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Commit 0ebcd4d7 authored by Célia Michotey's avatar Célia Michotey
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Change documentation directory and update code in consequence. GNP-5519.

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ABOUT.md deleted 100644 → 0
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# About this data portal
The purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories.
It is based on the [Breeding API (BrAPI)](https://brapi.org/) specifications and facilitates the access to genotype and phenotype datasets for crop and forest plants through an easy to use web interface.
It also provides a standard interface that can be accessed programatically through [web services](https://urgi.versailles.inra.fr/faidare/swagger-ui.html).
It is an extension of the generic [Data-Discovery portal](https://forgemia.inra.fr/urgi-is/data-discovery), a web portal that allows finding any type of data across several databases through a lightweight keyword based search.
FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.
It has been developed by [INRA-URGI](http://urgi.versailles.inra.fr/) in collaboration with [**Elixir Plant**](https://elixir-europe.org/communities/plant-sciences), [**Phenome-Emphasis.fr**](https://www.phenome-emphasis.fr/phenome_eng/Methodological-projects/MCP2-Distributed-Information-system) and [**Elixir-fr/IFB**](https://www.france-bioinformatique.fr).
If you want to join the FAIDARE federation, please read the [HOW TO JOIN guide](HOW-TO-JOIN.md) and [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
ABOUT.md 0 → 120000
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frontend/src/assets/faidare/ABOUT.md
\ No newline at end of file
HELP.md deleted 100644 → 0
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# Help section
> Note: this application is responsive, meaning that its rendering will adapt to the screen's size of your device, hence location of items below can be different than stated.
You can find data by building your own query using the fields available in the two tabs of the form:
* The `Germplasm` tab allow you to add criteria on plant material/germplasm (_e.g._ its name, genus or species).
* The `Trait` tab allow you to add criteria on trait(s) and/or variable(s) name(s).
In each field, one or several term(s) can be entered.
As you begin to type, a list of relevant suggestions is proposed to guide you in your search.
The query is launched as soon as at least one parameter is selected in the form.
The results are automatically updated if a parameter is added or removed.
To refine your search, you can add more specific filters by using the facets/categories on the left side.
> Note: applying several filters in the same facet/category will search for documents related to any of the selected terms (resulting in a `OR` operator between all the category's terms).
> In contrary, applying filters in different facets/categories will search for documents having both filters (resulting in an `AND` operator for the different facets).
\ No newline at end of file
HELP.md 0 → 120000
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frontend/src/assets/faidare/HELP.md
\ No newline at end of file
HOW-TO-JOIN.md deleted 100644 → 0
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# How to join FAIDARE federation?
If you want your information system to be part of the FAIDARE federation, we invite you to [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D) as soon as possible so that we can follow your progress and assist you if needed.
You will need to create a new `source` corresponding to your information system.
For this, you will have to set up your own [BrAPI](https://brapi.org/) endpoint and reference it in the sources of [Elixir's FAIDARE harvester](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis).
General information and considerations can be found on the [**Elixir Plant**](https://elixir-europe.org/communities/plant-sciences) web page.
## Creation of a BrAPI endpoint
To create a new endpoint, you should implement the BrAPI calls needed to give access to the data of your information system.
Those calls are documented in various formats on the [Developer resources](https://www.brapi.org/developers#) section of the BrAPI web site.
The BrAPI calls currently used by FAIDARE are:
* germplasm
* location
* ontology
* program
* study
* study/{studyDbId}/observationVariable
* study/{studyDbId}/germplasm
* study/{studyDbId}/observationUnit (can be resource intensive and therefore not implemented)
* trial
> Note that since the tool makes a backlink to your information system, we need a URL in the `DocumentationURL` field of the BrAPI for researchers to get more detailed information about the indexed entry directly in your information system.
To ensure the quality of your BrAPI endpoint, you can use the validation tools provided by the BrAPI community, especially [Brava](http://webapps.ipk-gatersleben.de/brapivalidator/).
If you have any question or need help implementing BrAPI calls, you can [contact the BrAPI community](https://brapi.org/).
## Referencement of a BrAPI endpoint
For your endpoint to be visible on FAIDARE, you have to declare it in the sources of [Elixir's FAIDARE harvester](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis).
To do this, you only have to create your own configuration file, according to the following template, and add it to the [`sources`](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis/tree/master/sources)` directory of the harvester:
```
{
"@context": {
"schema": "http://schema.org/",
"brapi": "https://brapi.org/"
},
"@type": "schema:DataCatalog",
"@id": "[information system URL]",
"schema:identifier": "[BrAPI endpoint name]",
"schema:name": "[information system name]",
"brapi:endpointUrl": "[BrAPI endpoint URL]"
}
```
Example: [URGI.json](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis/blob/master/sources/URGI.json)
```
{
"@context": {
"schema": "http://schema.org/",
"brapi": "https://brapi.org/"
},
"@type": "schema:DataCatalog",
"@id": "https://urgi.versailles.inra.fr/gnpis",
"schema:identifier": "URGI",
"schema:name": "URGI GnpIS",
"brapi:endpointUrl": "https://urgi.versailles.inra.fr/faidare/brapi/v1/"
}
```
If you have any question or need help referencing your endpoint, you can [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
## Data availability & update
[Elixir's FAIDARE harvester](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis) extract the metadata available from all declared sources (_i.e._ BrAPI endpoint) and index it into a centralised Elasticsearch cache.
The sources are reindexed regularly (once a month maximum) but if you want a reindexation following a major update on your side, please [inform us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
HOW-TO-JOIN.md 0 → 120000
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frontend/src/assets/faidare/HOW-TO-JOIN.md
\ No newline at end of file
LEGAL-MENTIONS.md deleted 100644 → 0
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# General Terms of Use
By browsing this web site, you acknowledge and accept its general terms of use described below.
## Intellectual property
Except where otherwise noted, content on this site is licensed under a [Creative Commons Attribution 4.0 International license](https://creativecommons.org/licenses/by/4.0/).
The logo is the property of INRA and you are not allowed to re-use it for your own work and purpose.
## Content
The portal maintained by INRA allows to find public data across a federation of databases.
The licences associated to data are therefore defined by the institutes in charge of them.
Users are sole responsible for the searches they carry out, as well as for the interpretation and for the use they make of the results.
The access to the web site can be interrupted at any moment and without prior warning in case of force majeure or if the editor decides to terminate its provision of service.
Users are informed that their use of the results should not infringe on current legislation or the recommendations of the French Data Protection Authority (CNIL) with respect to personal data.
Users are warned that the information must be used for strictly professional purposes only and downloading screen shots in order to constitute or enrich a database is contrary to French law and therefore forbidden, as is its use for commercial or advertising purposes (CNIL).
The portal may give access to personal and professional data concerning technical and scientific actors in relation with the data.
This information helps to identify and acknowledge the authors of the scientific works.
This personal information is attached to the produced datasets and follows the data life cycle.
## Hyperlinks
The portal links to external web sites.
INRA does not take responsibility of the content of these web site.
## Personal data
Technical data (date, hour, IP address of the computer of the visitor, pages viewed) are collected only for the statistical analysis of the usage of the portal.
These data are kept confidential and not transmitted to any other party.
They are stored on INRA’s private servers for 5 years.
During visits on URGI web site and its hosted applications, a cookie can be automatically installed on visitor’s web browsers to retrieve statistics on the pages that are visited and support improvements of the services provided by the web site.
Visitors can configure their web browsers in order to be informed of the setting of cookies and refuse them.
According to the European Regulation on the protection of personal data (EU Regulation 2016/679), you have the right to access, rectify, oppose and delete information about yourself.
If you wish to exercise this right and obtain information about yourself, please contact us:
- By [email](mailto:urgi-contact@inra.fr?subject=%5BData%20Discovery%5D%20GPDR%20request)
- Or via any other way available on our [contact form](https://urgi.versailles.inra.fr/Contact-us)
## Modifications
The editor might change the terms of use and user’s rights without prior warning.
Last update: 2019 June 25th
LEGAL-MENTIONS.md 0 → 120000
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frontend/src/assets/faidare/LEGAL-MENTIONS.md
\ No newline at end of file
frontend/package.json
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......@@ -32,8 +32,8 @@
"leaflet": "1.3.4",
"leaflet.markercluster": "1.4.1",
"moment": "2.24.0",
"ng-mocks": "^7.6.0",
"ngx-markdown": "^8.0.2",
"ng-mocks": "7.6.0",
"ngx-markdown": "8.0.2",
"ngx-moment": "3.3.0",
"popper.js": "1.14.6",
"rxjs": "6.4.0",
......
frontend/src/app/app-routing.module.ts
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......@@ -16,6 +16,7 @@ export const routes: Routes = [
{ path: 'join', component: MarkdownPageComponent, data: { mdFile: environment.joinUsMdFile } },
{ path: 'legal', component: MarkdownPageComponent, data: { mdFile: environment.legalMentionsMdFile } },
{ path: 'help', component: MarkdownPageComponent, data: { mdFile: environment.helpMdFile } },
{ path: 'HOW-TO-JOIN.md', redirectTo: '/join' },
];
......
frontend/src/app/markdown-page/markdown-page.component.spec.ts
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......@@ -28,6 +28,6 @@ describe('MarkdownPageComponent', () => {
it('should create', () => {
expect(component).toBeTruthy();
expect(component.mdFile).toEqual('assets/help.md');
expect(component.mdFile).toEqual('assets/HELP.md');
});
});
frontend/src/assets/faidare/ABOUT.md 0 → 100644
View file @ 0ebcd4d7
# About this data portal
The purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories.
It is based on the [Breeding API (BrAPI)](https://brapi.org/) specifications and facilitates the access to genotype and phenotype datasets for crop and forest plants through an easy to use web interface.
It also provides a standard interface that can be accessed programatically through [web services](https://urgi.versailles.inra.fr/faidare/swagger-ui.html).
It is an extension of the generic [Data-Discovery portal](https://forgemia.inra.fr/urgi-is/data-discovery), a web portal that allows finding any type of data across several databases through a lightweight keyword based search.
FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.
It has been developed by [INRA-URGI](http://urgi.versailles.inra.fr/) in collaboration with [**Elixir Plant**](https://elixir-europe.org/communities/plant-sciences), [**Phenome-Emphasis.fr**](https://www.phenome-emphasis.fr/phenome_eng/Methodological-projects/MCP2-Distributed-Information-system) and [**Elixir-fr/IFB**](https://www.france-bioinformatique.fr).
If you want to join the FAIDARE federation, please read the [HOW TO JOIN guide](HOW-TO-JOIN.md) and [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
frontend/src/assets/faidare/HELP.md 0 → 100644
View file @ 0ebcd4d7
# Help section
> Note: this application is responsive, meaning that its rendering will adapt to the screen's size of your device, hence location of items below can be different than stated.
You can find data by building your own query using the fields available in the two tabs of the form:
* The `Germplasm` tab allow you to add criteria on plant material/germplasm (_e.g._ its name, genus or species).
* The `Trait` tab allow you to add criteria on trait(s) and/or variable(s) name(s).
In each field, one or several term(s) can be entered.
As you begin to type, a list of relevant suggestions is proposed to guide you in your search.
The query is launched as soon as at least one parameter is selected in the form.
The results are automatically updated if a parameter is added or removed.
To refine your search, you can add more specific filters by using the facets/categories on the left side.
> Note: applying several filters in the same facet/category will search for documents related to any of the selected terms (resulting in a `OR` operator between all the category's terms).
> In contrary, applying filters in different facets/categories will search for documents having both filters (resulting in an `AND` operator for the different facets).
frontend/src/assets/faidare/HOW-TO-JOIN.md 0 → 100644
View file @ 0ebcd4d7
# How to join FAIDARE federation?
If you want your information system to be part of the FAIDARE federation, we invite you to [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D) as soon as possible so that we can follow your progress and assist you if needed.
You will need to create a new `source` corresponding to your information system.
For this, you will have to set up your own [BrAPI](https://brapi.org/) endpoint and reference it in the sources of [Elixir's FAIDARE harvester](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis).
General information and considerations can be found on the [Elixir Plant](https://elixir-europe.org/communities/plant-sciences) web page.
## Creation of a BrAPI endpoint
To create a new endpoint, you should implement the BrAPI calls needed to give access to the data of your information system.
Those calls are documented in various formats on the [Developer resources](https://www.brapi.org/developers#) section of the BrAPI web site.
The BrAPI calls currently used by FAIDARE are:
* germplasm
* location
* ontology
* program
* study
* study/{studyDbId}/observationVariable
* study/{studyDbId}/germplasm
* study/{studyDbId}/observationUnit (can be resource intensive and therefore not implemented)
* trial
> Note that since the tool makes a backlink to your information system, we need a URL in the `DocumentationURL` field of the BrAPI for researchers to get more detailed information about the indexed entry directly in your information system.
To ensure the quality of your BrAPI endpoint, you can use the validation tools provided by the BrAPI community, especially [Brava](http://webapps.ipk-gatersleben.de/brapivalidator/).
If you have any question or need help implementing BrAPI calls, you can [contact the BrAPI community](https://brapi.org/).
## Referencement of a BrAPI endpoint
For your endpoint to be visible on FAIDARE, you have to declare it in the sources of [Elixir's FAIDARE harvester](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis).
To do this, you only have to create your own configuration file, according to the following template, and add it to the [`sources`](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis/tree/master/sources) directory of the harvester:
```
{
"@context": {
"schema": "http://schema.org/",
"brapi": "https://brapi.org/"
},
"@type": "schema:DataCatalog",
"@id": "[information system URL]",
"schema:identifier": "[BrAPI endpoint name]",
"schema:name": "[information system name]",
"brapi:endpointUrl": "[BrAPI endpoint URL]"
}
```
Example: [URGI.json](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis/blob/master/sources/URGI.json)
```
{
"@context": {
"schema": "http://schema.org/",
"brapi": "https://brapi.org/"
},
"@type": "schema:DataCatalog",
"@id": "https://urgi.versailles.inra.fr/gnpis",
"schema:identifier": "URGI",
"schema:name": "URGI GnpIS",
"brapi:endpointUrl": "https://urgi.versailles.inra.fr/faidare/brapi/v1/"
}
```
If you have any question or need help referencing your endpoint, you can [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
## Data availability & update
[Elixir's FAIDARE harvester](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis) extract the metadata available from all declared sources (_i.e._ BrAPI endpoint) and index it into a centralised Elasticsearch cache.
The sources are reindexed regularly (once a month maximum) but if you want a reindexation following a major update on your side, please [inform us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
frontend/src/assets/faidare/LEGAL-MENTIONS.md 0 → 100644
View file @ 0ebcd4d7
# General Terms of Use
By browsing this web site, you acknowledge and accept its general terms of use described below.
## Intellectual property
Except where otherwise noted, content on this site is licensed under a [Creative Commons Attribution 4.0 International license](https://creativecommons.org/licenses/by/4.0/).
The logo is the property of INRA and you are not allowed to re-use it for your own work and purpose.
## Content
The portal maintained by INRA allows to find public data across a federation of databases.
The licences associated to data are therefore defined by the institutes in charge of them.
Users are sole responsible for the searches they carry out, as well as for the interpretation and for the use they make of the results.
The access to the web site can be interrupted at any moment and without prior warning in case of force majeure or if the editor decides to terminate its provision of service.
Users are informed that their use of the results should not infringe on current legislation or the recommendations of the French Data Protection Authority (CNIL) with respect to personal data.
Users are warned that the information must be used for strictly professional purposes only and downloading screen shots in order to constitute or enrich a database is contrary to French law and therefore forbidden, as is its use for commercial or advertising purposes (CNIL).
The portal may give access to personal and professional data concerning technical and scientific actors in relation with the data.
This information helps to identify and acknowledge the authors of the scientific works.
This personal information is attached to the produced datasets and follows the data life cycle.
## Hyperlinks
The portal links to external web sites.
INRA does not take responsibility of the content of these web site.
## Personal data
Technical data (date, hour, IP address of the computer of the visitor, pages viewed) are collected only for the statistical analysis of the usage of the portal.
These data are kept confidential and not transmitted to any other party.
They are stored on INRA’s private servers for 5 years.
During visits on URGI web site and its hosted applications, a cookie can be automatically installed on visitor’s web browsers to retrieve statistics on the pages that are visited and support improvements of the services provided by the web site.
Visitors can configure their web browsers in order to be informed of the setting of cookies and refuse them.
According to the European Regulation on the protection of personal data (EU Regulation 2016/679), you have the right to access, rectify, oppose and delete information about yourself.
If you wish to exercise this right and obtain information about yourself, please contact us:
- By [email](mailto:urgi-contact@inra.fr?subject=%5BData%20Discovery%5D%20GPDR%20request)
- Or via any other way available on our [contact form](https://urgi.versailles.inra.fr/Contact-us)
## Modifications
The editor might change the terms of use and user’s rights without prior warning.
Last update: 2019 June 25th
frontend/src/assets/faidare/about.md deleted 120000 → 0
View file @ 4d08d93c
../../../../ABOUT.md
\ No newline at end of file
frontend/src/assets/faidare/help.md deleted 120000 → 0
View file @ 4d08d93c
../../../../HELP.md
\ No newline at end of file
frontend/src/assets/faidare/join.md deleted 120000 → 0
View file @ 4d08d93c
../../../../HOW-TO-JOIN.md
\ No newline at end of file
frontend/src/assets/faidare/legal.md deleted 120000 → 0
View file @ 4d08d93c
../../../../LEGAL-MENTIONS.md
\ No newline at end of file
frontend/src/environments/environment.prod.ts
View file @ 0ebcd4d7
......@@ -22,10 +22,10 @@ export const environment = {
logo: 'assets/elixir_logo.png'
}
},
helpMdFile: 'assets/help.md',
aboutUsMdFile: 'assets/about.md',
joinUsMdFile: 'assets/join.md',
legalMentionsMdFile: 'assets/legal.md',
helpMdFile: 'assets/HELP.md',
aboutUsMdFile: 'assets/ABOUT.md',
joinUsMdFile: 'assets/HOW-TO-JOIN.md',
legalMentionsMdFile: 'assets/LEGAL-MENTIONS.md',
taxaLinks: {
NCBI: 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=',
ThePlantList: 'http://www.theplantlist.org/tpl1.1/record/',
......
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