference/html/cloud-deployment.html).
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For custom cloud deployments
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see [Spring Boot: Deploying to the Cloud](https://docs.spring.io/spring-boot/docs/current/reference/html/cloud-deployment.html)
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.
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To install as a system service see [Spring Boot: Installing Spring Boot Applications](https://docs.spring.io/spring-boot/docs/current/reference/html/deployment-install.html).
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To install as a system service
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see [Spring Boot: Installing Spring Boot Applications](https://docs.spring.io/spring-boot/docs/current/reference/html/deployment-install.html)
This file contains the database and SMTP credentials and various runtime
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configurations. Make sure it's only readable by the user that will run the
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instance.
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This file contains the database and SMTP credentials and various runtime configurations. Make sure it's only readable by
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the user that will run the instance.
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Documentation for options with their default values are available in [application.properties](https://github.com/PavlidisLab/rgr/blob/development/src/main/resources/application.properties).
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Documentation for options with their default values are available
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in [application.properties](https://github.com/PavlidisLab/rgr/blob/development/src/main/resources/application.properties)
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.
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That should be enough to get the Web service started. Now you can launch it by
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issuing the following command:
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That should be enough to get the Web service started. Now you can launch it by issuing the following command:
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```bash
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java -jar rdp-{{ config.extra.rdp_version }}.jar
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```
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If your email server is not properly configured, you will see an error from the
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Spring Actuator health check. You can detect further issues by looking at the
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If your email server is not properly configured, you will see an error from the Spring Actuator health check. You can
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detect further issues by looking at the
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`/admin/health` endpoint with administrative privilege.
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