A generic data portal that supports some basic interaction with Gen3 services like peregrine, sheepdog and fence.
npm install
See docs/guide_running_portal_locally.md for a step-by-step guide to running portal locally.
The portal's /dev.html path loads javascript and most css
from localhost. Test code under local development with this procedure:
npm install- launch the webpack dev server, and configure local code with the same configuration as the server to test against. For example - if we intend to test against qa.planx-pla.net, then:
HOSTNAME=qa.planx-pla.net NODE_ENV=auto bash ./runWebpack.sh
, or for qa-brain:
HOSTNAME=qa-brain.planx-pla.net NODE_ENV=auto bash ./runWebpack.sh
You can also use the autoprod value for NODE_ENV to do the auto setup, then run webpack in production mode, so it generates .js and .html files instead of launching the dev server - ex:
HOSTNAME=qa-brain.planx-pla.net NODE_ENV=autoprod GEN3_BUNDLE=all bash ./runWebpack.sh
Tiered-access settings can be configured through either the TIER_ACCESS_LEVEL environment variable (site-wide) or through the tierAccessLevel property on guppyConfig blocks for each Data Explorer tab in the gitops.json (index-scoped). To use the index-scoped config style, all guppyConfig blocks in the portal config must contain the tierAccessLevel property. See docs/portal_config.md for thorough example of portal config structure.
NOTE: To locally test site-wide Tiered Access features, the additional environment variables
TIER_ACCESS_LEVELandTIER_ACCESS_LIMITshould have the same values as the server's "global.tier_access_level" and "global.tier_access_limit" properties in itsmanifest.json.Example:
HOSTNAME=qa-brain.planx-pla.net TIER_ACCESS_LEVEL=regular TIER_ACCESS_LIMIT=50 NODE_ENV=auto bash ./runWebpack.sh
If the index-scoped tiered-access setting is used, the tierAccessLevel properties in the guppyConfig blocks in gitops.json should have the same values as the server's "guppyConfig[index].tier_access_level" in its manifest.json. Tabs should be configured with the same tiered-access level as the ES index they use.
-
Accept the self-signed certificate at https://localhost:9443/bundle.js
-
Load the test environment's
/dev.html- ex: https://qa-brian.planx-pla.net/dev.html
Most production commons currently load custom configuration via gitops. The configuration for a production commons is available in that commons' gitops repository (mostly https://github.com/uc-cdis/cdis-manifest), and can be copied for local development. The runWebpack.sh script automates this process when NODE_ENV is set to auto - ex:
HOSTNAME=qa-brain.planx-pla.net NODE_ENV=auto bash ./runWebpack.sh
Note: the legacy dev NODE_ENV is still available, but the APP environment must also be manually set to load the configuration that matches the dictionary from HOSTNAME - ex:
HOSTNAME=qa.planx-pla.net NODE_ENV=dev APP=dev bash ./runWebpack.sh
The portal webpack configurations selects between two application entry points at build time:
commons- the default data commons portalworkspace- a scaled down port for workspace accounts
We can use the https://remote/dev.html trick to test a local workspace build by setting the GEN3_BUNDLE variable to workspace:
HOSTNAME=qa.planx-pla.net GEN3_BUNDLE=workspace bash ./runWebpack.sh
That just changes the webpack config to serve the workspace bundle as bundle.js - which is what dev.html expects.
The protal Dockerfile runs a deploy time webpack build to incorporate
deploy-time configuration. The GEN3_BUNDLE environment variable determines which application gets built at run time.
To run Storybook:
npm run storybook
Build the container image first
docker build -t windmill .
Then run the container
docker run --rm -e HOSTNAME=qa.planx-pla.net -p 443:443 -ti windmill
You will then need to visit https://localhost and accept the self-signed certificate warnings
docker run -d --name=dataportal -p 80:80 quay.io/cdis/data-portal
The configurations of Homepage charts are specified data/config/.json, or gitops.json in gitops repo. For each common, we need to specify the following json entities:
"graphql": {
"boardCounts": [
{
"graphql": "_case_count",
"name": "Case",
"plural": "Cases"
},
{
"graphql": "_experiment_count",
"name": "Experiment",
"plural": "Experiments"
},
{
"graphql": "_aliquot_count",
"name": "Aliquot",
"plural": "Aliquots"
}
],
"chartCounts": [
{
"graphql": "_case_count",
"name": "Case"
},
{
"graphql": "_experiment_count",
"name": "Experiment"
},
{
"graphql": "_aliquot_count",
"name": "Aliquot"
}
],
"projectDetails": "boardCounts"
}
boardCountsare the counts that you want to display in the top-left of dashboard'schartCountsare the counts that you want to display in the bar chart of dashboard'sprojectDetailsare the counts that you want to display in the list of projects. It could be same asboardCounts, in this case, you only need to point toboardCounts.
Except the default case/file count charts, you could add more to the homepage, and those customized charts will be added to a carousel. We support categorical horizontal grouped bar charts, and the chart will be using data from Guppy, so make sure you correctly ETL them to your Elasticsearch database. The new added charts are configured in portal config's components.index.customHomepageChartConfig config, make sure configurations are correct. Example config (notice the comments won't work for JSON):
"customHomepageChartConfig": [
{
"chartType": "horizontalGroupedBar", // we currently only support this type
"dataType": "participant", // type name in your Elasticsearch db
"yAxisProp": "country", // field name for y axis
"xAxisProp": "ibd_affection_status", // field name for x axis
"constrains": {
"project_id": "jnkns-jenkins" // only support one constrains, could used to render charts for specific project or program
},
"chartTitle": "jnkns-jenkins project", // chart title
"logBase": 1, // optional, log base, default is 1,
"initialUnselectedKeys": ["no data", "Unknown"], // optional, an array of string, means the values those will be initially unselected
"subTitle": "number of cases by countries", // optional, by default it will be "number of ${dataTypePlural} by ${yAxisProp}"
"dataTypePlural": "cases" // optional, string, by default it will be `${dataType}s`
}
]
All the configurations of necessary certificates are define in src/.json. For each common, we need to specify the following json entities:
"components": {
"certs": {
"<certificate-name>": {
"title": "BloodPAC User agreement",
"description": "The agreement on what you can and need to do in a Commons.",
"questions": [
{
"name": "Things you can do after registration",
"question": "As a registered user, I can do the following things without any problem. Is it true or not:",
"options": ["Browse public Project", "Upload file", "Download file", "Invite people"],
"answer": 0,
"hint": "Some information about this question"
},
{
"name": "Things you need to do to become the registered user",
"question": "In order to be a register user, I must do the following things otherwise:",
"options": ["Agree the user agreement", "Accept a consent", "None of them", "Both of them"],
"answer": 2,
"hint": "Some information about this question"
},
{
"name": "Things you can do with data",
"question": "How can I share data with other people according to the policy of the commons",
"options": ["I can not share data", "I can only share data with BPA memebers", "I can share data with family", "I can share data with my wife"],
"answer": 1,
"hint": "Some information about this question"
}
]
}
}
}
Then, specify all the required certificates that need to be completed before using the portal in following entry:
"requiredCerts": ["<certificate-name>"]
Default is an empty list.
When styling components, we adhere to a few rules. We style using class selectors (.class-name instead of #class-name), and separate class names with hypens instead of camel case (.class-name instead of .className). The CSS file should be named {component}.css, and be in the same folder as the component. It is then imported into the component's .jsx file.
We are moving toward using the BEM methodology in terms of CSS organizational conventions. This means we are dividing chunks of code within a component into blocks, are avoiding nesting components, and are using the naming convention of {block}__{elements}--{modifer}. {element} and {modifier} are optional depending on the situation - see the BEM guidelines for more examples.
For our example, say we have a simple component called Component:
import './Component.css';
class Component extends React.Component {
render() {
return (
<div>
<h1>This is my component</h1>
<button>Submit</button>
<button>Cancel</button>
</div>
);
}
}
Our block would be .component, and elements in that block would consist of the buttons and the title. So our CSS would look like this, based on the BEM naming conventions:
.component { }
.component__title { }
.component__button { }
And the code would look like this:
import './Component.css';
class Component extends React.Component {
render() {
return (
<div className="component">
<h1 className="component__title">This is my component</h1>
<button className="component__button">Submit</button>
<button className="component__button">Cancel</button>
</div>
);
}
}
The buttons can also have modifiers - let's say we want two different colors depending on if the button is a submit button or a cancel button. Then our CSS and code would look something like this, respectively:
.component { }
.component__title { }
.component__button { }
.component__button--submit {
color: blue;
}
.component__button--cancel {
color: red;
}
import './Component.css';
class Component extends React.Component {
render() {
return (
<div className="component">
<h1 className="component__title">This is my component</h1>
<button className="component__button component__button--submit">Submit</button>
<button className="component__button component__button--cancel">Cancel</button>
</div>
);
}
}