From c0689d885615c0aeba4cb73df78105abde40e5ce Mon Sep 17 00:00:00 2001
From: lberti <lberti21@gmail.com>
Date: Mon, 4 Sep 2023 10:05:06 +0200
Subject: [PATCH 1/9] #187 delete data contribution guide from feelpp/toolbox
---
contribute/modules/girder/nav.adoc | 13 --
contribute/modules/girder/pages/README.adoc | 51 -------
contribute/modules/girder/pages/api_keys.adoc | 79 ----------
.../modules/girder/pages/python_scripts.adoc | 137 ------------------
4 files changed, 280 deletions(-)
delete mode 100644 contribute/modules/girder/nav.adoc
delete mode 100644 contribute/modules/girder/pages/README.adoc
delete mode 100644 contribute/modules/girder/pages/api_keys.adoc
delete mode 100644 contribute/modules/girder/pages/python_scripts.adoc
diff --git a/contribute/modules/girder/nav.adoc b/contribute/modules/girder/nav.adoc
deleted file mode 100644
index 9b4e4840..00000000
--- a/contribute/modules/girder/nav.adoc
+++ /dev/null
@@ -1,13 +0,0 @@
-* xref:README.adoc[How to contribute data with Girder]
-** xref:README.adoc#_what_is_girder[What is Girder]
-** xref:README.adoc#_file_access_options[File access options]
-*** xref:README.adoc#_web_browser_ui[Web brower UI]
-*** xref:README.adoc#_python_api[Python API]
-** xref:python_scripts.adoc[Python scripts examples]
-*** xref:python_scripts.adoc#_with_user_and_password[With user and password]
-**** xref:python_scripts.adoc#_what_not_to_do[What not to do]
-**** xref:python_scripts.adoc#_interactive_download[Interactive download]
-**** xref:python_scripts.adoc#_interactive_upload[Interactive upload]
-*** xref:api_keys.adoc#_using_api_keys[Using API keys]
-**** xref:api_keys.adoc#_download[Download]
-**** xref:api_keys.adoc#_upload[Upload]
diff --git a/contribute/modules/girder/pages/README.adoc b/contribute/modules/girder/pages/README.adoc
deleted file mode 100644
index 8357c6f2..00000000
--- a/contribute/modules/girder/pages/README.adoc
+++ /dev/null
@@ -1,51 +0,0 @@
-= Girder
-
-== What is Girder
-
-Girder is a data management platform.
-It can be used to store (large) files such as meshes, simulation results, etc...
-Read more about it in the {feelpp} xref:data:ROOT:data-storage.adoc[data manual] or
-link:http://girder.readthedocs.io/[on the official website].
-
-== File access options
-
-A big advantage of girder is that files can be accessed either with a nice user
-interface (in a web browser) or more programmatically (via CLI or programming
-interfaces).
-This is true for both upload and download.
-
-=== Web browser UI
-
-If you are new to Girder, you should start with the web user interface to
-discover the service.
-You are encouraged to read the documentation
-link:http://girder.readthedocs.io/[documentation] and especially the
-link:http://girder.readthedocs.io/en/latest/user-docs.html[user guide].
-For example, using a web browser, you can reach
-link:https://girder.math.unistra.fr/#collections[our server].
-
-|===
-| image:girder_web_ui.png[Web user interface,100%]
-|===
-
-NOTE: This is quite straightforward and it should illustrate important concepts
-and help better visualize the following section.
-
-=== Python API
-
-To download or upload a file using python, we have two options.
-We can either use a login system (user + password) or an API key.
-- With the user/password, we will need to provide a user and a password to
-access files, just like a human would do using the UI.
-- With an API key, the script only needs an API key.
-This means we do not need to have an account on the Girder server.
-
-In both cases, similar pieces of information are required:
-
-- an *address* (URL): to reach the server,
-- a *file ID*: to tell which file/directory we want to manipulate,
-- either a *user/password* pair or an *API key*: to grant access to the
-required file(s).
-
-Let's check out some
-xref:contribute:girder:python_scripts.adoc[scripts].
diff --git a/contribute/modules/girder/pages/api_keys.adoc b/contribute/modules/girder/pages/api_keys.adoc
deleted file mode 100644
index a77522a4..00000000
--- a/contribute/modules/girder/pages/api_keys.adoc
+++ /dev/null
@@ -1,79 +0,0 @@
-= Using API keys
-
-An API key grants access to a certain set of files, with various permissions.
-It is very useful and quite convenient to use.
-Since it is nothing more than a character string, one could think of it as a
-long and pseudorandom special password.
-
-NOTE: To learn how to set API keys, read
-link:http://girder.readthedocs.io/en/latest/user-guide.html#api-keys[this part]
-of the documentation.
-
-== Download
-
-To use an API key to download a file, see this script:
-
-[source, python]
-----
-#!/usr/bin/env python3
-
-
-# We need the girder client module.
-import girder_client
-
-# First, we initiate the client with the girder server address.
-gc = girder_client.GirderClient(apiUrl='https://girder.math.unistra.fr/api/v1')
-
-# We authenticate using only the API key
-gc.authenticate(apiKey='KEY') # <1>
-
-# We download the file using its file ID. The path indicates where the file
-# should be written (the full file name should be included at the end of the path)
-gc.downloadFile(fileId='FILEID', path='PATH') # <2>
-
-----
-
-<1> *KEY* is the only needed information to authenticate.
-
-<2> *FILEID* should be replaced by the actual Girder file ID and *PATH* should
-be the path where to store the results, including the desired file name and
-extension.
-
-
-== Upload
-
-To upload using an API key:
-
-[source, python]
-----
-#!/usr/bin/env python3
-
-
-# We need the girder client module.
-import girder_client
-
-# First, we initiate the client with the girder server address.
-gc = girder_client.GirderClient(apiUrl='https://girder.math.unistra.fr/api/v1')
-
-# We authenticate using only the API key
-gc.authenticate(apiKey='KEY') # <1>
-
-# /!\ This is mandatory: we have to open the file in read mode before
-# uploading it
-f = open('PATH', 'r') # <2>
-
-# Now we can upload the file <3>
-gc.uploadFile(parentId='PID', stream=f, name="NAME", size=SIZE, parentType='TYPE')
-
-----
-
-<1> *KEY* is the only needed information to authenticate.
-
-<2> *PATH* should be replaced by the full path to the file to read.
-*r* stands for "read mode".
-
-<3> *PID* should be replaced by the parent directory ID (on the Girder server).
-*f* is the read stream defined previously .
-*NAME* should be replaced by the desired file name (on the Girder server).
-*SIZE* should be replaced by the file size (in bytes).
-*TYPE* is either *folder*, *user*, or *collection*.
diff --git a/contribute/modules/girder/pages/python_scripts.adoc b/contribute/modules/girder/pages/python_scripts.adoc
deleted file mode 100644
index 34d94f40..00000000
--- a/contribute/modules/girder/pages/python_scripts.adoc
+++ /dev/null
@@ -1,137 +0,0 @@
-= Python scripts
-
-Here, we provide some python scripts to access files on Girder.
-To be able to use them, please install the girder client python module (read how
-link:http://girder.readthedocs.io/en/latest/python-client.html[here].
-)
-
-== With user and password
-
-=== What not to do
-
-WARNING: The following script is only meant as a first approach to understand
-how the module works.
-You should not use it because it requires your password to be written in clear
-in the script.
-Use the xref:python_scripts.adoc#_interactive_download[interactive version]
-instead.
-
-[source, python]
-----
-#!/usr/bin/env python3
-
-
-# We need the girder client module.
-import girder_client
-
-# First, we initiate the client with the girder server address.
-gc = girder_client.GirderClient(apiUrl='https://girder.math.unistra.fr/api/v1')
-
-# We authenticate using the username and the password.
-# /!\ This is for learning purpose.
-# For security reasons, you should never put your password in the script.
-gc.authenticate(username='USER', password='PASSWORD') # <1>
-
-# We download the file using its file ID. The path indicates where the file
-# should be written (the file name should be included at the end of the path)
-gc.downloadFile(fileId='FILEID', path='PATH') # <2>
-
-----
-<1> *USER* should be replaced by the Girder user name,
-*PASSWORD* by the corresponding password
-<2> *FILEID* should be replaced by the actual Girder file ID and *PATH* should
-be the path where to store the results, including the desired file name and
-extension.
-
-WARNING: If you don't supply the file name, the system will not warn you, it
-will *automatically generate one*, which could be confusing !
-
-IMPORTANT: Remember not to use this script. Try the
-xref:python_scripts.adoc#_interactive_download[interactive one] instead.
-
-
-=== Interactive download
-
-Here, we use a modified version of the _authenticate_ function to use
-interactive login.
-This means the password will be prompted for at run time.
-
-IMPORTANT: This implies the script can not be used in a fully automated way,
-because each execution of the script will require the user of the script to be
-present to type the password. For a safe and automatic access, use the
-xref:api_keys.adoc#_using_api_keys[API keys].
-
-[source, python]
-----
-#!/usr/bin/env python3
-
-
-# We need the girder client module.
-import girder_client
-
-# First, we initiate the client with the girder server address.
-gc = girder_client.GirderClient(apiUrl='https://girder.math.unistra.fr/api/v1')
-
-# We authenticate using the username, the password will be typed at runtime
-gc.authenticate(username='USER', interactive=True) # <1>
-
-# We download the file using its file ID. The path indicates where the file
-# should be written (the full file name should be included at the end of the path)
-gc.downloadFile(fileId='FILEID', path='PATH') # <2>
-
-----
-<1> *USER* should be replaced by the Girder user name, and because of the
-_interactive=True_ argument, the password will be prompted for at runtime.
-<2> *FILEID* should be replaced by the actual Girder file ID and *PATH* should be the path where to store the results, including the desired file name and extension.
-
-TIP: We can even prompt the user to type *both the user name and the password*
-by providing *only* the _interactive=True_ argument !
-This is a better solution when multiple users are likely to use the script only
-once or a handful of times each.
-
-WARNING: If you don't supply the file name, the system will not warn you, it
-will *automatically generate one*, which could be confusing !
-
-
-
-=== Interactive upload
-
-To upload a file, only a few changes are required.
-
-[source, python]
-----
-#!/usr/bin/env python3
-
-
-# We need the girder client module.
-import girder_client
-
-# First, we initiate the client with the girder server address.
-gc = girder_client.GirderClient(apiUrl='https://girder.math.unistra.fr/api/v1')
-
-# We authenticate using the username, the password will be typed at runtime
-gc.authenticate(username='USER', interactive=True) # <1>
-
-
-# /!\ This is mandatory: we have to open the file in read mode before
-# uploading it
-f = open('PATH', 'r') # <2>
-
-# Now we can upload the file <3>
-gc.uploadFile(parentId='PID', stream=f, name="NAME", size=SIZE, parentType='TYPE')
-
-----
-
-<1> *USER* should be replaced by the Girder user name, and because of the
-_interactive=True_ argument, the password will be prompted for at runtime.
-
-<2> *PATH* should be replaced by the full path to the file to read.
-*r* stands for "read mode".
-
-<3> *PID* should be replaced by the parent directory ID (on the Girder server).
-*f* is the read stream defined previously .
-*NAME* should be replaced by the desired file name (on the Girder server).
-*SIZE* should be replaced by the file size (in bytes).
-*TYPE* is either *folder*, *user*, or *collection*.
-
-NOTE: We should try and find a way to get the file size automatically.
From 103a0c85174e32e2247abb7d339bd8766425f74d Mon Sep 17 00:00:00 2001
From: lberti <lberti21@gmail.com>
Date: Mon, 4 Sep 2023 10:51:55 +0200
Subject: [PATCH 2/9] #187 restore girder readme page with partial
---
contribute/modules/ROOT/nav.adoc | 2 ++
contribute/modules/girder/images/README.adoc | 1 +
2 files changed, 3 insertions(+)
create mode 100644 contribute/modules/girder/images/README.adoc
diff --git a/contribute/modules/ROOT/nav.adoc b/contribute/modules/ROOT/nav.adoc
index 824ec254..261db55a 100644
--- a/contribute/modules/ROOT/nav.adoc
+++ b/contribute/modules/ROOT/nav.adoc
@@ -5,3 +5,5 @@
** xref:index.adoc#contrib-desc[an example or a benchmark description?]
** xref:index.adoc#contrib[an example or a benchmark?]
** xref:vtkjs.adoc[{vtkjs} files?]
+
+* xref:data:ROOT:partial$girder/README.adoc[How to contribute data with Girder]
\ No newline at end of file
diff --git a/contribute/modules/girder/images/README.adoc b/contribute/modules/girder/images/README.adoc
new file mode 100644
index 00000000..f39cf0fd
--- /dev/null
+++ b/contribute/modules/girder/images/README.adoc
@@ -0,0 +1 @@
+include::data:ROOT:partial$girder/README.adoc
\ No newline at end of file
From b39dbfe2af2df1e0fb3915d69b1cb013eb9e1b76 Mon Sep 17 00:00:00 2001
From: lberti <lberti21@gmail.com>
Date: Mon, 4 Sep 2023 10:59:57 +0200
Subject: [PATCH 3/9] #187 fix nav.adoc
---
contribute/modules/ROOT/nav.adoc | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/contribute/modules/ROOT/nav.adoc b/contribute/modules/ROOT/nav.adoc
index 261db55a..a6ee676e 100644
--- a/contribute/modules/ROOT/nav.adoc
+++ b/contribute/modules/ROOT/nav.adoc
@@ -6,4 +6,4 @@
** xref:index.adoc#contrib[an example or a benchmark?]
** xref:vtkjs.adoc[{vtkjs} files?]
-* xref:data:ROOT:partial$girder/README.adoc[How to contribute data with Girder]
\ No newline at end of file
+* xref:girder/README.adoc[How to contribute data with Girder]
\ No newline at end of file
From b4ef0cd99692ef99f4bd9a4d06f23830a68e0397 Mon Sep 17 00:00:00 2001
From: lberti <lberti21@gmail.com>
Date: Mon, 4 Sep 2023 11:09:55 +0200
Subject: [PATCH 4/9] #187 up navs
---
contribute/modules/ROOT/nav.adoc | 4 +---
contribute/modules/girder/nav.adoc | 13 +++++++++++++
2 files changed, 14 insertions(+), 3 deletions(-)
create mode 100644 contribute/modules/girder/nav.adoc
diff --git a/contribute/modules/ROOT/nav.adoc b/contribute/modules/ROOT/nav.adoc
index a6ee676e..d129db78 100644
--- a/contribute/modules/ROOT/nav.adoc
+++ b/contribute/modules/ROOT/nav.adoc
@@ -4,6 +4,4 @@
.How to contribute
** xref:index.adoc#contrib-desc[an example or a benchmark description?]
** xref:index.adoc#contrib[an example or a benchmark?]
-** xref:vtkjs.adoc[{vtkjs} files?]
-
-* xref:girder/README.adoc[How to contribute data with Girder]
\ No newline at end of file
+** xref:vtkjs.adoc[{vtkjs} files?]
\ No newline at end of file
diff --git a/contribute/modules/girder/nav.adoc b/contribute/modules/girder/nav.adoc
new file mode 100644
index 00000000..f13f54a2
--- /dev/null
+++ b/contribute/modules/girder/nav.adoc
@@ -0,0 +1,13 @@
+* xref:README.adoc[How to contribute data with Girder]
+ ** xref:README.adoc#_what_is_girder[What is Girder]
+ ** xref:README.adoc#_file_access_options[File access options]
+ *** xref:README.adoc#_web_browser_ui[Web brower UI]
+ *** xref:README.adoc#_python_api[Python API]
+ ** xref:python_scripts.adoc[Python scripts examples]
+ *** xref:python_scripts.adoc#_with_user_and_password[With user and password]
+ **** xref:python_scripts.adoc#_what_not_to_do[What not to do]
+ **** xref:python_scripts.adoc#_interactive_download[Interactive download]
+ **** xref:python_scripts.adoc#_interactive_upload[Interactive upload]
+ *** xref:api_keys.adoc#_using_api_keys[Using API keys]
+ **** xref:api_keys.adoc#_download[Download]
+ **** xref:api_keys.adoc#_upload[Upload]
\ No newline at end of file
From f415d5fc8ea52af0ce1b66a9695a18b9c2e61e30 Mon Sep 17 00:00:00 2001
From: lberti <lberti21@gmail.com>
Date: Mon, 4 Sep 2023 11:18:09 +0200
Subject: [PATCH 5/9] #187 mv Readme and add square bracket in partial
---
contribute/modules/girder/README.adoc | 1 +
contribute/modules/girder/images/README.adoc | 1 -
2 files changed, 1 insertion(+), 1 deletion(-)
create mode 100644 contribute/modules/girder/README.adoc
delete mode 100644 contribute/modules/girder/images/README.adoc
diff --git a/contribute/modules/girder/README.adoc b/contribute/modules/girder/README.adoc
new file mode 100644
index 00000000..7b87f3cd
--- /dev/null
+++ b/contribute/modules/girder/README.adoc
@@ -0,0 +1 @@
+include::data:ROOT:partial$girder/README.adoc[]
\ No newline at end of file
diff --git a/contribute/modules/girder/images/README.adoc b/contribute/modules/girder/images/README.adoc
deleted file mode 100644
index f39cf0fd..00000000
--- a/contribute/modules/girder/images/README.adoc
+++ /dev/null
@@ -1 +0,0 @@
-include::data:ROOT:partial$girder/README.adoc
\ No newline at end of file
From bb01cd3e75d591a1a303e7fbb5cfc2e208f03ba5 Mon Sep 17 00:00:00 2001
From: lberti <lberti21@gmail.com>
Date: Mon, 4 Sep 2023 11:25:28 +0200
Subject: [PATCH 6/9] #187 mv README.adoc into pages
---
contribute/modules/girder/{ => pages}/README.adoc | 0
1 file changed, 0 insertions(+), 0 deletions(-)
rename contribute/modules/girder/{ => pages}/README.adoc (100%)
diff --git a/contribute/modules/girder/README.adoc b/contribute/modules/girder/pages/README.adoc
similarity index 100%
rename from contribute/modules/girder/README.adoc
rename to contribute/modules/girder/pages/README.adoc
From f04740a0ea87396831ac50d6203922039996976a Mon Sep 17 00:00:00 2001
From: lberti <lberti21@gmail.com>
Date: Mon, 4 Sep 2023 11:34:29 +0200
Subject: [PATCH 7/9] #187 add pages referring to partials
---
contribute/modules/girder/pages/api_keys.adoc | 1 +
contribute/modules/girder/pages/python_scripts.adoc | 1 +
2 files changed, 2 insertions(+)
create mode 100644 contribute/modules/girder/pages/api_keys.adoc
create mode 100644 contribute/modules/girder/pages/python_scripts.adoc
diff --git a/contribute/modules/girder/pages/api_keys.adoc b/contribute/modules/girder/pages/api_keys.adoc
new file mode 100644
index 00000000..959e2b4a
--- /dev/null
+++ b/contribute/modules/girder/pages/api_keys.adoc
@@ -0,0 +1 @@
+include::data:ROOT:partial$girder/api_keys.adoc[]
\ No newline at end of file
diff --git a/contribute/modules/girder/pages/python_scripts.adoc b/contribute/modules/girder/pages/python_scripts.adoc
new file mode 100644
index 00000000..f8f86185
--- /dev/null
+++ b/contribute/modules/girder/pages/python_scripts.adoc
@@ -0,0 +1 @@
+include::data:ROOT:partial$girder/python_scripts.adoc[]
\ No newline at end of file
From 13db2c1088b4a23525323d639b42352be4a5f4c8 Mon Sep 17 00:00:00 2001
From: lberti <lberti21@gmail.com>
Date: Tue, 5 Sep 2023 09:24:00 +0200
Subject: [PATCH 8/9] #187 modify readme page
---
contribute/modules/girder/pages/README.adoc | 14 +++++++++++++-
1 file changed, 13 insertions(+), 1 deletion(-)
diff --git a/contribute/modules/girder/pages/README.adoc b/contribute/modules/girder/pages/README.adoc
index 7b87f3cd..323f510b 100644
--- a/contribute/modules/girder/pages/README.adoc
+++ b/contribute/modules/girder/pages/README.adoc
@@ -1 +1,13 @@
-include::data:ROOT:partial$girder/README.adoc[]
\ No newline at end of file
+= Girder
+
+== What is Girder
+
+Girder is a data management platform.
+It can be used to store (large) files such as meshes, simulation results, etc...
+Read more about it in the {feelpp} xref:data:ROOT:data-storage.adoc[data manual] or
+link:http://girder.readthedocs.io/[on the official website].
+
+include::data:ROOT:partial$girder/README.adoc[]
+
+Let's check out some
+xref:contribute:girder:python_scripts.adoc[scripts].
\ No newline at end of file
From 51fdfc20a9931e0b0378b7aceaec0b2c1dc458ef Mon Sep 17 00:00:00 2001
From: lberti <lberti21@gmail.com>
Date: Tue, 5 Sep 2023 10:13:15 +0200
Subject: [PATCH 9/9] #187 remove ref to python scripts
---
contribute/modules/girder/pages/README.adoc | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/contribute/modules/girder/pages/README.adoc b/contribute/modules/girder/pages/README.adoc
index 323f510b..0530e43c 100644
--- a/contribute/modules/girder/pages/README.adoc
+++ b/contribute/modules/girder/pages/README.adoc
@@ -7,7 +7,4 @@ It can be used to store (large) files such as meshes, simulation results, etc...
Read more about it in the {feelpp} xref:data:ROOT:data-storage.adoc[data manual] or
link:http://girder.readthedocs.io/[on the official website].
-include::data:ROOT:partial$girder/README.adoc[]
-
-Let's check out some
-xref:contribute:girder:python_scripts.adoc[scripts].
\ No newline at end of file
+include::data:ROOT:partial$girder/README.adoc[]
\ No newline at end of file