Merge branch 'master' into release_4.0.0

askomics · Mar 2, 2020 · 534acae · 534acae
2 parents d5de8cb + 3d80b6c
commit 534acae
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diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,20 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+
+# Build documentation with MkDocs
+mkdocs:
+  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt
diff --git a/askomics/react/src/routes/results/results.jsx b/askomics/react/src/routes/results/results.jsx
@@ -41,6 +41,7 @@ export default class Results extends Component {
       .then(response => {
         console.log(requestUrl, response.data)
         this.setState({
+          selected: [],
           results: response.data.remainingFiles,
           resultsPreview: [],
           headerPreview: [],

diff --git a/docs/configure.md b/docs/configure.md
@@ -19,11 +19,11 @@ All AskOmics configuration is set in `config/askomics.ini` files. When AskOmics
 
     - `debug` (`true` or `false`): Display debug log in console
     - `debug_ttl` (`true` or `false`): Keep converted rdf file. Set the to true can fill you disk, active only for debug purpose
-    - `reverse_proxy_path` (string): proxy path if AskOmics is accessible under a subpath
+    - `reverse_proxy_path` (string): Proxy path if AskOmics is accessible under a subpath
     - `subtitle` (string): Subtitle, displayed on the browser tab
     - `footer_message` (string): Custom message displayed on the AskOmics footer
     - `display_commit_hash` (`true` or `false`): diplay the commit hash of the current version in the AskOmics footer
-    - `data_directory` (path): where AskOmics store the data 
+    - `data_directory` (path): Where AskOmics store the data 
     - `database_path` (path): Path to the sqlite database
     - `disable_account_creation` (`true` or `false`): disable the possibility to create new accounts
     - `npreview` (int): Number of line displayed during integration 
@@ -41,6 +41,7 @@ All AskOmics configuration is set in `config/askomics.ini` files. When AskOmics
     - `smtp_password` (string): SMTP password
     - `smtp_connection` (string): SMTP connectin (starttls or null)
 
+
 - `virtuoso`
 
     - `triplestore` (string): Triplestore used. Can be virtuoso, fuseki or corese 

diff --git a/docs/contribute.md b/docs/contribute.md
@@ -14,7 +14,7 @@ git checkout -b my_new_feature
 
 Commit and push your modification to your [fork](https://help.github.com/articles/pushing-to-a-remote/). If your changes modify code, please ensure that is conform to [AskOmics style](#coding-style-guidlines)
 
-Write tests for your changes, and make sure that they [passes](dev.md#launch-continuous-integration-locally).
+Write tests for your changes, and make sure that they [passes](dev-deployment.md#launch-continuous-integration-locally).
 
 Open a pull request against the master branch of flaskomics. The message of your pull request should describe your modifications (why and how).
 

diff --git a/docs/production-deployment.md b/docs/production-deployment.md
@@ -80,12 +80,24 @@ Nginx is used to manage web redirection. Nginx configuration is in two files: `n
 
 ### AskOmics
 
-AskOmics configuration is set using enviroment variables. This variables are set in `askomics.env`. All entry if the `askomics.ini` file can be overrided in this file using 
-
-
-All properties defined in `askomics.ini` can be configured via the environment variables in `askomics.env`. The environment variable should be prefixed with `ASKO_` and have a format like `ASKO_$SECTION_$KEY`. $SECTION and $KEY are case sensitive. *E.g.* property `footer_message` in the `askomics` section should be configured as `ASKO_askomics_footer_message=Welcome to my AskOmics!`
+All properties defined in `askomics.ini` can be configured via the environment variables in `askomics.env`. The environment variable should be prefixed with `ASKO_` and have a format like `ASKO_$SECTION_$KEY`. $SECTION and $KEY are case sensitive. *E.g.* property `footer_message` in the `askomics` section should be configured as `ASKO_askomics_footer_message=Welcome to my AskOmics!`.
 
 !!! warning
     Change `ASKO_flask_secret_key` and `ASKO_askomics_password_salt` to random string
 
 For more information about AskOmics configuration, see [configuration](configure.md) section.
+
+#### First user
+
+environment variables can also be used to create a user into AskOmics at first start. For this, use `CREATE_USER=true` User information can be configured with the following environment variables:
+
+- `USER_FIRST_NAME`: User first name (default: Ad)
+- `USER_LAST_NAME`: User last name (default: Min)
+- `USER_USERNAME`: Username (default: admin)
+- `USER_PASSWORD`: Password (default: admin)
+- `USER_EMAIL`: User email (default: admin@example.com)
+- `USER_APIKEY`: User API key (default: admin)
+- `GALAXY_API_KEY`: Galaxy URL linked to the user (optional)
+- `GALAXY_URL`: User Galaxy API Key (optional)
+
+The user will be created only if the users table of the database is empty.
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,2 +1 @@
-mkdocs
-fontawesome_markdown
+mkdocs==1.0.4
diff --git a/docs/usage_external.md b/docs/usage_external.md
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -12,7 +12,6 @@ theme:
     - javascript
 markdown_extensions:
   - admonition
-  - fontawesome_markdown
   - toc:
       permalink: true
       toc_depth: 1