ODM-11357: sdk bearer token support (#25)

Author: natalyatodorova

docs/usage/tools/odm-sdk/configuration.md

@@ -8,7 +8,8 @@
 
 ### Configure
 
-1. Obtain a token by logging in to ODM and clicking on the profile link under the username.
+1. Retrieve an Access (Bearer) Token, or obtain an API token by logging into ODM and clicking the profile link under
+    the username.
 
     See an example for Public user below:
 
@@ -25,11 +26,12 @@
 
 3. Type ‘add’ to enter a new user, enter an alias for the user.
 4. Enter the host name, which should be of the format: https://domain_name/.
-5. Then select authentication method by token (1) and input the content of the token you received in step 2:
+5. Then select suitable authentication method (1 or 2) and input the content of the token you received in step 1:
 
     ```shell
     1) by token
-    2) by email and password
+    2) by access token
+    3) by email and password
     Select authentication: 1
     Host: https://domain_name/
     Please specify Genestack API token for "my_user":

docs/usage/tools/odm-sdk/terminal/dictionaries-and-ontologies/loading-new-ontology.md

@@ -7,6 +7,7 @@ This article explains how to load custom dictionaries (ontologies) in ODM.
 ## Requirements
 
 - Configured odm-sdk. See [Configured odm-sdk](../../configuration.md)
+- User should have Bearer Token or API token. See [Getting a Genestack API token](https://odm-user-guide.readthedocs.io/en/latest/doc-odm-user-guide/getting-a-genestack-api-token.html#token-label)
 - A file describing dictionaries, e.g.: [dictionaries.json](loading-new-ontology/dictionaries.json)
 - One or more dictionaries in CSV, JSON, OWL, OBO or TTL formats, hosted at FTP or HTTP web addresses, see [dictionary example](http://purl.obolibrary.org/obo/go.owl)
 
@@ -28,6 +29,12 @@ Multiple dictionaries can be supplied by repeating the section in curly brackets
 
 ## Running the command to import dictionaries
 
+To explore the full list of supported arguments use the following command:
+
+```bash
+odm-update-dictionary -h
+```
+
 Run the following command from your terminal:
 
 ```shell

docs/usage/tools/odm-sdk/terminal/study/curation-script.md

@@ -10,13 +10,19 @@ assist in the matching process.
 ## Requirements
 
 - Configured odm-sdk. See [Configured odm-sdk](../../configuration.md)
-- The user should be a member of Curator group and have API token. See [Getting a Genestack API token](https://odm-user-guide.readthedocs.io/en/latest/doc-odm-user-guide/getting-a-genestack-api-token.html#token-label)
+- The user should be a member of Curator group and have Bearer Token or API token. See [Getting a Genestack API token](https://odm-user-guide.readthedocs.io/en/latest/doc-odm-user-guide/getting-a-genestack-api-token.html#token-label)
 - File with curation rules. How to correctly write such file is described [below](#metadata-mapping-rules).
 
     **Example**: [rules.json](curation-script/rules.json) written for sample metadata [samples.tsv](curation-script/samples.tsv).
 
 ## Curation script usage
 
+To explore the full list of supported arguments use the following command:
+
+```bash
+odm-curate-study -h
+```
+
 Curation can be carried out by running the Python metadata curation script `odm-curate-study`.
 This can be used to perform automated curation of metadata associated with experiments and assays on Genestack.
 The script takes as input the accessions of Genestack study or studies which should contain the samples to be curated.
@@ -34,14 +40,6 @@ Space is used as a separator in case of multiple studies. Example:
 odm-curate-study --rules rules.json GSF000100 GSF000200 -H GENESTACK_ENDPOINT_ADDR
 ```
 
-If the template specified for the curation differs from the template already associated with the study then the study is
-not curated and a warning is given in the logs.
-To explore the full list of supported arguments use the following command:
-
-```bash
-odm-curate-study -h
-```
-
 You can test a curation rule before applying it with the --dry-run parameter. This will connect to the server and report
 matches in the task output log (see later) but not actually change any data.
 

docs/usage/tools/odm-sdk/terminal/study/deleting-study.md

@@ -3,10 +3,16 @@
 ## Requirements
 
 - Configured odm-sdk. See [Configured odm-sdk](../../configuration.md)
-- The user should have the "Manage organisation” permission and have API token. See [Getting a Genestack API token](https://odm-user-guide.readthedocs.io/en/latest/doc-odm-user-guide/getting-a-genestack-api-token.html#token-label)
+- The user should have the "Manage organisation" permission and have Bearer Token or API token. See [Getting a Genestack API token](https://odm-user-guide.readthedocs.io/en/latest/doc-odm-user-guide/getting-a-genestack-api-token.html#token-label)
 
 ## Instructions
 
+To explore the full list of supported arguments use the following command:
+
+```bash
+odm-delete-study -h
+```
+
 !!!warning Warning
 
     1. Only users with the “Manage organisation” permission can delete studies.

docs/usage/tools/odm-sdk/terminal/study/sharing-study.md

@@ -3,10 +3,16 @@
 ## Requirements
 
 - Configured odm-sdk. See [Configured odm-sdk](../../configuration.md)
-- The user should be a member of Curator group and have API token. See [Getting a Genestack API token](https://odm-user-guide.readthedocs.io/en/latest/doc-odm-user-guide/getting-a-genestack-api-token.html#token-label)
+- The user should be a member of Curator group and have Bearer Token or API token. See [Getting a Genestack API token](https://odm-user-guide.readthedocs.io/en/latest/doc-odm-user-guide/getting-a-genestack-api-token.html#token-label)
 
 ## Instructions
 
+To explore the full list of supported arguments use the following command:
+
+```bash
+odm-share-study -h
+```
+
 !!!note "Please note that there are several limitations:"
 
     1. The script should be launched under the study owner user.

docs/usage/tools/odm-sdk/terminal/templates/create-or-update-template.md

@@ -7,12 +7,18 @@ Loaded templates are available to all users on the instance.
 ## Requirements
 
 - Configured odm-sdk. See [Configured odm-sdk](../../configuration.md)
-- The user should have the "Set up templates" permission and API token. See [Getting a Genestack API token](https://odm-user-guide.readthedocs.io/en/latest/doc-odm-user-guide/getting-a-genestack-api-token.html#token-label)
+- The user should have the "Set up templates" permission and Bearer Token or API token. See [Getting a Genestack API token](https://odm-user-guide.readthedocs.io/en/latest/doc-odm-user-guide/getting-a-genestack-api-token.html#token-label)
 - A template settings json file, e.g.: [default_ODM_template_settings.json](default_ODM_template_settings.json)
 - A template json file, e.g.: [Default_ODM_Template.json](Default_ODM_Template.json)
 
 ## Instructions
 
+To explore the full list of supported arguments use the following command:
+
+```bash
+odm-update-template -h
+```
+
 1. Download or create a template json file (see Requirements). Templates are collections of fields with rules determining whether the field is required, which dictionary to use (if any) etc.
 
     ```text

docs/usage/tools/odm-sdk/terminal/templates/delete-template.md

@@ -5,6 +5,7 @@ This article describes how to delete templates in ODM.
 ## Requirements
 
 - Configured odm-sdk. See [Configured odm-sdk](../../configuration.md)
+- The user should have the "Manage organisation" permission and have Bearer Token or API token. See [Getting a Genestack API token](https://odm-user-guide.readthedocs.io/en/latest/doc-odm-user-guide/getting-a-genestack-api-token.html#token-label)
 
 !!!warning
 
@@ -15,6 +16,12 @@ This article describes how to delete templates in ODM.
 
 ## Instructions
 
+To explore the full list of supported arguments use the following command:
+
+```bash
+odm-delete-template -h
+```
+
 1. Before a template deletion all the studies which have this template set should be manually changed: another template which is not going to be deleted should be applied (for example, Default template). Apply template manually via the UI.
 2. Run delete template script and follow its login instructions, replacing the host name with the name of the instance the script will apply to. The script will print “Success” or an error stacktrace in case of an error.