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ci-bot committed Jul 6, 2024
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58 changes: 29 additions & 29 deletions latest/index.html
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Expand Up @@ -1147,7 +1147,7 @@ <h2 id="default-setup">
</li>
<li>
a reverse
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/proxy">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/proxy">
proxy
</a>
container is created and routes traffic to (2) and (3) through localhost subdomains, in the form:
Expand Down Expand Up @@ -1194,11 +1194,11 @@ <h3 id="docker-compose-env-variables">
</h3>
<p>
They are used to modify existing services where whenever enabling the feature requires changes in multiple services. They also have the advantage, compared to docker profiles, of not needing to define a new profile when a new combination of features becomes available. To set an env variable for docker compose, either assign it in the shell or change the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/.env">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/.env">
.env
</a>
file. To later unset it, either unset it from the shell or assign it an empty value, either in the shell or in the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/.env">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/.env">
.env
</a>
file.
Expand Down Expand Up @@ -1578,15 +1578,15 @@ <h4 id="dev-configuration">
<p>
<img alt="⚠" class="twemoji" src="https://cdn.jsdelivr.net/gh/jdecked/twemoji@15.0.3/assets/svg/26a0.svg" title=":warning:"/>
As the DEV containers pull from upstream/latest, there is no guarantee of their functioning outside of releases. If they fail to start, try, as a first option, to build the image from a tag (e.g.
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/frontend/compose.dev.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/frontend/compose.dev.yaml">
build context
</a>
) using the
<a href="https://docs.docker.com/reference/cli/docker/image/build/#git-repositories">
TAG
</a>
and then git checkout to that tag (e.g. set
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/frontend/compose.dev.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/frontend/compose.dev.yaml">
GITHUB_REPO
</a>
including the branch using the same syntax and value as the build context).
Expand Down Expand Up @@ -1622,7 +1622,7 @@ <h3 id="service-specific-config">
</p>
<p>
Every service folder (inside the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services">
services
</a>
parent directory) contains its configuration and some instructions, at least for the non-third-party containers.
Expand All @@ -1633,7 +1633,7 @@ <h3 id="service-specific-config">
frontend
</a>
, the user can change any file in the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/frontend/config">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/frontend/config">
frontend config
</a>
folder, for which instructions are available in the
Expand Down Expand Up @@ -1661,15 +1661,15 @@ <h3 id="entrypoints">
frontend
</code>
composability, it is useful to specify its configuration through multiple JSON files, with different scopes, which are then merged by a
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/frontend/entrypoints/merge_json.sh">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/frontend/entrypoints/merge_json.sh">
init script
</a>
. For this reason, one can define service-specific
<code>
entrypoints
</code>
(e.g.
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/frontend/entrypoints">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/frontend/entrypoints">
frontend ones
</a>
) which can be run inside the container, before the service starts (i.e. before the docker compose
Expand All @@ -1681,22 +1681,22 @@ <h3 id="entrypoints">
entrypoints
</code>
folder below the outermost service (e.g.
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/entrypoints">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/entrypoints">
this one
</a>
).
</p>
<p>
To ease the iterative execution of multiple init scripts, one can leverage the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/entrypoints/loop_entrypoints.sh">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/entrypoints/loop_entrypoints.sh">
loop_entrypoints
</a>
utility, which loops alphabetically over
<code>
/docker-entrypoinst/*.sh
</code>
and executes each. This is in use in some services (e.g. in the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/frontend/compose.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/frontend/compose.yaml">
frontend
</a>
), so one can add additional init steps by mounting them, one by one, as volumes inside the container in the
Expand All @@ -1718,7 +1718,7 @@ <h4 id="if-the-service-does-not-support-entrypoints-yet-one-needs-to">
<ol>
<li>
mount the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/entrypoints/loop_entrypoints.sh">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/entrypoints/loop_entrypoints.sh">
loop_entrypoint.sh
</a>
as a volume inside the container
Expand Down Expand Up @@ -1746,7 +1746,7 @@ <h4 id="if-the-service-does-not-support-entrypoints-yet-one-needs-to">
</ol>
<p>
See for example
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/frontend/compose.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/frontend/compose.yaml">
here
</a>
.
Expand Down Expand Up @@ -1804,7 +1804,7 @@ <h2 id="select-the-services">
</h2>
<p>
The user can selectively decide the containers to spin up and the dependencies will be resolved accordingly. The available services are in the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services">
services
</a>
folder and are called consistently.
Expand Down Expand Up @@ -1912,7 +1912,7 @@ <h3 id="basic">
<ol>
<li>
create a dedicated folder in the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services">
services
</a>
one *
Expand Down Expand Up @@ -1942,7 +1942,7 @@ <h3 id="basic">
</li>
<li>
include the reference to (3) to the global
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/compose.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/compose.yaml">
compose include list
</a>
*
Expand All @@ -1960,11 +1960,11 @@ <h3 id="basic">
services
</code>
folder relative to the affected service, and in (6) add it to its inclusion list. See an example of a service relative
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services">
services folder here
</a>
and a
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/compose.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/compose.yaml">
relative inclusion list here
</a>
.
Expand All @@ -1981,7 +1981,7 @@ <h4 id="supported-os-architectures">
docker compose up
</code>
on different platforms, for example on MAC with arm64 architecture. See for example the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/searchapi/compose.yaml#L3">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/searchapi/compose.yaml#L3">
searchapi compose
</a>
.
Expand Down Expand Up @@ -2012,11 +2012,11 @@ <h3 id="advanced">
</li>
<li>
eventually, include any service, in the service-specific folder which is specific to the service and not shared by other, more general services, e.g.
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services">
here
</a>
. This folder should also include different versions of the same service, e.g. v3 and v4
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services">
here
</a>
</li>
Expand All @@ -2039,7 +2039,7 @@ <h3 id="advanced">
compose.base.yaml
</code>
file, e.g.
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/v4/compose.base.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/v4/compose.base.yaml">
here
</a>
, which should contain the
Expand All @@ -2058,22 +2058,22 @@ <h3 id="advanced">
compose.&lt;ENV&gt;.yaml
</code>
file, e.g.
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/v4/compose.elastic.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/v4/compose.elastic.yaml">
backend v4 compose.elastic.yaml
</a>
, with the additional/override config, specific to the enabled feature
</li>
<li>
create a symlink from
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/.empty.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/.empty.yaml">
.empty.yaml
</a>
to each
<code>
.compose.&lt;ENV&gt;.yaml
</code>
, e.g.
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/v4/.compose.elastic.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/v4/.compose.elastic.yaml">
here
</a>
. This is used whenever the
Expand All @@ -2100,7 +2100,7 @@ <h3 id="advanced">
ENV
</code>
is not set. See an example
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/v4/compose.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/v4/compose.yaml">
here
</a>
</li>
Expand All @@ -2110,7 +2110,7 @@ <h3 id="advanced">
backend
</code>
service, add the selective include in the parent compose.yaml, e.g.
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/compose.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/compose.yaml">
here
</a>
</li>
Expand All @@ -2123,7 +2123,7 @@ <h3 id="advanced">
here
</a>
, e.g. like
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/v4/compose.base.yaml">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/v4/compose.base.yaml">
here
</a>
</p>
Expand Down
10 changes: 5 additions & 5 deletions latest/services/backend/services/keycloak/index.html
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Expand Up @@ -732,11 +732,11 @@ <h2 id="configuration-options">
</h2>
<p>
The Keycloak configuration is set by the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/keycloak/config/.env">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/keycloak/config/.env">
.env file
</a>
and the realm created is in
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/keycloak/config/facility-realm.json">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/keycloak/config/facility-realm.json">
facility-realm.json file
</a>
.
Expand All @@ -760,7 +760,7 @@ <h2 id="default-configuration">
</h2>
<p>
The default configuration
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/keycloak/config/.env">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/keycloak/config/.env">
.env file
</a>
creates the
Expand Down Expand Up @@ -819,11 +819,11 @@ <h2 id="default-configuration">
</code>
(an array of strings).
The name of the claim can be configured either in
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/v3/config/login-callbacks.js">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/v3/config/login-callbacks.js">
login-callbacks.js
</a>
for v3 or with
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/v4/config/.oidc.env">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/v4/config/.oidc.env">
environment variables
</a>
for v4.
Expand Down
6 changes: 3 additions & 3 deletions latest/services/backend/services/ldap/index.html
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Original file line number Diff line number Diff line change
Expand Up @@ -732,7 +732,7 @@ <h2 id="configuration-options">
</h2>
<p>
The OpenLDAP configuration is set by the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/ldap/config/.env">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/ldap/config/.env">
.env file
</a>
.
Expand All @@ -746,7 +746,7 @@ <h2 id="configuration-options">
</p>
<p>
You can add other users by editing the
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/ldap/config/ldifs/02-users.ldif">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/ldap/config/ldifs/02-users.ldif">
ldif file
</a>
.
Expand All @@ -761,7 +761,7 @@ <h2 id="default-configuration">
</h2>
<p>
The default configuration
<a href="https://github.com/SciCatProject/scicatlive/blob/219/merge/services/backend/services/ldap/config/.env">
<a href="https://github.com/SciCatProject/scicatlive/blob/main/services/backend/services/ldap/config/.env">
.env file
</a>
creates the
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