Documentation update

README.md

@@ -16,37 +16,67 @@ The program to perform the following actions:
 * cancel: cancel a private object and its dependent objects (**under development**)
 * release: release a private object immediately to the public (**under development**)
 
-## The tool dependencies in LINUX
+## Tool dependencies
 
 * curl
-* Genshi
-* subprocess
-* shlex
-* json
-* argparse
-* hashlib
-* ftplib
-* uuid
-* datetime
-* lxml
-* pandas
+* python 2.7+ including following packages:
+  * Genshi
+  * lxml
+  * pandas
 
 ## Installation
 
 ```
 pip install ena-upload-cli
 ```
 
+> Be aware that Windows can give problems with the `curl` commands executed by the script. Check that curl is available in your PATH.
+
 ## Usage
+
 ```
-ENA_upload [-h] --action {add,modify} [--study STUDY]
-                  --center CENTER_NAME --webin_id
-                  WEBIN_ID --password PASSWORD
+usage: ENA_upload [-h] --action {add,modify,cancel,release} [--study STUDY]
                   [--sample SAMPLE] [--experiment EXPERIMENT] [--run RUN]
-                  [--data [FILE [FILE ...]]] 
+                  [--data [FILE [FILE ...]]] --center CENTER_NAME --webin_id
+                  WEBIN_ID (--password PASSWORD | --secret SECRET) [-d]
+
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --action {add,modify,cancel,release}
+                         add: add an object to the archive
+                         modify: modify an object in the 
+  --study STUDY         table of STUDY object
+  --sample SAMPLE       table of SAMPLE object
+  --experiment EXPERIMENT
+                        table of EXPERIMENT object
+  --run RUN             table of RUN object
+  --data [FILE [FILE ...]]
+                        data for submission
+  --center CENTER_NAME  specific to your Webin account
+  --webin_id WEBIN_ID   the usermane of your Webin account
+  --password PASSWORD   the password of your Webin account
+  --secret SECRET       .secret file containing the password  of your Webin account
+  -d, --dev             Flag to use the dev/sandbox endpoint of ENA.
 ```
 
-Mandatory arguments: --action, --center, --webin_id, --password.
+Mandatory arguments: --action, --center, --webin_id, --password or --secret.
+
+### ENA Webin
+
+A Webin can be made [here](https://www.ebi.ac.uk/ena/submit/sra/#home) if you don't have one already. The *--webin_id* parameter makes use of the full username looking like: `Webin-XXXXX`. Visit [Webin online](https://www.ebi.ac.uk/ena/submit/webin) to check on your submissions or [dev Webin](https://wwwdev.ebi.ac.uk/ena/submit/webin) to check on test submissions.
+
+### The password parameter
+
+To avoid exposing you password through the terminal history, it is recommended to make use of a `.secret` file, containing your password on the first line. Use instead of the *--password* parameter in the ena-upload-cli tool the *--secret* parameter to specify the location of the .secret file.
+
+
+### dev instance
+
+
+By default the submission will be done using following url to ENA: https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA
+
+Use the *--dev* flag if you want to do a test submission using the tool by the sandbox dev instance of ENA: https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA. A TEST submission will be discarded within 24 hours
 
 ## Test the tool
 
@@ -69,8 +99,12 @@ outputs:
 
 test command: **add metadata and sequence data**
 
- `python ena_upload.py --action add --center 'your_center_name' --webin_id your_id --password your_password --study example_tables/ENA_template_studies.tsv --sample example_tables/ENA_template_samples.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz`
+ `ena_upload --action add --center 'your_center_name' --webin_id your_id --password your_password --study example_tables/ENA_template_studies.tsv --sample example_tables/ENA_template_samples.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz --dev`
 
  test command: **modify a metadata**
 
- `python ena_upload.py --action modify --center 'your_center_name' --webin_id your_id --password your_password --study example_tables/ENA_template_studies-2020-05-01T14\:21.tsv`
+ `ena_upload --action modify --center 'your_center_name' --webin_id your_id --password your_password --study example_tables/ENA_template_studies-2020-05-01T1421.tsv --dev`
+
+test command **.secret file**
+
+`ena-upload-cli --action add --center "VIB - UGENT" --webin_id Webin-56059 --study example_tables/ENA_template_studies.tsv --sample example_tables/ENA_template_samples.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz --dev --secret .secret`