README.md 12.7 KB
Newer Older
1
2
# Rare project - Data discovery

3
4
5
6
7
- [Rare project - Data discovery](#rare-project---data-discovery)
  - [Contribute](#contribute)
    - [Data](#data)
    - [Code](#code)
  - [Setup](#setup)
8
    - [Requirements](#requirements)
9
    - [Data handling](#data-handling)
10
11
12
13
14
15
    - [Backend](#backend)
    - [Frontend](#frontend)
  - [Build](#build)
  - [CI](#ci)
  - [Documentation](#documentation)
  - [Harvest](#harvest)
16
    - [Portability](#portability)
17
18
19
  - [Indices and aliases](#indices-and-aliases)
  - [Spring Cloud config](#spring-cloud-config)
  - [Building other apps](#building-other-apps)
20
  - [Configuration](#configuration)
21

22
23
## Contribute

24
If you want to install the program locally, it's cool, just keep reading at [Setup section and beyond](#setup).
25
26
27

### Data

28
You might probably want to know how to contribute to the federation of data. That's great, let's have a look at the [WheatIS/Plant guide](./HOW-TO-JOIN-WHEATIS-AND-PLANT-FEDERATIONS.md) or the [RARe guide](./HOW-TO-JOIN-RARe-FEDERATION.md) to know how to.
29

30
31
32
### Code

If you do want to contribute to code, that's great also, have a look at [CONTRIBUTING.md](./CONTRIBUTING.MD).
33

34
35
## Setup

36
37
38
39
40
41
42
43
44
45
46
47
48
49
### Requirements

The application itself is running under a Java OpenJDK 8+: <https://openjdk.java.net/install/>

For getting the data, you need to install Git LFS: <https://git-lfs.github.com/>

The indexing process depends on the following tools, you need to have them installed and available in your `PATH` variable:

- JQ 1.6+: <https://stedolan.github.io/jq/>
- GNU Parallel (recent enough version): <https://www.gnu.org/software/parallel/>
- GNU coreutils (sed, date...): <https://www.gnu.org/software/coreutils/>
- GNU GZIP: <https://git.savannah.gnu.org/cgit/gzip.git>
- GNU Bash v4+: <https://www.gnu.org/software/bash/>

50
51
### Data handling

52
At the moment, all data is located next to the code in the `data` directory. If you want to have a look at the code only, you can ignore this directory at git clone step by setting the variable `GIT_LFS_SKIP_SMUDGE=1`, ie.:
53
54
55
56
57
58
59
60
61
62
63
64

```sh
GIT_LFS_SKIP_SMUDGE=1 git clone git@forgemia.inra.fr:urgi-is/data-discovery.git
```

After clone done, if you want to fetch some of the data (for instance for RARe only), let's run:

```sh
$ git lfs pull -I data/rare/
Downloading LFS objects: 100% (16/16), 8.8 MB | 0 B/s
```

65
66
### Backend

67
The project uses Spring (5.x) for the backend, with Spring Boot.
68
69
70
71
72

You need to install:

- a recent enough JDK8

73
74
75
The docker images need quite a bit of resources,
so make sure you have at least 4g of RAM configured (Docker Desktop / Resources / Memory).

76
The application expects to connect on an Elasticsearch instance running on `http://127.0.0.1:9200`.
Exbrayat Cédric's avatar
Exbrayat Cédric committed
77
78
To have such an instance, simply run:

Raphaël Flores's avatar
Raphaël Flores committed
79
80
81
```sh
docker-compose up
```
Exbrayat Cédric's avatar
Exbrayat Cédric committed
82

Raphaël Flores's avatar
Raphaël Flores committed
83
And this will start Elasticsearch and a Kibana instance (allowing to explore the data on <http://localhost:5601>).
Exbrayat Cédric's avatar
Exbrayat Cédric committed
84

85
86
87
Then at the root of the application, run `./gradlew build` to download the dependencies.
Then run `./gradlew bootRun` to start the app.

88
You can stop the Elasticsearch and Kibana instances by running:
Exbrayat Cédric's avatar
Exbrayat Cédric committed
89

Raphaël Flores's avatar
Raphaël Flores committed
90
91
92
```sh
docker-compose stop
```
93
94

or run:
95

Raphaël Flores's avatar
Raphaël Flores committed
96
97
98
```sh
docker-compose down
```
99

100
to also remove the stopped containers as well as any networks that were created.
Exbrayat Cédric's avatar
Exbrayat Cédric committed
101

102
103
### Frontend

104
The project uses Angular (8.x) for the frontend, with the Angular CLI.
105
106
107

You need to install:

Raphaël Flores's avatar
Raphaël Flores committed
108
- a recent enough NodeJS (ie. v12 LTS) is required for Angular 8.
109
110
111
112
113
- Yarn as a package manager (see [here to install](https://yarnpkg.com/en/docs/install))

Then in the `frontend` directory, run `yarn` to download the dependencies.
Then run `yarn start` to start the app, using the proxy conf to reroute calls to `/api` to the backend.

Raphaël Flores's avatar
Raphaël Flores committed
114
The application will be available on:
115
116

- <http://localhost:4000/rare-dev> for RARe (runs with: `yarn start:rare` or simply `yarn start`)
117
- <http://localhost:4000/rare-dev> for RARe with basket (runs with: `yarn start:rare-with-basket`)
118
- <http://localhost:4100/wheatis-dev> for WheatIS (runs with: `yarn start:wheatis`)
119
- <http://localhost:4200/data-discovery-dev> for DataDiscovery (runs with: `yarn start:data-discovery`)
120
121

See [./frontend/package.json (scripts section)](./frontend/package.json) for other yarn commands.
122
123
124
125
126

## Build

To build the app, just run:

Raphaël Flores's avatar
Raphaël Flores committed
127
128
129
```sh
./gradlew assemble
```
130
131
132

or

Raphaël Flores's avatar
Raphaël Flores committed
133
134
135
```sh
./gradlew assemble -Papp=wheatis
```
136
or
137

Raphaël Flores's avatar
Raphaël Flores committed
138
```sh
139
./gradlew assemble -Papp=rare-with-basket
Raphaël Flores's avatar
Raphaël Flores committed
140
```
141

142
This will build a standalone jar at `backend/build/libs/`, that you can run with either:
143

Raphaël Flores's avatar
Raphaël Flores committed
144
145
```sh
java -jar backend/build/libs/rare.jar
146
java -jar backend/build/libs/rare-with-basket.jar
Raphaël Flores's avatar
Raphaël Flores committed
147
148
149
java -jar backend/build/libs/wheatis.jar
java -jar backend/build/libs/data-discovery.jar
```
Raphaël Flores's avatar
Raphaël Flores committed
150

151
And the full app running on:
152

153
- <http://localhost:8080/rare-dev>
154
155
156
- <http://localhost:8080/rare-dev>
- <http://localhost:8180/wheatis-dev>
- <http://localhost:8280/data-discovery-dev>
157
158
159
160
161

## CI

The `.gitlab-ci.yml` file describes how Gitlab is running the CI jobs.

162
163
164
It uses a base docker image named `urgi/docker-browsers`
available on [DockerHub](https://hub.docker.com/r/urgi/docker-browsers/)
and [INRA-MIA Gitlab](https://forgemia.inra.fr/urgi-is/docker-rare).
Raphaël Flores's avatar
Raphaël Flores committed
165
The image is based on `openjdk:8` and adds all stuff needed to run the tests
166
(ie. a Chrome binary with a headless Chrome in `--no-sandbox` mode).
167
168
169
170
171
172

We install `node` and `yarn` in `/tmp` (this is not the case for local builds)
to avoid symbolic links issues on Docker.

You can approximate what runs on CI by executing:

Raphaël Flores's avatar
Raphaël Flores committed
173
174
175
```sh
docker run --rm -v "$PWD":/home/rare -w /home/rare urgi/docker-browsers ./gradlew build
```
Jean-Baptiste Nizet's avatar
Jean-Baptiste Nizet committed
176

177
178
Or also run a gitlab-runner as Gitlab-CI would do (minus the environment variables and caching system):

Raphaël Flores's avatar
Raphaël Flores committed
179
180
181
```sh
gitlab-runner exec docker test
```
182
183
184
185
186

## Documentation

An API documentation describing most of the webservices can be generated using the
build task `asciidoctor`, which executes tests and generates documentation based on snippets generated
187
by these tests. The documentation is generated in the folder `backend/build/asciidoc/html5/index.html`
188

Raphaël Flores's avatar
Raphaël Flores committed
189
190
191
```sh
./gradlew asciidoctor
```
192

Jean-Baptiste Nizet's avatar
Jean-Baptiste Nizet committed
193
194
## Harvest

195
Before all, if you have cloned the repository without fetching the data (see [Data handling](#data-handling) section), take care to get it before running any indexing script.
196
197
198

### Portability

199
200
201
202
203
204
205
206
Feedback related to portability on MacOS and other GNU/Linux distro is really welcomed.

For MacOS, care to use latest GNU Parallel and Bash v4 versions, not the version provided by default via Brew.
Install the following packages to be able to run the scripts:

```sh
brew install gnu-sed coreutils parallel
```
207

208
Harvesting (i.e. importing JSON documents into Elasticsearch) consists in creating the necessary index and aliases and Elasticsearch templates.
Jean-Baptiste Nizet's avatar
Jean-Baptiste Nizet committed
209

Raphaël Flores's avatar
Raphaël Flores committed
210
To create the index and its aliases execute the script below for local dev environment:
211

Raphaël Flores's avatar
Raphaël Flores committed
212
213
214
```sh
./scripts/index.sh -app rare|wheat|data-discovery --local
```
Jean-Baptiste Nizet's avatar
Jean-Baptiste Nizet committed
215

216
The -app parameter will trigger a harvest of the resources stored in the Git LFS directories `data/rare`, `data/wheatis` and `data/data-discovery` respectively.
Raphaël Flores's avatar
Raphaël Flores committed
217

218
219
## Indices and aliases

220
The application uses several physical indices:
221

222
- one to store physical resources, containing the main content
223
- one to store suggestions, used for the search type-ahead feature only
Raphaël Flores's avatar
Raphaël Flores committed
224
225

Both indices must be created explicitly before using the application. If not, requests to the web services will return errors.
226

227
Each index and alias below refers to `rare` application in `dev` environment, the equivalent shall be created for `wheatis` and `data-discovery` app in `dev` environment as same as in `beta` or `staging` or `prod` environments. For brevity, only `rare-dev` is explained here.
Raphaël Flores's avatar
Raphaël Flores committed
228
229
{: .alert .alert-info}

230
231
232
233
234
235
236
237
The application doesn't use the physical resources index directly. Instead, it uses two aliases, that must be created before using the application:

- `rare-dev-resource-alias` is the alias used by the application to store and search for documents
- `rare-dev-suggestions-alias` is the alias used by the application to store and search for suggestions, only used for completion service.

In normal operations, these two aliases should refer to physical indices having a timestamp such as `rare-dev-tmstp1579877133-suggestions` and `rare-dev-tmstp1579877133-resource-index`. Those timestamps allow for reindexing data without breaking another runnning application having another timestamp. The alias switch being done atomicly, we always see data in the web interface.

Using two aliases is useful when deleting obsolete documents. This is actually done by removing everything and then harvesting the new JSON files again, to re-populate the index from scratch.
238

239
240
## Spring Cloud config

241
On bootstrap, the application will try to connect to a remote Spring Cloud config server to fetch its configuration. The details of this remote server are filled in the `bootstrap.yml` file. By default, it tries to connect to the local server on <http://localhost:8888> but it can of course be changed, or even configured via the `SPRING_CONFIG_URI` environment variable.
242
243
244

It will try to fetch the configuration for the application name `rare`, and the default profile.
If such a configuration is not found, it will then fallback to the local `application.yml` properties.
245

246
247
248
To avoid running the Spring Cloud config server every time when developing the application,
all the properties are still available in `application.yml` even if they are configured on the remote Spring Cloud server as well.

249
If you want to use the Spring Cloud config app locally, see <https://forgemia.inra.fr/urgi-is/data-discovery-config>
250

251
The configuration is currently only read on startup, meaning the application has to be reboot if the configuration is changed on the Spring Cloud server. For a dynamic reload without restarting the application, see <http://cloud.spring.io/spring-cloud-static/Finchley.SR1/single/spring-cloud.html#refresh-scope>
252
to check what has to be changed.
253

Raphaël Flores's avatar
Raphaël Flores committed
254
In case of testing configuration from the config server, one may use a dedicated branch on `data-discovery-config` project and append the `--spring.cloud.config.label=<branch name to test>` parameter when starting the application's executable jar, or use the corresponding Spring [env variable](https://docs.spring.io/spring-boot/docs/current/reference/html/spring-boot-features.html#boot-features-external-config-relaxed-binding-from-environment-variables). More info on [how to pass a parameter to a Spring Boot app](https://docs.spring.io/spring-boot/docs/current/reference/html/boot-features-external-config.html#boot-features-external-config).
255

256
257
## Building other apps

258
259
260
261
By default, the built application is RARe (without basket, i.e. without the possibility to add accessions to a basket
and create an accession order on the rare-basket application). 
But this project actually allows building other
applications (RARe with basket and WheatIS, for the moment, but more could come).
262
263
264
265

To build a different app, specify an `app` property when building. For example, to assemble
the WheatIS app, run the following command

Raphaël Flores's avatar
Raphaël Flores committed
266
267
268
```sh
./gradlew assemble -Papp=wheatis
```
269

270
271
You can also run the backend WheatIS application using

Raphaël Flores's avatar
Raphaël Flores committed
272
273
274
```sh
./gradlew bootRun -Papp=wheatis
```
275

276
277
278
279
280
281
282
283
284
285
286
287
To assemble the RARe app with support for adding accessions to a basket, run the following command

```sh
./gradlew assemble -Papp=rare-with-basket
```

You can also run the backend RARe application with basket support using

```sh
./gradlew bootRun -Papp=rare-with-basket
```

288
289
Adding this property has the following consequences:

290
291
292
293
294
- the generated jar file (in `backend/build/libs`) is named `wheatis.jar` (resp. `rare-with-basket.jar` instead of `rare.jar`;
- the Spring active profile in `bootstrap.yml` is `wheatis-app` (resp. `rare-with-basket-app`) instead of `rare-app`;
- the frontend application built and embedded inside the jar file is the WheatIS frontend application 
(resp. the RARe application with basket support) instead of the RARe frontend application, i.e. the frontend command 
`yarn build:wheatis` (resp. `yarn build:rare-with-basket`) is executed instead of the command `yarn:rare`.
295

296
Since the active Spring profile is different, all the properties specific to this profile
297
are applied. In particular:
298
299
300

- the context path of the application is `/wheatis-dev` instead of `/rare-dev`;
- the Elasticsearch prefix used for the index aliases is different.
301

Raphaël Flores's avatar
Raphaël Flores committed
302
See the `backend/src/main/resources/application.yml` file for details.
303
304

You can adapt the elasticsearch index used with the following parameter
305

Raphaël Flores's avatar
Raphaël Flores committed
306
307
308
```sh
java -jar backend/build/libs/data-discovery.jar --data-discovery.elasticsearch-prefix="data-discovery-staging-"
```
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325

## Configuration

The RARe and RARe with basket applications can be configured to apply an implicit filtering on the searches,
aggregations, and pillar list. There is currently only one implicit filter that can be added, which is a filter on the 
pillar name.

To activate it, add the following YAML configuration under the appropriate profile:

```yaml
rare:
  implicit-terms:
    PILLAR:
      - Pilier Forêt
      - Pilier Micro-organisme
```