major refactoring

.gitignore

@@ -13,3 +13,5 @@ __pycache__
 paper/paper.pdf
 paper/jats/
 venv
+
+.qodo

README.md

@@ -23,7 +23,8 @@ First, clone the repository on your local machine and then install the package u
 ```bash
 $ git clone https://github.com/PRIDE-Archive/pridepy
 $ cd pridepy
-$ pip install .
+$ poetry build
+$ pip install dist/*.whl
 ```
 
 Install with setup.py: 
@@ -34,73 +35,126 @@ $ cd pridepy
 $ poetry build
 $ pip install dist/pridepy-{version}.tar.gz
 ```
+# Usage and Documentation
 
-# Examples
+This Python CLI tool, built using the Click module, 
+already provides detailed usage instructions for each command. To avoid redundancy and potential clutter in this README, you can access the usage instructions directly from the CLI
+Use the below command to view a list of commands available:
 
-Download all the raw files from a dataset(eg: PXD012353).
-Warning: Raw files are generally large in size, so it may take some time to download depending on the number of files and file sizes.
+```bash
+$ pridepy --help
+Usage: pridepy [OPTIONS] COMMAND [ARGS]...
 
-`-p`: in download specifies protocol (ftp default): 
-   - **ftp**: FTP protocol
-   - **aspera**: using the aspera protocol
-   - **globus**: PRIDE globus endpoint (_the data is downloaded through https_)
+Options:
+  --help  Show this message and exit.
+
+Commands:
+  download-all-public-raw-files   Download all public raw files...
+  download-file-by-name           Download a single file from a...
+  get-files-by-filter             get paged files :return:
+  get-files-by-project-accession  get files by project accession...
+  get-private-files               Get private files by project...
+  get-projects                    get paged projects :return:
+  get-projects-by-accession       get projects by accession... 
+  stream-files-metadata           Stream all files metadata in...
+  stream-projects-metadata        Stream all projects metadata...
+
+```
+> [!NOTE]
+> Please make sure you are using Python3, not Python 2.7 version.
+
+## Downloading a project from PRIDE Archive
+
+The main purpose of this tool is to download data from the PRIDE Archive. Here, how to download all the raw files from a dataset(eg: PXD012353).
 
 ```bash
 $ pridepy download-all-public-raw-files -a PXD012353 -o /Users/yourname/Downloads/foldername/ -p aspera
 ```
+- `-a` flag is used to specify the project accession number.
+- `-o` flag is used to specify the output directory. 
+- `-p` flag is used to specify the protocol (**aspera, ftp, globus**)
+
+> [!IMPORTANT]
+> Currently, pridepy supports multiple protocols for downloading including ftp, aspera, globus, s3. ftp, aspera uses those protocols to download the files; the pridepy includes the aspera client. For globus and s3, the tool uses https of both services endpoints. Read the whitepaper to know more about the performance of each protocol.
+
+Additional options: 
+
+- `-skip` flag is used to skip the download of files that already exist in the output directory.
+- `--aspera_maximum_bandwidth` flag is used to specify the maximum bandwidth for the Aspera download. The default value is 100M.
+- `--checksum_check` flag is used to check the checksum of the downloaded files. The default value is False.
+
+## Download single file by name
+
+Users instead of downloading an entire project files may be interested in downloading a single file if they know it by name. Here is how to download a single file by name.
 
-Download single file by name:
 ```bash
 $ pridepy download-file-by-name -a PXD022105 -o /Users/yourname/Downloads/foldername/ -f checksum.txt -p globus
 ```
 
->**NOTE**: Currently we use Globus URLs (when `-p globus` is used) via HTTPS, not the Globus protocol. For more information about Globus, see [Globus documentation](https://www.globus.org/data-transfer).
+Please be aware that the additional parameters are the same as the previous command [Downloading a project from PRIDE Archive](#downloading-a-project-from-pride-archive).
 
-Search projects with keywords and filters
-```bash
-$ pridepy search-projects-by-keywords-and-filters --filter accession==PXD012353
+## Download project files by category
+
+Users may be interested in downloading files by category. Here is how to download files by category. The different categories are available in the PRIDE Archive: 
 
-$ pridepy search-projects-by-keywords-and-filters --keyword PXD012353
+- RAW: Raw data files  
+- PEAK: Peak list files 
+- SEARCH: Search engine output files 
+- OTHER: Other files
+- RESULT: Result files
+- SPECTRUM LIBRARIES: Spectrum libraries
+- FASTA: FASTA files
+
+```bash
+$ pridepy download-files-by-category -a PXD022105 -o /Users/yourname/Downloads/foldername/ -c RAW -p ftp
 ```
 
-Stream metadata of all projects as json and write it to a file
+Please be aware that the additional parameters are the same as the previous command [Downloading a project from PRIDE Archive](#downloading-a-project-from-pride-archive).
+
+>[!IMPORTANT]
+> We also implemented a direct command to download RAW files from a project which is the most common use case.
+
+## Download private files
+
+Users and especially reviewers may be interested in downloading private files. Here is how to download private files. 
+
+First, the user can list the private files of a project:
+
 ```bash
-$ pridepy stream-projects-metadata -o all_pride_projects.json
+$ pridepy list-private-files -a PXD022105 -u yourusername -p yourpassword
 ```
 
-Stream metadata of all files as json and write it to a file. Project accession can be specified as an optional parameter
+This command will list the private files of the project PXD022105. Including the file name, file size, and download link.
+
+Then the user can download the private files:
+
 ```bash
-$ pridepy stream-files-metadata -o all_pride_files.json
-OR
-$ pridepy stream-files-metadata -o PXD005011_files.json -a PXD005011
+$ pridepy download-file-by-name -a PXD022105 -o /Users/yourname/Downloads/foldername/ --username yourusername --password yourpassword -f checksum.txt 
 ```
 
-This Python CLI tool, built using the Click module, 
-already provides detailed usage instructions for each command. To avoid redundancy and potential clutter in this README, you can access the usage instructions directly from the CLI
-Use the below command to view a list of commands available:
+>[!WARNING]
+> To download preivate files, the user should use the same command as downloading a single file by name. The only difference is that the user should provide the username and password. However, protocol in this case is unnecessary as the tool will use the https protocol to download the files. At the moment we only allow this protocol because of the infrastructure of PRIDE private files (read the whitepaper for more information).
+
+## Streamming metadata
+
+One of the great features of PRIDE and pridepy is the ability to stream metadata of all projects and files. This is useful for users who want to analyze the metadata of all projects and files locally.
+
+Stream metadata of all projects as JSON and write it to a file: 
 
 ```bash
-$ pridepy --help
-Usage: pridepy [OPTIONS] COMMAND [ARGS]...
+$ pridepy stream-projects-metadata -o all_pride_projects.json
+```
 
-Options:
-  --help  Show this message and exit.
+Stream all files metadata in a specific project as JSON and write it to a file: 
 
-Commands:
-  download-all-public-raw-files   Download all public raw files...
-  download-file-by-name           Download a single file from a...
-  get-files-by-filter             get paged files :return:
-  get-files-by-project-accession  get files by project accession...
-  get-private-files               Get private files by project...
-  get-projects                    get paged projects :return:
-  get-projects-by-accession       get projects by accession... 
-  stream-files-metadata           Stream all files metadata in...
-  stream-projects-metadata        Stream all projects metadata...
-
+```bash
+$ pridepy stream-files-metadata -o all_pride_files_metadata.json
 ```
-# NOTE
+Stream the files metadata of a specific project as JSON and write it to a file: 
 
-Please make sure you are using Python3, not Python 2.7 version.
+```bash
+$ pridepy stream-files-metadata -o PXD005011_files.json -a PXD005011
+```
 
 # White paper
 

pridepy/authentication/authentication.py

@@ -27,11 +27,7 @@ def get_token(self, username, password):
         url = self.base_url + "/login"
         headers = {"Content-type": "application/json", "Accept": "text/plain"}
         credentials = (
-            '{"Credentials":{"username":"'
-            + username
-            + '", "password":"'
-            + password
-            + '"}}'
+            '{"Credentials":{"username":"' + username + '", "password":"' + password + '"}}'
         )
 
         response = requests.post(url, data=credentials, headers=headers)
@@ -55,8 +51,4 @@ def validate_token(self, token):
 
         response = requests.post(url, headers=headers)
 
-        return (
-            response.ok
-            and response.status_code == 200
-            and response.text == "Token Valid"
-        )
+        return response.ok and response.status_code == 200 and response.text == "Token Valid"