README.md 14.3 KB
Newer Older
1
2
# Rare project - Data discovery

Célia Michotey's avatar
Célia Michotey committed
3
[[_TOC_]]
4

5
6
## Contribute

7
If you want to install the program locally, it's cool, just keep reading at [Setup section and beyond](#setup).
8
9
10

### Data

11
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.
12

13
14
15
### Code

If you do want to contribute to code, that's great also, have a look at [CONTRIBUTING.md](./CONTRIBUTING.MD).
16

17
18
## Setup

19
20
21
22
23
24
25
26
27
28
29
30
31
32
### 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/>

33

34
35
### Data handling

36
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.:
37
38
39
40
41
42
43
44
45
46
47
48

```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
```

49
50
51
52
53
54
Git might request you to enable additional parameters, which is acceptable:

```sh
git config lfs.https://forgemia.inra.fr/urgi-is/data-discovery.git/info/lfs.locksverify true
```

55
56
### Backend

57
The project uses Spring (5.x) for the backend, with Spring Boot.
58
59
60
61
62

You need to install:

- a recent enough JDK8

63
64
65
The docker images need quite a bit of resources,
so make sure you have at least 4g of RAM configured (Docker Desktop / Resources / Memory).

66
The application expects to connect on an Elasticsearch instance running on `http://127.0.0.1:9200`.
Exbrayat Cédric's avatar
Exbrayat Cédric committed
67
68
To have such an instance, simply run:

Raphaël Flores's avatar
Raphaël Flores committed
69
70
71
```sh
docker-compose up
```
Exbrayat Cédric's avatar
Exbrayat Cédric committed
72

Raphaël Flores's avatar
Raphaël Flores committed
73
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
74

75
76
77
Then at the root of the application, run `./gradlew build` to download the dependencies.
Then run `./gradlew bootRun` to start the app.

78
You can stop the Elasticsearch and Kibana instances by running:
Exbrayat Cédric's avatar
Exbrayat Cédric committed
79

Raphaël Flores's avatar
Raphaël Flores committed
80
81
82
```sh
docker-compose stop
```
83

84
or run the following command to also remove the stopped containers as well as any networks that were created:
85

Raphaël Flores's avatar
Raphaël Flores committed
86
87
88
```sh
docker-compose down
```
89

90
91
### Frontend

92
The project uses Angular (8.x) for the frontend, with the Angular CLI.
93
94
95

You need to install:

Raphaël Flores's avatar
Raphaël Flores committed
96
- a recent enough NodeJS (ie. v12 LTS) is required for Angular 8.
97
98
99
100
101
- 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
102
The application will be available on:
103
104

- <http://localhost:4000/rare-dev> for RARe (runs with: `yarn start:rare` or simply `yarn start`)
Raphaël Flores's avatar
Raphaël Flores committed
105
- <http://localhost:4000/brc4env-dev> for RARe with basket (runs with: `yarn start:brc4env`)
106
- <http://localhost:4100/wheatis-dev> for WheatIS (runs with: `yarn start:wheatis`)
107
- <http://localhost:4200/data-discovery-dev> for DataDiscovery (runs with: `yarn start:data-discovery`)
108
109

See [./frontend/package.json (scripts section)](./frontend/package.json) for other yarn commands.
110
111
112
113
114

## Build

To build the app, just run:

Raphaël Flores's avatar
Raphaël Flores committed
115
116
117
```sh
./gradlew assemble
```
118
119
120

or

Raphaël Flores's avatar
Raphaël Flores committed
121
122
123
```sh
./gradlew assemble -Papp=wheatis
```
124

125
or
126

Raphaël Flores's avatar
Raphaël Flores committed
127
```sh
128
./gradlew assemble -Papp=brc4env
Raphaël Flores's avatar
Raphaël Flores committed
129
```
130

131
This will build a standalone jar at `backend/build/libs/`, that you can run with either:
132

Raphaël Flores's avatar
Raphaël Flores committed
133
134
```sh
java -jar backend/build/libs/rare.jar
135
java -jar backend/build/libs/brc4env.jar
Raphaël Flores's avatar
Raphaël Flores committed
136
137
138
java -jar backend/build/libs/wheatis.jar
java -jar backend/build/libs/data-discovery.jar
```
Raphaël Flores's avatar
Raphaël Flores committed
139

140
And the full app running on:
141

142
143
144
- <http://localhost:8080/rare-dev>
- <http://localhost:8180/wheatis-dev>
- <http://localhost:8280/data-discovery-dev>
145
- <http://localhost:8580/brc4env-dev>
146
147
148
149
150

## CI

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

151
152
153
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
154
The image is based on `openjdk:8` and adds all stuff needed to run the tests
155
(ie. a Chrome binary with a headless Chrome in `--no-sandbox` mode).
156
157
158
159
160
161

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
162
163
164
```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
165

166
167
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
168
169
170
```sh
gitlab-runner exec docker test
```
171
172
173
174
175

## 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
176
by these tests. The documentation is generated in the folder `backend/build/asciidoc/html5/index.html`
177

Raphaël Flores's avatar
Raphaël Flores committed
178
179
180
```sh
./gradlew asciidoctor
```
181

Jean-Baptiste Nizet's avatar
Jean-Baptiste Nizet committed
182
183
## Harvest

184
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.
185

186
187
### TL;DR

Raphaël Flores's avatar
Raphaël Flores committed
188
Data indexing to your local Elasticsearch is done using the following command. Note that your local Elasticsearch instance should be already runing using `docker-compose up`:
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207

```sh
docker run -t --volume $(pwd)/data:/opt/data/ --volume /tmp/bulk:/tmp/bulk/ --network=container:elasticsearch registry.forgemia.inra.fr/urgi-is/docker-rare/data-discovery-loader:latest --help
```

Example for indexing RARe data:

```sh
docker run -t --volume $(pwd)/data:/opt/data/ --volume /tmp/bulk:/tmp/bulk/ --network=container:elasticsearch registry.forgemia.inra.fr/urgi-is/docker-rare/data-discovery-loader:latest -host elasticsearch -app rare -env dev
```

If you need to spread the load on several CPUs, duplicate the value of `host` argument to simulate several Elasticsearch nodes, ie. below to use 4 CPUs:

```sh
docker run -t --volume $(pwd)/data:/opt/data/ --volume /tmp/bulk:/tmp/bulk/ --network=container:elasticsearch registry.forgemia.inra.fr/urgi-is/docker-rare/data-discovery-loader:latest -host "elasticsearch elasticsearch elasticsearch elasticsearch" -app rare -env dev
```

Output logs should be available in directory `/tmp/bulk/rare-dev`.

208
209
### Portability

210
211
#### Docker

Raphaël Flores's avatar
Raphaël Flores committed
212
[TL;DR](#TLDR) section above expects to have an available docker image on the forgemia docker registry. You can update or push such an image using the following:
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228

```sh
# build the image
docker build -t registry.forgemia.inra.fr/urgi-is/docker-rare/data-discovery-loader:latest .

# Login before pushing the image
docker login registry.forgemia.inra.fr/urgi-is/docker-rare -u <your ForgeMIA username>

# push the built image
docker push registry.forgemia.inra.fr/urgi-is/docker-rare/data-discovery-loader:latest
```

That should ease the indexing of data without having to craft a dedicated environment, which is explained below.

#### UNIX/BSD

229
230
231
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.
232
233
Don't use zsh!

234
235
236
237
238
Install the following packages to be able to run the scripts:

```sh
brew install gnu-sed coreutils parallel
```
239

240
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
241

Raphaël Flores's avatar
Raphaël Flores committed
242
To create the index and its aliases execute the script below for local dev environment:
243

Raphaël Flores's avatar
Raphaël Flores committed
244
```sh
Raphaël Flores's avatar
Raphaël Flores committed
245
./scripts/index.sh -app rare|brc4env|wheatis|data-discovery --local
Raphaël Flores's avatar
Raphaël Flores committed
246
```
Jean-Baptiste Nizet's avatar
Jean-Baptiste Nizet committed
247

Raphaël Flores's avatar
Raphaël Flores committed
248
The `-app` parameter will trigger a harvest of the resources stored in the Git LFS subdirectories `data/rare` and `data/data-discovery` filtered or not (`wheatis` and `brc4env` rely on `data-discovery` and `rare` data respectively).
Raphaël Flores's avatar
Raphaël Flores committed
249

250
251
## Indices and aliases

252
The application uses several physical indices:
253

254
- one to store physical resources, containing the main content
255
- one to store suggestions, used for the search type-ahead feature only
Raphaël Flores's avatar
Raphaël Flores committed
256
257

Both indices must be created explicitly before using the application. If not, requests to the web services will return errors.
258

259
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
260
261
{: .alert .alert-info}

262
263
264
265
266
267
268
269
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.
270

271
272
## Spring Cloud config

273
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.
274
275
276

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.
277

278
279
280
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.

281
If you want to use the Spring Cloud config app locally, see <https://forgemia.inra.fr/urgi-is/data-discovery-config>
282

283
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>
284
to check what has to be changed.
285

286
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) (_ie._ `SPRING_CLOUD_CONFIG_LABEL`). 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).
287

288
289
## Building other apps

Raphaël Flores's avatar
Raphaël Flores committed
290
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, WheatIS and DataDiscovery for the moment, but more could come).
291
292
293
294

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
295
296
297
```sh
./gradlew assemble -Papp=wheatis
```
298

299
300
You can also run the backend WheatIS application using

Raphaël Flores's avatar
Raphaël Flores committed
301
302
303
```sh
./gradlew bootRun -Papp=wheatis
```
304

305
306
307
To assemble the RARe app with support for adding accessions to a basket, run the following command

```sh
308
./gradlew assemble -Papp=brc4env
309
310
311
312
313
```

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

```sh
314
./gradlew bootRun -Papp=brc4env
315
316
```

317
318
Adding this property has the following consequences:

Raphaël Flores's avatar
Raphaël Flores committed
319
320
- the generated jar file (in `backend/build/libs`) is named `wheatis.jar` (resp. `brc4env.jar` instead of `rare.jar`);
- the Spring active profile in `bootstrap.yml` is `wheatis-app` (resp. `brc4env-app`) instead of `rare-app`);
321
- 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:brc4env`) is executed instead of the command `yarn:rare`.
322

323
Since the active Spring profile is different, all the properties specific to this profile
324
are applied. In particular:
325
326
327

- the context path of the application is `/wheatis-dev` instead of `/rare-dev`;
- the Elasticsearch prefix used for the index aliases is different.
328

Raphaël Flores's avatar
Raphaël Flores committed
329
See the `backend/src/main/resources/application.yml` file for details.
330
331

You can adapt the elasticsearch index used with the following parameter
332

Raphaël Flores's avatar
Raphaël Flores committed
333
334
335
```sh
java -jar backend/build/libs/data-discovery.jar --data-discovery.elasticsearch-prefix="data-discovery-staging-"
```
336

337
338
339
340
341
342
For debuging:

```sh
java -jar backend/build/libs/data-discovery.jar --debug
```

343
344
345
## Configuration

The RARe and RARe with basket applications can be configured to apply an implicit filtering on the searches,
346
aggregations, and pillar list. There is currently only one implicit filter that can be added, which is a filter on the pillar name.
347
348
349
350
351
352
353
354
355
356

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

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