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7 changes: 3 additions & 4 deletions docs/api.md
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Expand Up @@ -14,9 +14,8 @@ Authorization: Bearer {accessToken}

Passing the authorization token via `auth` query parameter is deprecated as of 1.4.0.

Keep in mind that the token you use is tied to a user that has permissions.
What you can see through the API will be restricted to what the corresponding
user is authorized to read.
Keep in mind that the token you use is tied to a user that has permissions. What you can see through the API will be
restricted to what the corresponding user is authorized to read.

## List all users

Expand Down Expand Up @@ -55,7 +54,7 @@ GET /api/users/search HTTP/1.1
By name:

- `nameLike` a name in the user profile
- `prefix` a boolean `true` or `false` as to whether the name search is matching a prefix
- `prefix` a boolean `true` or `false` whether the name search is matching a prefix

By description:

Expand Down
100 changes: 51 additions & 49 deletions docs/customization.md
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Expand Up @@ -15,16 +15,17 @@ update the software.
## Gene information and GO terms

By default, RDP will retrieve the latest gene information from NCBI, and GO terms
from [Ontobee](http://www.ontobee.org/ontology/OBI). Users genes and GO terms will be updated after a
successful update.
from [Ontobee](http://www.ontobee.org/ontology/OBI). Users genes and GO terms will be updated after a successful update.

Gene information are obtained from [NCBI Gene FTP server](https://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/)
with URLs stored in the database. You can retrieve these with the following query:

```sql
select taxon_id, scientific_name, gene_url from taxon;
```
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`

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`

Genes' GO term annotations are also obtained from NCBI:

Expand All @@ -38,23 +39,23 @@ GO terms, on the other hand, are obtained from Ontobee:
rdp.settings.cache.term-file=http://purl.obolibrary.org/obo/go.obo
```



## Taxon

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.
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 taxon, set their `active` column to `1` in the database.

For example, the following will activate the mouse taxon:

```sql
update taxon set active = 1 where taxon_id = 10090;
```
Every time the new model organisams are added to the application, they will have to be activated in this manner.

Every time the new model organisms are added to the application, they will have to be activated in this manner.

## Ortholog mapping

There is an ortholog mapping file that is included with the application and will automatically
populate the database on startup. The ortholog mappings are based
There is an ortholog mapping file that is included with the application and will automatically populate the database on
startup. The ortholog mappings are based
on [DIOPT](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-357).

The default value points to a classpath resource included within RDP archive:
Expand All @@ -63,11 +64,13 @@ The default value points to a classpath resource included within RDP archive:
rdp.settings.cache.ortholog-file=classpath:cache/DIOPT_filtered_data_May2021.gz
```

It would also be possible to use another orthology resource, as long as it has the same format. For example, to use the NCBI gene orthologs:
It would also be possible to use another ortholog resource, as long as it has the same format. For example, to use the
NCBI gene orthologs:

```ini
rdp.settings.cache.orthologs-file=ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_orthologs.gz
```

As with other remotely downloaded files, this would be updated monthly.

## Organ systems
Expand All @@ -80,17 +83,17 @@ and updated monthly.
rdp.settings.cache.organ-file=http://purl.obolibrary.org/obo/uberon.obo
```

Only a select few organ systems are active by default. You can activate more by running the following SQL command with a
Uberon identifier of your choice:
Only a select few organ systems are active by default. You can activate more by running the following SQL command with
an Uberon identifier of your choice:

```sql
update organ_info
set active = true
where uberon_id = '<uberon_id>';
```

If you activate a non-default organ system, consider adding an icon for it by
following the instructions in the [Style and static resources](#style-and-static-resources)
If you activate a non-default organ system, consider adding an icon for it by following the instructions in
the [Style and static resources](#style-and-static-resources)
section below.

To disable organ systems altogether, set the following in your configuration:
Expand All @@ -101,8 +104,8 @@ rdp.settings.organs.enabled=false

## Loading data from disk

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
working directory of the Web application:
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 working directory of the Web application:

```ini
#this setting relates only to gene info files. Files for all taxons will be stord under gene/
Expand All @@ -119,9 +122,9 @@ rdp.settings.cache.organ-file=file:uberon.obo
rdp.settings.cache.ortholog-file=file:DIOPT_filtered_data_March2020.txt
```

With `rdp.settings.load-from-disk` enabled, the basename from the `gene_url` (mentioned above) will
be used in conjustion with `rdp.settings.gene-files-location`. For example *Homo
sapiens* taxon would be retrieved from `genes/Homo_sapiens.gene_info.gz`
With `rdp.settings.load-from-disk` enabled, the basename from the `gene_url` (mentioned above) will be used in
conjunction with `rdp.settings.gene-files-location`. For example *Homo sapiens* taxon would be retrieved
from `genes/Homo_sapiens.gene_info.gz`

## International data

Expand All @@ -131,40 +134,40 @@ do not have HTTPS setup for you domain, you can consult the following guides on
- [medium.com/@raupach/how-to-install-lets-encrypt-with-tomcat-3db8a469e3d2](https://medium.com/@raupach/how-to-install-lets-encrypt-with-tomcat-3db8a469e3d2)
- [community.letsencrypt.org/t/configuring-lets-encrypt-with-tomcat-6-x-and-7-x/32416](https://community.letsencrypt.org/t/configuring-lets-encrypt-with-tomcat-6-x-and-7-x/32416)

Registries can access each other public data by enabling `rdp.settings.isearch.enabled` and setting up the `rdp.settings.isearch.apis` in
the `application.properties` file to contain a comma-delimited list of partner registry URLs.
Registries can access each other public data by enabling `rdp.settings.isearch.enabled` and setting up
the `rdp.settings.isearch.apis` in the `application.properties` file to contain a comma-delimited list of partner
registry URLs.

```ini
rdp.settings.isearch.enabled=true
rdp.settings.isearch.apis=https://register.rare-diseases-catalyst-network.ca/
```

A secure communication between different instances is achieved using a special search token which gets appended to remote queries. Currently there is one
token that is used by all partner registries.
A secure communication between different instances is achieved using a special search token which gets appended to
remote queries. Currently, there is one token that is used by all partner registries.

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.
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.

The token is added to the `application.properties` file in the following way:

```ini
rdp.settings.isearch.search-token=hrol3Y4z2OE0ayK227i8oHTLDjPtRfb4
```


On the receiving side, the partner registry must create a user that is used to perform privileged searches.

This is usually done by creating a remote administrative account:

```sql
insert into user ( email, enabled, password, privacy_level, description, last_name, name, shared, hide_genelist, contact_email_verified)
values(concat(rand(),"@rdmm.com"), 0, md5(rand()), 0, "remote admin profile", "", "", false, false, false);
values(concat(rand(),'@rdmm.com'), 0, md5(rand()), 0, 'remote admin profile', '', '', false, false, false);
insert into user_role (user_id,role_id) values ((select max(user_id) from user), 1);
insert into user_role (user_id,role_id) values ((select max(user_id) from user), 2);
select max(user_id) from user;
```



Let's assume that the created user's ID was 522. The partner would then add the token to
its `rdp.settings.isearch.auth-tokens` setting along any existing tokens.

Expand All @@ -173,12 +176,13 @@ rdp.settings.isearch.user-id=522
rdp.settings.isearch.auth-tokens=jLb22QZzsaT6/w3xwDHBObmZPypJgXfb,hrol3Y4z2OE0ayK227i8oHTLDjPtRfb4
```

This allows you to query private data from the partner registry when logged in as an administrator on your own
registry.
This allows you to query private data from the partner registry when logged in as an administrator on your own registry.

## Gene Tiers

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.
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.

To enable only TIER1 and TIER2, and thus disabling GO terms-related features, add the following to your configuration:

Expand All @@ -189,8 +193,7 @@ rdp.settings.enabled-tiers=TIER1,TIER2
## Researcher position

Researcher positions can be enabled or disabled by setting the
`rdp.settings.profile.enabled-researcher-positions` to a list of desired
values.
`rdp.settings.profile.enabled-researcher-positions` to a list of desired values.

For the moment, only one value is defined `PRINCIPAL_INVESTIGATOR`.

Expand All @@ -203,21 +206,20 @@ To disable this feature, just leave the setting blank.
## Researcher categories

Researcher categories can be enabled or disabled by setting the
`rdp.settings.profile.enabled-researcher-categories` to a list of desired
values.
`rdp.settings.profile.enabled-researcher-categories` to a list of desired values.

```ini
rdp.settings.profile.enabled-researcher-categories=IN_SILICO,IN_VIVO
```

The available values are:

- `IN_VIVO`
- `IN_VITRO_BIOCHEMICAL`
- `IN_VITRO_CELLS`
- `IN_VITRO_STRUCTURAL`
- `IN_SILICO`
- `OTHER`
- `IN_VIVO`
- `IN_VITRO_BIOCHEMICAL`
- `IN_VITRO_CELLS`
- `IN_VITRO_STRUCTURAL`
- `IN_SILICO`
- `OTHER`

To disable this feature, just leave the setting blank.

Expand All @@ -230,11 +232,9 @@ rdp.settings.privacy.enabled-levels=PUBLIC,SHARED,PRIVATE
rdp.settings.privacy.enabled-gene-levels=PUBLIC,SHARED,PRIVATE
```

Note that any value enabled for genes that is not also enabled for profiles
will be ignored.
Note that any value enabled for genes that is not also enabled for profiles will be ignored.

To allow user to modify the privacy level of their profile and individual
genes, set the following properties:
To allow user to modify the privacy level of their profile and individual genes, set the following properties:

```ini
rdp.settings.privacy.customizable-level=true
Expand All @@ -258,7 +258,8 @@ rdp.settings.privacy.enable-anonymized-search-results=false

## Customizing the application's messages

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
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
[messages.properties](https://github.com/PavlidisLab/rgr/blob/master/src/main/resources/messages.properties)

You can use suffixed like `messages_en_CA.properties` for region-specific customization.
Expand All @@ -275,15 +276,16 @@ the `rdp.settings.faq-file` parameter:
rdp.settings.faq-file=file:faq.properties
```

In the file, each entry requires two parts: `rdp.faq.questions.<q_key>` and `rdp.faq.answers.<q_key>` which hold the question and the corresponding
answer, respectively.
In the file, each entry requires two parts: `rdp.faq.questions.<q_key>` and `rdp.faq.answers.<q_key>` which hold the
question and the corresponding answer, respectively.

```ini
rdp.faq.questions.<q_key>=A relevant question.
rdp.faq.answers.<q_key>=A plausible answer.
```

The provided default file can be found in [faq.properties](https://github.com/PavlidisLab/rgr/tree/master/src/main/resources/faq.properties).
The provided default file can be found
in [faq.properties](https://github.com/PavlidisLab/rgr/tree/master/src/main/resources/faq.properties).

## Style and static resources

Expand Down
26 changes: 15 additions & 11 deletions docs/deployment.md
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Expand Up @@ -13,9 +13,9 @@ Set `-Dserver.port=<port>` to adjust the port the embedded webserver is listenin

### Fast random number generation

Specify `-Djava.security.egd=file:/dev/urandom` this if you receive logs such as: _"Creation of SecureRandom instance for
session ID generation using [SHA1PRNG] took [235,853] milliseconds."_ The secure random calls may be blocking as there is
not enough entropy to feed them in `/dev/random`.
Specify `-Djava.security.egd=file:/dev/urandom` this if you receive logs such as: _"Creation of SecureRandom instance
for session ID generation using [SHA1PRNG] took [235,853] milliseconds."_ The secure random calls may be blocking as
there is not enough entropy to feed them in `/dev/random`.

### Proxy configuration

Expand All @@ -27,7 +27,8 @@ Likewise, you can set up a proxy for FTP connections with `-Dftp.proxyHost` and

1. Create a working directory for the web service: `mkdir -p /project/directory`
2. Move into that directory: `cd /project/directory`
3. Download the latest release: `wget -O rdp-{{ config.extra.rdp_version }}.jar https://github.com/PavlidisLab/rdp/releases/download/v{{ config.extra.rdp_version }}/rdp-{{ config.extra.rdp_version }}.jar`
3. Download the latest
release: `wget -O rdp-{{ config.extra.rdp_version }}.jar https://github.com/PavlidisLab/rdp/releases/download/v{{ config.extra.rdp_version }}/rdp-{{ config.extra.rdp_version }}.jar`
4. Create `application.properties`, and optionally `faq.properties` and
`messages.properties` if you want to [customize messages](customization.md#customizing-the-applications-messages).
5. Test your setup: `java -jar rdp-{{ config.extra.rdp_version }}.jar`
Expand All @@ -36,11 +37,10 @@ Likewise, you can set up a proxy for FTP connections with `-Dftp.proxyHost` and

## Integration with systemd

If you are not using a container technology such as Docker, we recommend that
you use a systemd service unit to deploy your RDP instance.
If you are not using a container technology such as Docker, we recommend that you use a systemd service unit to deploy
your RDP instance.

Create a file under `/etc/systemd/system/rdp.service` with the following
content:
Create a file under `/etc/systemd/system/rdp.service` with the following content:

```Ini
[Unit]
Expand All @@ -63,7 +63,7 @@ WantedBy=multi-user.target

### Apache

Create a standard virtual host seection with the following proxies:
Create a standard virtual host section with the following proxies:

```
ProxyPass / http://localhost:<port>/
Expand All @@ -72,6 +72,10 @@ ProxyPassReverse / http://localhost:<port>/

## More information

For custom cloud deployments see [Spring Boot: Deploying to the Cloud](https://docs.spring.io/spring-boot/docs/current/reference/html/cloud-deployment.html).
For custom cloud deployments
see [Spring Boot: Deploying to the Cloud](https://docs.spring.io/spring-boot/docs/current/reference/html/cloud-deployment.html)
.

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).
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)
.
25 changes: 12 additions & 13 deletions docs/installation.md
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Expand Up @@ -16,13 +16,12 @@ Download the [latest jar distribution](https://github.com/PavlidisLab/rgr/releas
wget https://github.com/PavlidisLab/rgr/releases/download/v{{ config.extra.rdp_version }}/rdp-{{ config.extra.rdp_version }}.jar
```

The jar contains the core application, including an embedded webserver (Tomcat 8.5.x),
a task scheduler, an in-memory cache, and much more!
The jar contains the core application, including an embedded webserver (Tomcat 8.5.x), a task scheduler, an in-memory
cache, and much more!

## Setup the MySQL database
## Set up the MySQL database

Create the database and an associated user that the application will use to
store and retrieve data.
Create the database and an associated user that the application will use to store and retrieve data.

```sql
create database <database name> character set utf8mb4 collate utf8mb4_general_ci;
Expand Down Expand Up @@ -54,21 +53,21 @@ spring.mail.properties.mail.smtp.auth=true
spring.mail.properties.mail.smtp.starttls.enable=true
```

This file contains the database and SMTP credentials and various runtime
configurations. Make sure it's only readable by the user that will run the
instance.
This file contains the database and SMTP credentials and various runtime configurations. Make sure it's only readable by
the user that will run the instance.

Documentation for options with their default values are available in [application.properties](https://github.com/PavlidisLab/rgr/blob/development/src/main/resources/application.properties).
Documentation for options with their default values are available
in [application.properties](https://github.com/PavlidisLab/rgr/blob/development/src/main/resources/application.properties)
.

That should be enough to get the Web service started. Now you can launch it by
issuing the following command:
That should be enough to get the Web service started. Now you can launch it by issuing the following command:

```bash
java -jar rdp-{{ config.extra.rdp_version }}.jar
```

If your email server is not properly configured, you will see an error from the
Spring Actuator health check. You can detect further issues by looking at the
If your email server is not properly configured, you will see an error from the Spring Actuator health check. You can
detect further issues by looking at the
`/admin/health` endpoint with administrative privilege.

## Create an administrative account
Expand Down
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