Update to pass all checks

.github/workflows/code_quality.yml

@@ -22,6 +22,7 @@ jobs:
         with:
           node-version: '18'
       - run: npm install --global remark-cli remark-validate-links remark-lint-no-dead-urls
+      - run: remark --version
       - run: make remark
 
   Flake_8_syntax_errors:

.remarkrc

@@ -7,9 +7,15 @@
     },
     "lint-no-dead-urls": {
       "skipLocalhost": true,
+      "deadOrAliveOptions": {
+        "timeout": 20000,
+        "maxRetries": 2
+      },
       "skipUrlPatterns": [
         "https://security.stackexchange.com",
-        "https://github.com/LayerManager/layman/issues/"
+        "https://github.com/LayerManager/layman/issues/",
+        "https://github.com/LayerManager/layman/blob/",
+        "https://docs.geoserver.org/2.21.x/en/api/"
       ]
     }
   }

CHANGELOG.md

@@ -210,7 +210,7 @@
 - If you are using environment variable [`OAUTH2_CALLBACK_URL`](doc/env-settings.md#oauth2_callback_url), change only its URL path from `/client/authn/oauth2-liferay/callback` to `/client/authn/oauth2-provider/callback`. Keep protocol, domain, and port unchanged.
 - Stop using environment variable `LAYMAN_AUTHN_OAUTH2_PROVIDERS`, it has no effect to Layman anymore. There is exactly one OAuth2 provider Python module now, no need to set it.
 - Stop using environment variable `FLASK_ENV`, it has no effect to Layman anymore.
-  - If you used environment variable `FLASK_ENV` with value `development`, add new environment variable [`FLASK_DEBUG`](https://flask.palletsprojects.com/en/2.3.x/config/?highlight=flask_debug#DEBUG):
+  - If you used environment variable `FLASK_ENV` with value `development`, add new environment variable [`FLASK_DEBUG`](https://flask.palletsprojects.com/en/stable/config/?highlight=flask_debug#DEBUG):
     ```
     FLASK_DEBUG=1
     ```
@@ -579,10 +579,10 @@ make timgen-build
 ### Changes
 - [#167](https://github.com/LayerManager/layman/issues/167) Allow publishing also raster geospatial data using [POST Workspace Layers](doc/rest.md#post-workspace-layers) and [PATCH Workspace Layer](doc/rest.md#patch-workspace-layer).
   - Following formats are supported:
-     - [GeoTIFF](https://gdal.org/drivers/raster/gtiff.html) 
-     - [JPEG2000](https://gdal.org/drivers/raster/jp2openjpeg.html)
-     - [PNG](https://gdal.org/drivers/raster/png.html)
-     - [JPEG](https://gdal.org/drivers/raster/jpeg.html)
+     - [GeoTIFF](https://gdal.org/en/stable/drivers/raster/gtiff.html) 
+     - [JPEG2000](https://gdal.org/en/stable/drivers/raster/jp2openjpeg.html)
+     - [PNG](https://gdal.org/en/stable/drivers/raster/png.html)
+     - [JPEG](https://gdal.org/en/stable/drivers/raster/jpeg.html)
   - Following input combinations of bands and color interpretations are supported:
     - 1 band: Gray
     - 1 band: Palette
@@ -742,7 +742,7 @@ make timgen-build
     - Parameter *style* accepts also QGIS layer style (QML). Layman Test Client enables to select also `*.qml` files.
     - Endpoint [GET Workspace Layer](doc/rest.md#get-workspace-layer) returns in `style` attribute also `type`, either `"sld"` or `"qml"`.
     - Endpoint [GET Workspace Layer Style](doc/rest.md#get-workspace-layer-style) returns SLD style or QML style.
-    - Treat attribute names in QML (also known as '[launder](https://gdal.org/drivers/vector/pg.html#layer-creation-options)').
+    - Treat attribute names in QML (also known as '[launder](https://gdal.org/en/stable/drivers/vector/pg.html#layer-creation-options)').
     - New docker container with QGIS server called `qgis` in demo configuration.
     - New directory [LAYMAN_QGIS_DATA_DIR](doc/env-settings.md#LAYMAN_QGIS_DATA_DIR) is used to store [layer QGS files](doc/data-storage.md#filesystem).
     - [WMS](doc/endpoints.md#web-map-service) is moved to dedicated [GeoServer workspace](doc/data-storage.md#geoserver) whose name is composed from Layman's [workspace](doc/models.md#workspace) name and suffix `_wms`. [WFS](doc/endpoints.md#web-feature-service) remains in GeoServer workspace whose name is equal to Layman's workspace name.

README.md

@@ -7,8 +7,8 @@ Publishing geospatial data online through [REST API](doc/rest.md).
   - [**layer**](doc/models.md#layer): visual representation of single vector or raster dataset, including raster [timeseries](doc/models.md#timeseries)
   - [**map**](doc/models.md#map): collection of layers
 - Accepts **vector** layer data in [GeoJSON](https://en.wikipedia.org/wiki/GeoJSON), [ShapeFile](https://en.wikipedia.org/wiki/Shapefile), or [PostGIS table](https://postgis.net/) identified by [PostgreSQL connection URI](https://www.postgresql.org/docs/15/libpq-connect.html#id-1.7.3.8.3.6)
-- Accepts **raster** layer data in [GeoTIFF](https://gdal.org/drivers/raster/gtiff.html), [JPEG2000](https://gdal.org/drivers/raster/jp2openjpeg.html), [PNG](https://gdal.org/drivers/raster/png.html), and [JPEG](https://gdal.org/drivers/raster/jpeg.html) formats
-- Accepts layer **style** in [Styled Layer Descriptor](https://ogc.org/standard/sld), [Symbology Encoding](https://ogc.org/standard/se), and [QGIS Style File Format](https://docs.qgis.org/3.16/en/docs/user_manual/appendices/qgis_file_formats.html#qml-the-qgis-style-file-format) (for vector data only) formats
+- Accepts **raster** layer data in [GeoTIFF](https://gdal.org/en/stable/drivers/raster/gtiff.html), [JPEG2000](https://gdal.org/en/stable/drivers/raster/jp2openjpeg.html), [PNG](https://gdal.org/en/stable/drivers/raster/png.html), and [JPEG](https://gdal.org/en/stable/drivers/raster/jpeg.html) formats
+- Accepts layer **style** in [Styled Layer Descriptor](https://www.ogc.org/publications/standard/sld/), [Symbology Encoding](https://www.ogc.org/publications/standard/se/), and [QGIS Style File Format](https://docs.qgis.org/3.16/en/docs/user_manual/appendices/qgis_file_formats.html#qml-the-qgis-style-file-format) (for vector data only) formats
 - Accepts **map** definition in [HSLayers Map Composition](https://github.com/hslayers/map-compositions) format
 - Even large files can be easily uploaded from browser thanks to asynchronous chunk upload
 - [OAuth2 authentication](doc/security.md#authentication)
@@ -35,7 +35,7 @@ Publishing geospatial data online through [REST API](doc/rest.md).
 
     You can check your kernel version with `uname -r`.
 - Docker Engine v20.10.13+ including Docker Compose v2+
-  - installation instructions for [centos 7](https://docs.docker.com/install/linux/docker-ce/centos/), including docker-compose-plugin installation
+  - installation instructions for [centos 7](https://docs.docker.com/engine/install/centos/), including docker-compose-plugin installation
 
 **Optionally**
 - linux or any tool to run tasks defined in Makefile using `make` command
@@ -106,7 +106,7 @@ Then you can log in with automatically provided Wagtail user `layman` and passwo
 Layman's source code provides settings suitable for development, testing and demo purposes. Furthermore, there exists [`Makefile`](Makefile) with predefined commands for each purpose including starting all necessary services (both in background and foreground) and stoping it.
 
 Layman's configuration is split into three levels:
-- `docker-compose.*.yml` files used as [docker-compose configuration files](https://docs.docker.com/compose/compose-file/) with most general settings of docker containers including volume mappings, port mappings, container names and startup commands
+- `docker-compose.*.yml` files used as [docker-compose configuration files](https://docs.docker.com/reference/compose-file/) with most general settings of docker containers including volume mappings, port mappings, container names and startup commands
 - `.env*` files with environment settings of both build stage and runtime of docker containers
 - `src/layman_settings.py` Python module with settings of Layman's Python modules for runtime
 
@@ -170,7 +170,7 @@ When providing **external dependencies**, check their production-related documen
 - [PostgreSQL 13.3](https://www.postgresql.org/docs/13/admin.html) & [PostGIS 3.1](http://postgis.net/docs/manual-3.1/performance_tips.html)
 - [QGIS Server 3.16.1](https://docs.qgis.org/3.10/en/docs/user_manual/working_with_ogc/server/index.html)
 - [GeoServer 2.21.2](https://geoserver.org/release/2.21.2/)
-- [Redis 4.0](https://redis.io/topics/admin)
+- [Redis 4.0](https://redis.io/docs/latest/operate/oss_and_stack/management/admin/)
 - [Micka v2020.014](https://github.com/hsrs-cz/Micka/releases/tag/v2020.014), see also [configuration](deps/micka/sample/confs/config.local.neon) of [dockerized Micka](https://github.com/LayerManager/docker-micka).
 
 Within PostgreSQL, you need to provide one database for Layman and one database for Micka. For Layman, you also need to provide one user [LAYMAN_PG_USER](doc/env-settings.md#LAYMAN_PG_USER) who needs enough privileges to create new schemas in [LAYMAN_PG_DBNAME](doc/env-settings.md#LAYMAN_PG_DBNAME) database. The user also needs access to `public` schema where PostGIS must be installed.
@@ -190,8 +190,8 @@ After providing external dependencies there is time to provide **internal depend
 **System-level** dependencies includes
 - python 3.8+
 - [python3-lxml](https://lxml.de/installation.html)
-- [ogr2ogr](https://gdal.org/programs/ogr2ogr.html) utility of [gdal](https://gdal.org/) 3.3+
-- [chromium-browser](https://chromium.org/) 90+ and corresponding version of [chromedriver](https://chromedriver.chromium.org/)
+- [ogr2ogr](https://gdal.org/en/stable/programs/ogr2ogr.html) utility of [gdal](https://gdal.org/) 3.3+
+- [chromium-browser](https://www.chromium.org/) 90+ and corresponding version of [chromedriver](https://developer.chrome.com/docs/chromedriver/)
 - [pipenv](https://pypi.org/project/pipenv/)
 - [node.js](https://nodejs.org/) 18 & npm 8 for running Layman Test Client
 - [node.js](https://nodejs.org/) 16 & npm 8 for running Timgen

doc/dependencies.md

@@ -35,12 +35,12 @@
 | --- | --- | --- | --- | --- | --- |
 | [flask](http://flask.pocoo.org/) | BSD License | Pipfile | prod | bin | to build REST API |
 | [celery](https://github.com/celery/celery) | BSD 3-Clause | Pipfile | prod | bin | asynchronous task runner |
-| [redis-py](https://github.com/andymccurdy/redis-py) | MIT | Pipfile | prod | bin | |
+| [redis-py](https://github.com/redis/redis-py) | MIT | Pipfile | prod | bin | |
 | [unidecode](https://github.com/avian2/unidecode) | GNU GPL v2 | Pipfile | prod | bin | |
 | [psycopg2-binary](https://github.com/psycopg/psycopg2) | GNU LGPL | Pipfile | prod | bin | |
 | [requests](https://requests.readthedocs.io/) | Apache License 2.0 | Pipfile | prod | bin | |
 | [owslib](https://github.com/geopython/OWSLib) | BSD 3-Clause | Pipfile | prod | bin | |
-| [jsonschema](https://github.com/Julian/jsonschema) | MIT | Pipfile | prod | bin | |
+| [jsonschema](https://github.com/python-jsonschema/jsonschema) | MIT | Pipfile | prod | bin | |
 | [flower](https://github.com/mher/flower) | BSD 3-Clause | Pipfile | prod | bin | to monitor celery tasks |
 | [selenium](https://www.chromium.org/) | Apache License 2.0 | Dockerfile | prod | bin | for client-side map rendering and integration testing |
 | [cacheout](https://github.com/dgilland/cacheout) | MIT | Pipfile | prod | bin | |
@@ -51,7 +51,7 @@
 | [pytest](https://pytest.org/) | MIT License | Pipfile | test | bin | |
 | [flake8](https://flake8.pycqa.org/) | MIT | Pipfile | test | bin | code style checker |
 | [pycodestyle](https://pycodestyle.pycqa.org/) | MIT | Pipfile | test | bin | code style checker |
-| [pylint](https://github.com/PyCQA/pylint) | GNU GPL v2 | Pipfile | test | bin | code style checker |
+| [pylint](https://github.com/pylint-dev/pylint) | GNU GPL v2 | Pipfile | test | bin | code style checker |
 | [autopep8](https://github.com/hhatto/autopep8) | MIT | Pipfile | test | bin | to automatically fix code style |
 | [pytest-rerunfailures](https://github.com/pytest-dev/pytest-rerunfailures) | MPL | Pipfile | test | bin | to automatically rerun flaky tests |
 | [pytest-timeout](https://pypi.org/project/pytest-timeout/) | MIT | Pipfile | test | bin | to automatically stop tests after given timeout |
@@ -89,5 +89,5 @@
 | [layermanager/docker-postgis](https://github.com/layermanager/docker-postgis) | MIT | docker-compose.yml | dev | bin | |
 | [jirikcz/micka](https://github.com/LayerManager/docker-micka) | GNU GPL v3 | docker-compose.yml | prod-external | bin | |
 | [samtux/micka](https://github.com/samtux/docker-micka) | GNU GPL v3 | jirikcz/micka | prod-external | src | |
-| [docker-library/redis](https://github.com/docker-library/redis) | BSD 3-Clause | docker-compose.yml | prod | bin | |
+| [docker-library/redis](https://github.com/redis/docker-library-redis) | BSD 3-Clause | docker-compose.yml | prod | bin | |
 | [plantuml/plantuml](https://hub.docker.com/r/plantuml/plantuml) | GNU GPL v3 | Makefile | dev | bin | render PlantUML images |

doc/endpoints.md

@@ -2,7 +2,7 @@
 To use [headers for GeoServer's Proxy URL](https://docs.geoserver.org/2.21.x/en/user/configuration/globalsettings.html#use-headers-for-proxy-url) see [client proxy documentation](client-proxy.md).
 
 ## Web Map Service
-[Web Map Service (WMS)](https://ogc.org/standard/wms) endpoint is implemented using combination of Layman's authentication proxy, Layman's WMS proxy, and [GeoServer](https://docs.geoserver.org/2.21.x/en/user/services/wms/reference.html).
+[Web Map Service (WMS)](https://www.ogc.org/publications/standard/wms/) endpoint is implemented using combination of Layman's authentication proxy, Layman's WMS proxy, and [GeoServer](https://docs.geoserver.org/2.21.x/en/user/services/wms/reference.html).
 
 The authentication proxy understands same [authentication credentials](security.md#authentication) as Layman REST API (e.g. OAuth2 credentials) and passes the request to GeoServer with credentials understandable by GeoServer.
 
@@ -15,7 +15,7 @@ WMS respects [publication access rights](security.md#publication-access-rights).
 GetLegendGraphic query is answered directly by GeoServer for layers with SLD style and can be parametrized according to [GeoServer documentation](https://docs.geoserver.org/latest/en/user/services/wms/get_legend_graphic/index.html). For layers with QML style is such query redirected by GeoServer to QGIS server and can be parametrized according to [QGIS documentation](https://docs.qgis.org/3.16/en/docs/server_manual/services.html?highlight=getlegendgraphic#getlegendgraphics). 
 
 ## Web Feature Service
-[Web Feature Service (WFS)](https://ogc.org/standard/wfs) endpoint is implemented using combination of Layman's authentication proxy, Layman's WFS proxy, and [GeoServer](https://docs.geoserver.org/2.21.x/en/user/services/wfs/reference.html).
+[Web Feature Service (WFS)](https://www.ogc.org/publications/standard/wfs/) endpoint is implemented using combination of Layman's authentication proxy, Layman's WFS proxy, and [GeoServer](https://docs.geoserver.org/2.21.x/en/user/services/wfs/reference.html).
 
 The authentication proxy behaves in the same way as in case of [WMS](#web-map-service).
 
@@ -31,4 +31,4 @@ WFS respects [publication access rights](security.md#publication-access-rights).
 For layers in `EPSG:5514` and WFS requests in `CRS:84`, the features may have wrong coordinates by hundreds of meters. For requests in `EPSG:4326`, coordinates are correct.
 
 ## Catalogue Service
-[Catalogue Service (CSW)](https://ogc.org/standard/cat) is implemented using [Micka](https://github.com/hsrs-cz/Micka).
+[Catalogue Service (CSW)](https://www.ogc.org/publications/standard/cat/) is implemented using [Micka](https://github.com/hsrs-cz/Micka).

doc/env-settings.md

@@ -109,7 +109,7 @@ Internal URL of REST API [Current User](rest.md#current-user) endpoint.
 Internal URL (only protocol & host & port, without path) of Layman's REST API.
 
 ### LTC_REDIS_URL
-URL of [Redis logical database](https://redis.io/commands/select) including database number where Layman Test Client stores user sessions including authentication credentials.
+URL of [Redis logical database](https://redis.io/docs/latest/commands/select/) including database number where Layman Test Client stores user sessions including authentication credentials.
 
 ### LTC_SESSION_SECRET
 See [`secret` at express-session documentation](https://www.npmjs.com/package/express-session#secret).
@@ -126,7 +126,7 @@ To enable not-so-secure SSL communication (UnsafeLegacyRenegotiation), set `NODE
 ## Connection to Redis
 
 ### LAYMAN_REDIS_URL
-URL of [Redis logical database](https://redis.io/commands/select) including database number. Layman stores internal data about publications and users in this database. By default, Layman flushes the whole logical database on every startup! See also [LAYMAN_SKIP_REDIS_LOADING](#LAYMAN_SKIP_REDIS_LOADING).
+URL of [Redis logical database](https://redis.io/docs/latest/commands/select/) including database number. Layman stores internal data about publications and users in this database. By default, Layman flushes the whole logical database on every startup! See also [LAYMAN_SKIP_REDIS_LOADING](#LAYMAN_SKIP_REDIS_LOADING).
 
 ## Connection to PostgreSQL
 
@@ -197,10 +197,10 @@ Filesystem directory where data published on QGIS are stored, including styles.
 HTTP Basic Authentication credentials for communication with [CSW](#CSW_URL) encoded as `user:password`.
 
 ### CSW_URL
-Internal URL of [OGC Catalogue Service v2.0.2](https://ogc.org/standard/cat) endpoint. Tested with [Micka](http://micka.bnhelp.cz/).
+Internal URL of [OGC Catalogue Service v2.0.2](https://www.ogc.org/publications/standard/cat/) endpoint. Tested with [Micka](https://www.bnhelp.cz/produkty/metadata/).
 
 ### CSW_PROXY_URL
-Public URL of [OGC Catalogue Service v2.0.2](https://ogc.org/standard/cat) endpoint. Tested with [Micka](http://micka.bnhelp.cz/).
+Public URL of [OGC Catalogue Service v2.0.2](https://www.ogc.org/publications/standard/cat/) endpoint. Tested with [Micka](https://www.bnhelp.cz/produkty/metadata/).
 
 ### MICKA_ACCEPTED_VERSION
 Version of Micka that Layman will accept on startup encoded as `version:revision`, e.g. `2020.014:2020-04-15.01`. Also, on one of '>=' or '==' prefixes can be used with obvious meaning, `e.g. >=2020.014:2020-04-15.01`. For prefix '>=', version and revision are compared independently as strings. If the variable is not set, a version defined in [`src/layman_settings.py`](../src/layman_settings.py) will be accepted. If none prefix is used, value is compared as with '=='.
@@ -211,13 +211,13 @@ String with public domain and optionally port, e.g. `<domain>` or `<domain>:<por
 ## Flask settings
 
 ### FLASK_APP
-See [Flask documentation](https://flask.palletsprojects.com/en/2.3.x/cli/?highlight=flask_app#environment-variables-from-dotenv).
+See [Flask documentation](https://flask.palletsprojects.com/en/stable/cli/?highlight=flask_app#environment-variables-from-dotenv).
 
 ### FLASK_DEBUG
-See [Flask documentation](https://flask.palletsprojects.com/en/2.3.x/config/?highlight=flask_debug#DEBUG).
+See [Flask documentation](https://flask.palletsprojects.com/en/stable/config/?highlight=flask_debug#DEBUG).
 
 ### FLASK_SECRET_KEY
-See [Flask documentation](https://flask.palletsprojects.com/en/2.3.x/config/?highlight=secret_key#SECRET_KEY).
+See [Flask documentation](https://flask.palletsprojects.com/en/stable/config/?highlight=secret_key#SECRET_KEY).
 
 ## Docker settings
 

doc/metadata.md

@@ -1,6 +1,6 @@
 # Metadata
 
-Layman is able to publish partial metadata records to [OGC Catalogue Service](https://ogc.org/standard/cat) [Micka](http://micka.bnhelp.cz/). Records are partial because Layman does not know all metadata properties. Below are listed
+Layman is able to publish partial metadata records to [OGC Catalogue Service](https://www.ogc.org/publications/standard/cat/) [Micka](https://www.bnhelp.cz/produkty/metadata/). Records are partial because Layman does not know all metadata properties. Below are listed
 - [metadata properties that are known to Layman](#metadata-properties-known-to-layman) 
 - [metadata properties unknown to Layman](#metadata-properties-unknown-to-layman), that Layman is aware of.