files: add support for uploading multiple files

cap_client/cli/files_cli.py

@@ -28,7 +28,7 @@
 import click
 
 from cap_client.api import FilesAPI
-from cap_client.utils import ColoredGroup, json_dumps, logger, pid_option
+from cap_client.utils import ColoredGroup, json_dumps, logger, pid_option, load_file_names_from_directory
 
 pass_api = click.make_pass_decorator(FilesAPI, ensure=True)
 
@@ -62,31 +62,61 @@ def get(api, pid):
     default=False,
     help="Bypasses prompts..Say YES to everything",
 )
+@click.option(
+    '--dir-files',
+    '-df',
+    type=click.Path(exists=True),
+    help='Upload all the files individually of the specified directory.',
+)
 @click.argument(
-    'file',
+    'path',
+    nargs=-1,
     type=click.Path(exists=True),
 )
 @logger
 @pass_api
-def upload(api, pid, file, output_filename, yes_i_know):
+def upload(api, pid, path, output_filename, yes_i_know, dir_files):
     """Upload a file to your analysis."""
-    if os.path.isdir(file):
-        if yes_i_know or click.confirm(
-                '{} is a directory. Do you want to upload a tarball?'.format(
-                    file)):
-            api.upload_directory(
+    if not path and not dir_files:
+        click.echo("Error: Missing argument 'PATH' or option 'DIR_FILES'.")
+        return
+
+    file_names = list(path) if path else []
+    if dir_files:
+        file_names += load_file_names_from_directory(dir_files)
+        if file_names:
+            if not yes_i_know and not click.confirm(
+                "{} contains {} files. Do you want to upload them individually?".format(
+                    dir_files, len(file_names)
+                )
+            ):
+                click.echo("Use 'PATH' argument for uploading as tarball.")
+                return
+        else:
+            click.echo("No files found in parent directory {}.".format(dir_files))
+
+    for _file in file_names:
+        if os.path.isdir(_file):
+            if yes_i_know or click.confirm(
+                "{} is a directory. Do you want to upload a tarball?".format(_file)
+            ):
+                api.upload_directory(
+                    pid=pid,
+                    filepath=_file,
+                    output_filename=output_filename,
+                )
+                click.echo("Directory {} uploaded successfully.".format(_file))
+            else:
+                click.echo("Use --dir-files for uploading files individually.")
+                click.echo("Aborting upload of {}.".format(_file))
+                continue
+        elif os.stat(_file).st_size != 0:
+            api.upload_file(
                 pid=pid,
-                filepath=file,
+                filepath=_file,
                 output_filename=output_filename,
             )
-    else:
-        api.upload_file(
-            pid=pid,
-            filepath=file,
-            output_filename=output_filename,
-        )
-
-    click.echo("File uploaded successfully.")
+            click.echo("File {} uploaded successfully.".format(_file))
 
 
 @files.command()
@@ -129,7 +159,7 @@ def download(api, pid, filename, output_file, yes_i_know):
 @logger
 @pass_api
 def remove(api, pid, filename):
-    """Removefile from deposit with given pid."""
+    """Remove a file from deposit with given pid."""
     api.remove(pid=pid, filename=filename)
 
     click.echo("File {} removed.".format(filename))

cap_client/utils.py

@@ -95,6 +95,15 @@ def load_num(ctx, param, value):
                 raise BadParameter('Not a valid number.')
 
 
+def load_file_names_from_directory(dir_path):
+    """Return the list of file names inside the directory."""
+    filenames = []
+    for root, d_names, f_names in os.walk(dir_path):
+        for f in f_names:
+            filenames.append(os.path.join(root, f))
+    return filenames
+
+
 class NotRequiredIf(click.Option):
     """
     Mutually exclusive REQUIRED arguments.

docs/chapters/files.md

@@ -1,6 +1,6 @@
 ## Files
 
-The `files` command group allows the user to manage files attached to their analyses, as well as upload local files and attach them to an analysis.
+The `files` command group allows users to manage files attached to their analyses and upload local files and attach them to analysis. The supported commands are the following:
 
 ```
 **[terminal]
@@ -15,18 +15,24 @@ Options:
 Commands:
   download  Download file uploaded with given deposit.
   get       Get list of files attached to analysis with given PID.
-  remove    Removefile from deposit with given pid.
+  remove    Remove a file from deposit with given PID.
   upload    Upload a file to your analysis.
 ```
 
+### Download a file from an analysis
 
-#### Download a file from an analysis
+#### Description
 
-**Description:**
+- Allows the user to download a previously attached file to a specified analysis.
+- The supported options are the following:
 
-Allows the user to download a file, that was previously attached to a specified analysis.
+| Name               | Type   | Desc                                                  |
+| :----------------- | :----- | :---------------------------------------------------- |
+| FILENAME           | TEXT   | The name of the file to be downloaded  [required]     |
+| --pid / -p         | TEXT   | Your analysis PID (Persistent Identifier)  [required] |
+| --output-file / -o | PATH   | Download file as                                      |
 
-**Usage:**
+#### Usage
 
 ```
 **[terminal]
@@ -40,22 +46,18 @@ File saved as FILENAME.
 File saved as dir/NEWFILE.
 ```
 
-**Options:**
+### Retrieve all the files of an analysis
+
+#### Description
+
+- Allows the user to get a list of the files attached to an analysis with a given PID.
+- The supported options are the following:
 
 | Name               | Type   | Desc                                                  |
 | :----------------- | :----- | :---------------------------------------------------- |
-| FILENAME           | TEXT   | The name of the file to be downloaded  [required]     |
 | --pid / -p         | TEXT   | Your analysis PID (Persistent Identifier)  [required] |
-| --output-file / -o | PATH   | Download file as                                      |
 
-
-#### Retrieve all the files of an analysis
-
-**Description:**
-
-Allows the user to get a list of the files, attached to an analysis with a given PID.
-
-**Usage:**
+#### Usage
 
 ```
 **[terminal]
@@ -70,63 +72,66 @@ Allows the user to get a list of the files, attached to an analysis with a given
 ]
 ```
 
-**Options:**
+### Remove a file from an analysis
+
+#### Description
+
+- Allows the user to get a list of the files attached to an analysis with a given PID.
+- The supported options are the following:
 
 | Name               | Type   | Desc                                                  |
 | :----------------- | :----- | :---------------------------------------------------- |
 | --pid / -p         | TEXT   | Your analysis PID (Persistent Identifier)  [required] |
-
-
-#### Remove a file from an analysis
-
-**Description:**
-
-Allows the user to get a list of the files, attached to an analysis with a given PID.
-
-**Usage:**
+#### Usage
 
 ```
 **[terminal]
 **[prompt user@pc]**[path ~]**[delimiter  $ ]**[command cap-client files remove --pid <analysis-pid> FILENAME]
 File FILENAME removed.
 ```
 
-**Options:**
-
-| Name               | Type   | Desc                                                  |
-| :----------------- | :----- | :---------------------------------------------------- |
-| --pid / -p         | TEXT   | Your analysis PID (Persistent Identifier)  [required] |
+### Upload a file to an analysis
 
+#### Description
 
-#### Upload a file to an analysis
+- Allows the user to upload and attach a file to analysis or a whole directory as a tar.gz file.
+- The command enables the user to upload a single file of any type, as well as a whole directory. After a prompt asks the user for confirmation, the directory will be zipped and uploaded as a `.tar.gz` file.
+- To avoid the prompt and enable the usage of cap-client inside a CLI script, the flag `--yes-i-know` can be added.
+- The supported options are the following:
 
-**Description:**
+| Name                   | Type   | Desc                                                         |
+| :--------------------- | :----- | :----------------------------------------------------------- |
+| FILE                   | TEXT   | The name of the file/s to be uploaded [required]             |
+| --pid / -p             | TEXT   | Your analysis PID (Persistent Identifier)  [required]        |
+| --output-filename / -o | PATH   | Upload file as..                                             |
+| --yes-i-know           | FLAG   | Bypasses prompts..Say YES to everything                      |
+| --dir-files / -df      | TEXT   | Upload all the files individually of the specified directory.|
 
-Allows the user to upload and attach a file to an analysis, or a whole directory as a tar.gz file.
+#### Usage
 
-**Usage:**
+```
+**[terminal]
+**[prompt user@pc]**[path ~]**[delimiter  $ ]**[command cap-client files upload --pid <analysis-pid> FILE1]
+File File1 uploaded successfully.
+```
 
 ```
 **[terminal]
-**[prompt user@pc]**[path ~]**[delimiter  $ ]**[command cap-client files upload --pid <analysis-pid> FILE]
-File uploaded successfully.
+**[prompt user@pc]**[path ~]**[delimiter  $ ]**[command cap-client files upload --pid <analysis-pid> FILE1 FILE2]
+File File1 uploaded successfully.
+File File2 uploaded successfully.
 ```
 
 ```
 **[terminal]
 **[prompt user@pc]**[path ~]**[delimiter  $ ]**[command cap-client files upload --pid <analysis-pid> --yes-i-know DIR]
-File uploaded successfully.
+Directory DIR uploaded successfully.
 ```
 
-**Extended Description:**
-
-The command enables the user to upload a single file of any type, as well as a whole directory. After a prompt asks the user for confirmation, the directory will be zipped and uploaded as a `.tar.gz` file. In order to avoid the prompt, and enable the usage of CAP-Client inside a cli script, the flag `--yes-i-know` can be added.
-
-**Options:**
-
-| Name                   | Type   | Desc                                                  |
-| :--------------------- | :----- | :---------------------------------------------------- |
-| FILE                   | TEXT   | The name of the file to be downloaded  [required]     |
-| --pid / -p             | TEXT   | Your analysis PID (Persistent Identifier)  [required] |
-| --output-filename / -o | PATH   | Upload file as                                        |
-| --yes-i-know           | FLAG   | Bypasses prompts..Say YES to everything               |
+```
+**[terminal]
+**[prompt user@pc]**[path ~]**[delimiter  $ ]**[command cap-client files upload --pid <analysis-pid> --dir-files DIR]
+File DIR/File1 uploaded successfully.
+File DIR/File2 uploaded successfully.
+...
+```