[arvados] created: 2.1.0-2850-ge35720b45
git repository hosting
git at public.arvados.org
Wed Aug 17 21:36:31 UTC 2022
at e35720b456048c4fafcbb267cb8297522284ed61 (commit)
commit e35720b456048c4fafcbb267cb8297522284ed61
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Wed Aug 17 17:36:11 2022 -0400
19180: Document how to do various project operations at the command line
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/doc/_config.yml b/doc/_config.yml
index 148e1a166..f195986a1 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -188,6 +188,7 @@ navbar:
- admin/health-checks.html.textile.liquid
- admin/management-token.html.textile.liquid
- Data Management:
+ - admin/project-management.html.textile.liquid
- admin/collection-versioning.html.textile.liquid
- admin/collection-managed-properties.html.textile.liquid
- admin/restricting-upload-download.html.textile.liquid
diff --git a/doc/admin/group-management.html.textile.liquid b/doc/admin/group-management.html.textile.liquid
index dddfe13ac..764204296 100644
--- a/doc/admin/group-management.html.textile.liquid
+++ b/doc/admin/group-management.html.textile.liquid
@@ -55,7 +55,7 @@ arv link list --filters '[["link_class", "=", "permission"],
["head_uuid", "=", "the_group_uuid"]]' | jq .items[].tail_uuid
</pre>
-h2. Share a project with a group
+h2(#share-project). Share a project with a group
This will give all members of the group @can_manage@ access.
@@ -78,7 +78,7 @@ arv link list --filters '[["link_class", "=", "permission"],
["tail_uuid", "=", "the_group_uuid"]]' | jq .items[].head_uuid
</pre>
-h2. Stop sharing a project with a group
+h2(#stop-sharing-project). Stop sharing a project with a group
This will remove access for members of the group.
diff --git a/doc/admin/project-management.html.textile.liquid b/doc/admin/project-management.html.textile.liquid
new file mode 100644
index 000000000..6b3daa830
--- /dev/null
+++ b/doc/admin/project-management.html.textile.liquid
@@ -0,0 +1,68 @@
+---
+layout: default
+navsection: admin
+title: Project management
+...
+
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+This page describes how to manage projects at the command line.
+
+h2. Create a Project
+
+Projects are entries in the "groups" table with @"group_class": "project"@.
+
+<pre>
+arv group create --group '{"group_class": "project", "owner_uuid": "the_parent_project_uuid", "name": "My new Project"}'
+</pre>
+
+h2. Move a collection into a Project
+
+Move a collection by assigning it to a new owner.
+
+<pre>
+arv collection update --uuid the_collection_uuid --collection '{"owner_uuid": "the_project_uuid"}'
+</pre>
+
+h2. Get Project contents
+
+Lists everything owned by the project.
+
+<pre>
+arv group contents --uuid the_project_uuid
+</pre>
+
+h2. Move a Project
+
+Move a project by assigning it to a new owner.
+
+<pre>
+arv group create --uuid the_project_uuid --group '{"owner_uuid": "the_new_parent_project_uuid"}'
+</pre>
+
+h2. Put a Project in the trash
+
+Trashing a project recursively includes all of its contents (collections, subprojects, workflows, etc). This sets @trash_at@ to now and @delete_at@ to the time period @Collection.DefaultTrashLifetime@ in the future. When @delete_at@ is reached, the project and all of its contents are deleted permanently.
+
+<pre>
+arv group delete --uuid the_project_uuid
+</pre>
+
+h2. Recover a Project from the trash
+
+
+<pre>
+arv group untrash --uuid the_project_uuid
+</pre>
+
+h2. Share a project with a user group
+
+See "Share a project with a group":group-management.html#share-project
+
+h2. Stop sharing a project with a user group
+
+See "Stop sharing a project with a group":group-management.html#stop-sharing-project
diff --git a/doc/sdk/python/cookbook.html.textile.liquid b/doc/sdk/python/cookbook.html.textile.liquid
index f3186ebbb..53330dcbe 100644
--- a/doc/sdk/python/cookbook.html.textile.liquid
+++ b/doc/sdk/python/cookbook.html.textile.liquid
@@ -10,14 +10,36 @@ Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-h2. Cancel a container request
+# "Cancel a container request":#cancel-a-container-request
+# "Cancel all container requests":#cancel-all-container-requests
+# "List completed container requests":#list-completed-container-requests
+# "Get input of a CWL workflow":#get-input-of-a-cwl-workflow
+# "Get output of a CWL workflow":#get-output-of-a-cwl-workflow
+# "Get state of a CWL workflow":#get-state-of-a-cwl-workflow
+# "List input of child requests":#list-input-of-child-requests
+# "List output of child requests":#list-output-of-child-requests
+# "List failed child requests":#list-failed-child-requests
+# "Get log of a child request":#get-log-of-a-child-request
+# "Create a collection sharing link":#sharing-link
+# "Combine two or more collections":#combine-two-or-more-collections
+# "Upload a file into a new collection":#upload-a-file-into-a-new-collection
+# "Download a file from a collection":#download-a-file-from-a-collection
+# "Copy files from a collection to a new collection":#copy-files-from-a-collection-to-a-new-collection
+# "Copy files from a collection to another collection":#copy-files-from-a-collection-to-another-collection
+# "Delete a file from an existing collection":#delete-a-file-from-an-existing-collection
+# "Listing records with paging":#listing-records-with-paging
+# "Querying the vocabulary definition":#querying-the-vocabulary-definition
+# "Translating between vocabulary identifiers and labels":#translating-between-vocabulary-identifiers-and-labels
+# "Create a Project":#create-a-project
+
+h2(#cancel-a-container-request). Cancel a container request
{% codeblock as python %}
import arvados
arvados.api().container_requests().update(uuid=container_request_uuid, body={"priority": 0}).execute()
{% endcodeblock %}
-h2. Cancel all container requests
+h2(#cancel-all-container-requests). Cancel all container requests
{% codeblock as python %}
import arvados
@@ -27,7 +49,7 @@ for container_request in result:
api.container_requests().update(uuid=container_request["uuid"], body={"priority": 0}).execute()
{% endcodeblock %}
-h2. List completed container requests
+h2(#list-completed-container-requests). List completed container requests
{% codeblock as python %}
import arvados
@@ -42,7 +64,7 @@ for container_request in result:
print("%s, %s, %s" % (container_request["uuid"], container_request["name"], "Success" if container["exit_code"] == 0 else "Failed"))
{% endcodeblock %}
-h2. Get input of a CWL workflow
+h2(#get-input-of-a-cwl-workflow). Get input of a CWL workflow
{% codeblock as python %}
import arvados
@@ -52,7 +74,7 @@ container_request = api.container_requests().get(uuid=container_request_uuid).ex
print(container_request["mounts"]["/var/lib/cwl/cwl.input.json"])
{% endcodeblock %}
-h2. Get output of a CWL workflow
+h2(#get-output-of-a-cwl-workflow). Get output of a CWL workflow
{% codeblock as python %}
import arvados
@@ -64,7 +86,7 @@ collection = arvados.collection.CollectionReader(container_request["output_uuid"
print(collection.open("cwl.output.json").read())
{% endcodeblock %}
-h2. Get state of a CWL workflow
+h2(#get-state-of-a-cwl-workflow). Get state of a CWL workflow
{% codeblock as python %}
import arvados
@@ -93,7 +115,7 @@ container_request_uuid = 'zzzzz-xvhdp-zzzzzzzzzzzzzzz'
print(get_cr_state(container_request_uuid))
{% endcodeblock %}
-h2. List input of child requests
+h2(#list-input-of-child-requests). List input of child requests
{% codeblock as python %}
import arvados
@@ -112,7 +134,7 @@ for c in child_requests["items"]:
print(" %s" % m["portable_data_hash"])
{% endcodeblock %}
-h2. List output of child requests
+h2(#list-output-of-child-requests). List output of child requests
{% codeblock as python %}
import arvados
@@ -131,7 +153,7 @@ for c in child_requests["items"]:
print("%s -> %s" % (c["name"], uuid_to_pdh[c["output_uuid"]]))
{% endcodeblock %}
-h2. List failed child requests
+h2(#list-failed-child-requests). List failed child requests
{% codeblock as python %}
import arvados
@@ -149,7 +171,7 @@ for c in cancelled_child_containers["items"]:
print("%s (%s)" % (child_containers[c["uuid"]]["name"], child_containers[c["uuid"]]["uuid"]))
{% endcodeblock %}
-h2. Get log of a child request
+h2(#get-log-of-a-child-request). Get log of a child request
{% codeblock as python %}
import arvados
@@ -177,7 +199,7 @@ token = api.api_client_authorizations().create(body={"api_client_authorization":
print("%s/c=%s/t=%s/_/" % (download, collection_uuid, token["api_token"]))
{% endcodeblock %}
-h2. Combine two or more collections
+h2(#combine-two-or-more-collections). Combine two or more collections
Note, if two collections have files of the same name, the contents will be concatenated in the resulting manifest.
@@ -185,7 +207,7 @@ Note, if two collections have files of the same name, the contents will be conca
import arvados
import arvados.collection
api = arvados.api()
-project_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
+project_uuid = "zzzzz-j7d0g-zzzzzzzzzzzzzzz"
collection_uuids = ["zzzzz-4zz18-aaaaaaaaaaaaaaa", "zzzzz-4zz18-bbbbbbbbbbbbbbb"]
combined_manifest = ""
for u in collection_uuids:
@@ -195,7 +217,7 @@ newcol = arvados.collection.Collection(combined_manifest)
newcol.save_new(name="My combined collection", owner_uuid=project_uuid)
{% endcodeblock %}
-h2. Upload a file into a new collection
+h2(#upload-a-file-into-a-new-collection). Upload a file into a new collection
{% codeblock as python %}
import arvados
@@ -217,7 +239,7 @@ c.save_new(name=collection_name, owner_uuid=project_uuid)
print("Saved %s to %s" % (collection_name, c.manifest_locator()))
{% endcodeblock %}
-h2. Download a file from a collection
+h2(#download-a-file-from-a-collection). Download a file from a collection
{% codeblock as python %}
import arvados
@@ -237,7 +259,7 @@ with c.open(filename, "rb") as reader:
print("Finished downloading %s" % filename)
{% endcodeblock %}
-h2. Copy files from a collection to a new collection
+h2(#copy-files-from-a-collection-to-a-new-collection). Copy files from a collection to a new collection
{% codeblock as python %}
import arvados.collection
@@ -258,7 +280,7 @@ target.save_new(name=target_name, owner_uuid=target_project)
print("Created collection %s" % target.manifest_locator())
{% endcodeblock %}
-h2. Copy files from a collection to another collection
+h2(#copy-files-from-a-collection-to-another-collection). Copy files from a collection to another collection
{% codeblock as python %}
import arvados.collection
@@ -277,7 +299,7 @@ for f in files_to_copy:
target.save()
{% endcodeblock %}
-h2. Delete a file from an existing collection
+h2(#delete-a-file-from-an-existing-collection). Delete a file from an existing collection
{% codeblock as python %}
import arvados
@@ -287,7 +309,7 @@ c.remove("file2.txt")
c.save()
{% endcodeblock %}
-h2. Listing records with paging
+h2(#listing-records-with-paging). Listing records with paging
Use the @arvados.util.keyset_list_all@ helper method to iterate over all the records matching an optional filter. This method handles paging internally and returns results incrementally using a Python iterator. The first parameter of the method takes a @list@ method of an Arvados resource (@collections@, @container_requests@, etc).
@@ -299,7 +321,7 @@ for c in arvados.util.keyset_list_all(api.collections().list, filters=[["name",
print("got collection " + c["uuid"])
{% endcodeblock %}
-h2. Querying the vocabulary definition
+h2(#querying-the-vocabulary-definition). Querying the vocabulary definition
The Python SDK provides facilities to interact with the "active metadata vocabulary":{{ site.baseurl }}/admin/metadata-vocabulary.html in the system. The developer can do key and value lookups in a case-insensitive manner:
@@ -319,7 +341,7 @@ voc['size']['Small'].identifier
# Example output: 'IDVALSIZES2'
{% endcodeblock %}
-h2. Translating between vocabulary identifiers and labels
+h2(#translating-between-vocabulary-identifiers-and-labels). Translating between vocabulary identifiers and labels
Client software might need to present properties to the user in a human-readable form or take input from the user without requiring them to remember identifiers. For these cases, there're a couple of conversion methods that take a dictionary as input like this:
@@ -331,4 +353,22 @@ voc.convert_to_labels({'IDTAGIMPORTANCES': 'IDVALIMPORTANCES1'})
# Example output: {'Importance': 'Critical'}
voc.convert_to_identifiers({'creature': 'elephant'})
# Example output: {'IDTAGANIMALS': 'IDVALANIMALS3'}
-{% endcodeblock %}
\ No newline at end of file
+{% endcodeblock %}
+
+h2(#create-a-project). Create a Project
+
+{% codeblock as python %}
+import arvados
+
+parent_project_uuid = "zzzzz-j7d0g-zzzzzzzzzzzzzzz"
+project_name = "My project"
+
+g = arvados.api().groups().create(body={
+ "group": {
+ "group_class": "project",
+ "owner_uuid": parent_project_uuid,
+ "name": project_name,
+ }}).execute()
+
+print("New project uuid is", g["uuid"])
+{% endcodeblock %}
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list