These options are shared by download-all-public-raw-files, download-all-public-category-files, download-file-by-name, and download-files-by-list:

pridepy download-all-public-raw-files \
  -a PXD008644 \
  -o ./downloads/PXD008644 \
  --checksum-check

Continue an interrupted download safely by adding --skip-if-downloaded-already:

pridepy download-all-public-raw-files \
  -a PXD008644 \
  -o ./downloads/PXD008644 \
  --skip-if-downloaded-already \
  --checksum-check

pridepy download-all-public-category-files \
  -a PXD022105 \
  -o ./downloads/PXD022105 \
  -c RAW,SEARCH

-c, --category takes one or more comma-separated categories. Valid values: RAW, PEAK, SEARCH, RESULT, SPECTRUM_LIBRARY, OTHER, FASTA.

pridepy download-file-by-name \
  -a PXD022105 \
  -f checksum.txt \
  -o ./downloads/PXD022105 \
  --checksum-check

-f, --file-name is the file to download.

pridepy download-files-by-list \
  -a PXD001819 \
  -F files.txt \
  -o ./downloads/PXD001819 \
  --checksum-check

files.txt is one filename per line (blank lines and # comments are ignored). Each filename is resolved against the project metadata and downloaded via the same batch + protocol-fallback engine as download-all-public-raw-files. Use -f a.raw,b.raw,c.raw instead of -F for a small inline list (you can combine both).

pridepy download-files-by-url \
  -F urls.txt \
  -o ./downloads/urls

urls.txt is one fully-qualified URL per line. Schemes http, https, and ftp are dispatched to the matching downloader. Use -u, --urls for one or more comma-separated URLs, e.g. --urls https://a.com/x.raw,ftp://b.com/y.raw (URLs containing literal commas must use a manifest file instead).

Command-specific options:

List the files of a private project with your PRIDE credentials:

pridepy list-private-files -a PXD022105 -u YOUR_USER -p YOUR_PASSWORD

Download a private file by passing --username/--password to download-file-by-name:

pridepy download-file-by-name \
  -a PXD022105 \
  -f checksum.txt \
  -o ./downloads/private \
  --username YOUR_USER \
  --password YOUR_PASSWORD

download-px-raw-files resolves the dataset's ProteomeXchange XML and downloads the RAW files it references, regardless of which repository hosts them:

pridepy download-px-raw-files \
  -a PXD039236 \
  -o ./downloads/PXD039236

Datasets that do not have a ProteomeXchange accession — or where you already know the native accession — can be downloaded directly. The standard download commands accept MassIVE, JPOST, and iProX accessions transparently:

# MassIVE (FTPS at massive-ftp.ucsd.edu)
pridepy download-all-public-raw-files \
  -a MSV000082297 \
  -o ./downloads/MSV000082297

# JPOST (PROXI listing + ftp.jpostdb.org)
pridepy download-all-public-raw-files \
  -a JPST002311 \
  -o ./downloads/JPST002311

# iProX (ProteomeXchange XML + anonymous HTTP at download.iprox.org)
pridepy download-all-public-raw-files \
  -a IPX0017413000 \
  -o ./downloads/IPX0017413000

How each repository is enumerated:

• MassIVE walks the FTPS tree at massive-ftp.ucsd.edu (the server requires TLS). If FTP/FTPS is blocked by the network, pridepy automatically falls back to HTTPS: it lists the dataset from the GNPS2 file index (datasetcache.gnps2.org) and downloads each file from the ProteoSAFe endpoint at massive.ucsd.edu (byte-identical to the FTPS copy).
• JPOST lists files through the JSON PROXI endpoint at https://repository.jpostdb.org/proxi/datasets/<JPSTxxxxxx> and downloads from ftp.jpostdb.org over plain FTP. The PROXI listing avoids the source-IP connection limit JPOST enforces on FTP.
• iProX fetches the dataset's ProteomeXchange XML from http://download.iprox.org/<accession>/PX_<accession>.xml, then downloads each referenced file from the same host over anonymous HTTP (with Range support for resume). iProX also exposes Aspera (faspe://) with username/password for very large bulk transfers; pridepy uses the public HTTP endpoint so no iProX credentials are required.

download-all-public-raw-files retrieves the files stored under the dataset's raw/ collection, saving them under output_folder with the dataset's sub-directory layout preserved (so identically-named files in different collections don't overwrite each other). These direct downloads support resume (REST for FTP, byte-Range for HTTP), per-file retries, parallel workers (-w up to 3), and post-transfer size verification against the server-reported size.

You can also request a specific collection from these repositories through the same category interface:

pridepy download-all-public-category-files \
  -a MSV000082297 \
  -o ./downloads/MSV000082297-results \
  -c RESULT

from pridepy.download.client import Client

client = Client()
raw_files = client.get_all_raw_file_list("PXD008644")
print(f"RAW files: {len(raw_files)}")
print(raw_files[0]["fileName"])

For MassIVE / JPOST / iProX accessions, the same method returns the files found under the dataset's raw/ collection:

from pridepy.download.client import Client

client = Client()
for accession in ("MSV000082297", "JPST002311", "IPX0017413000"):
    raw_files = client.get_all_raw_file_list(accession)
    print(f"{accession} raw files: {len(raw_files)}")