abcupload 1.0.0__py3-none-any.whl

abcupload/__init__.py

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+"""ABCOMICS Genomic Data Upload Tool."""
+
+__version__ = "1.0.0"
+__author__  = "Khadim Gueye"

abcupload/__main__.py

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+from abcupload.cli import main
+
+main()

abcupload/cli.py

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+# Author: Khadim Gueye
+# ABCOMICS Genomic Data Upload Tool
+# Handles: URL signing (POST) + file upload (PUT), progress, duplicate detection, test mode.
+
+from __future__ import annotations
+
+import argparse
+import glob
+import os
+import re
+import sys
+from pathlib import Path
+from typing import Generator, Optional
+
+import requests
+from rich import box
+from rich.console import Console
+from rich.panel import Panel
+from rich.progress import (
+    BarColumn,
+    DownloadColumn,
+    Progress,
+    TextColumn,
+    TimeRemainingColumn,
+    TransferSpeedColumn,
+)
+from rich.table import Table
+from rich.text import Text
+
+from abcupload import __version__
+
+PROD_API = "https://abcomics-upload-492456311172.europe-west1.run.app"
+TEST_API = "https://abcomics-test-upload-492456311172.europe-west1.run.app"
+
+ALLOWED_SUFFIXES = {
+    ".fastq", ".fq", ".fastq.gz", ".fq.gz", ".fastq.bz2", ".fq.bz2",
+    ".fasta", ".fa", ".fna", ".faa", ".ffn", ".frn",
+    ".fasta.gz", ".fa.gz", ".fna.gz", ".faa.gz",
+    ".bam", ".sam", ".cram",
+    ".bai", ".crai", ".csi", ".tbi",
+    ".vcf", ".vcf.gz", ".bcf", ".bcf.gz",
+    ".gff", ".gff3", ".gtf", ".bed",
+    ".gff.gz", ".gff3.gz", ".gtf.gz", ".bed.gz",
+    ".csv", ".tsv",
+}
+
+console     = Console()
+err_console = Console(stderr=True)
+
+
+# ── Helpers ───────────────────────────────────────────────────────────────────
+
+def _has_bio_ext(name: str) -> bool:
+    lower = name.lower()
+    for ext in sorted(ALLOWED_SUFFIXES, key=len, reverse=True):
+        if lower.endswith(ext):
+            return True
+    return False
+
+
+def _human_size(n: int) -> str:
+    for unit in ("B", "KB", "MB", "GB", "TB"):
+        if n < 1024 or unit == "TB":
+            return f"{n:.1f} {unit}" if unit != "B" else f"{n} B"
+        n /= 1024  # type: ignore[assignment]
+    return str(n)
+
+
+# ── File resolution ───────────────────────────────────────────────────────────
+
+def resolve_files(data_arg: str) -> list[Path]:
+    """Return a list of Paths from a directory, glob, or comma-separated list."""
+    path = Path(data_arg)
+
+    if path.is_dir():
+        files = sorted(f for f in path.iterdir() if f.is_file() and _has_bio_ext(f.name))
+        if not files:
+            console.print(f"  [yellow]![/] No bioinformatics files found in: [bold]{data_arg}[/]")
+        return files
+
+    results: list[Path] = []
+    for part in data_arg.split(","):
+        part = part.strip()
+        if not part:
+            continue
+        matches = sorted(glob.glob(part))
+        if matches:
+            results.extend(Path(m) for m in matches if Path(m).is_file())
+        elif Path(part).is_file():
+            results.append(Path(part))
+        else:
+            console.print(f"  [yellow]![/] No match: [bold]{part}[/]")
+
+    return results
+
+
+# ── API call — get signed URL ─────────────────────────────────────────────────
+
+def get_upload_url(
+    api_url: str,
+    api_key: str,
+    username: str,
+    project_id: str,
+    filename: str,
+    overwrite: bool = False,
+) -> tuple[str, dict]:
+    """POST to the API to get a GCS signed upload URL.
+
+    Returns (status, data) where status is 'ok', 'exists', or 'error'.
+    """
+    payload: dict = {"username": username, "project_id": project_id, "filename": filename}
+    if overwrite:
+        payload["overwrite"] = True
+
+    try:
+        resp = requests.post(
+            f"{api_url}/generate-upload-url",
+            json=payload,
+            headers={"X-API-Key": api_key},
+            timeout=30,
+        )
+    except requests.exceptions.ConnectionError:
+        return "error", {"error": "Connection failed. Check your internet connection."}
+    except requests.exceptions.Timeout:
+        return "error", {"error": "Request timed out (30 s)."}
+    except requests.exceptions.RequestException as exc:
+        return "error", {"error": str(exc)}
+
+    try:
+        data = resp.json()
+    except ValueError:
+        data = {"error": f"Non-JSON response (HTTP {resp.status_code})"}
+
+    if resp.status_code == 409:
+        return "exists", data
+    if resp.status_code != 200:
+        return "error", data
+    return "ok", data
+
+
+# ── File upload — PUT to GCS ──────────────────────────────────────────────────
+
+def upload_to_gcs(file_path: Path, upload_url: str) -> tuple[bool, str]:
+    """Upload a file to GCS via a signed PUT URL with a rich progress bar."""
+    file_size = file_path.stat().st_size
+
+    with Progress(
+        TextColumn("     "),
+        BarColumn(bar_width=34),
+        "[progress.percentage]{task.percentage:>3.0f}%",
+        DownloadColumn(),
+        TransferSpeedColumn(),
+        TimeRemainingColumn(),
+        console=console,
+        transient=True,
+    ) as progress:
+        task = progress.add_task("upload", total=file_size)
+
+        def _reader() -> Generator[bytes, None, None]:
+            with open(file_path, "rb") as fh:
+                while True:
+                    chunk = fh.read(65536)
+                    if not chunk:
+                        break
+                    progress.advance(task, len(chunk))
+                    yield chunk
+
+        try:
+            resp = requests.put(
+                upload_url,
+                data=_reader(),
+                headers={
+                    "Content-Type":   "application/octet-stream",
+                    "Content-Length": str(file_size),
+                },
+                timeout=None,
+            )
+        except requests.exceptions.RequestException as exc:
+            return False, str(exc)
+
+    if resp.status_code == 200:
+        return True, ""
+    return False, f"HTTP {resp.status_code}"
+
+
+# ── Per-file orchestration ────────────────────────────────────────────────────
+
+def upload_one(
+    file_path: Path,
+    username: str,
+    project_id: str,
+    api_key: str,
+    test_mode: bool,
+    overwrite: bool,
+    index: int,
+    total: int,
+) -> str:
+    """Upload a single file. Returns 'ok', 'fail', or 'skip'."""
+    api_url  = TEST_API if test_mode else PROD_API
+    filename = file_path.name
+    size_str = _human_size(file_path.stat().st_size)
+
+    console.print(f"  [{index}/{total}] [bold]{filename}[/]  [dim]{size_str}[/]")
+
+    status, data = get_upload_url(api_url, api_key, username, project_id, filename, overwrite)
+
+    if status == "exists":
+        console.print("     [yellow]![/] File already exists in your project directory.")
+        try:
+            answer = input("     Overwrite? [y/N] ").strip().lower()
+        except (EOFError, KeyboardInterrupt):
+            answer = "n"
+        if answer == "y":
+            status, data = get_upload_url(
+                api_url, api_key, username, project_id, filename, overwrite=True
+            )
+        else:
+            console.print("     [dim]−[/] Skipped.")
+            return "skip"
+
+    if status != "ok":
+        err_msg = data.get("error", "Unknown error")
+        console.print(f"     [red]✗[/] {err_msg}")
+        return "fail"
+
+    upload_url = data.get("upload_url", "")
+    if not upload_url:
+        console.print("     [red]✗[/] Could not retrieve upload URL.")
+        return "fail"
+
+    ok, err_msg = upload_to_gcs(file_path, upload_url)
+
+    if ok:
+        console.print("     [green]✓[/] Uploaded successfully")
+        if test_mode and "auto_delete" in data:
+            console.print(f"     [dim]{data['auto_delete']}[/]")
+        return "ok"
+
+    console.print(f"     [red]✗[/] Upload failed: {err_msg}")
+    return "fail"
+
+
+# ── Display helpers ───────────────────────────────────────────────────────────
+
+def print_banner(username: str, project_id: str, test_mode: bool) -> None:
+    mode = (
+        Text("TEST  ·  files deleted after 24 h", style="bold yellow")
+        if test_mode
+        else Text("Production", style="bold green")
+    )
+    grid = Table.grid(padding=(0, 2))
+    grid.add_column(style="dim")
+    grid.add_column()
+    grid.add_row("User",    f"[bold]{username}[/]")
+    grid.add_row("Project", f"[bold]{project_id}[/]")
+    grid.add_row("Mode",    mode)
+    console.print(Panel(
+        grid,
+        title=f"[bold blue]ABCOMICS[/] Genomic Upload  [dim]v{__version__}[/]",
+        border_style="blue",
+        padding=(0, 1),
+    ))
+    console.print()
+
+
+def print_summary(results: dict) -> None:
+    total = sum(results.values())
+    tbl = Table(box=box.SIMPLE, show_header=False, padding=(0, 1))
+    tbl.add_column(style="dim", width=10)
+    tbl.add_column()
+    tbl.add_row("Total", f"{total} file(s)")
+    if results["ok"]:
+        tbl.add_row("Uploaded", f"[green]{results['ok']}[/]")
+    if results["fail"]:
+        tbl.add_row("Failed",   f"[red]{results['fail']}[/]")
+    if results["skip"]:
+        tbl.add_row("Skipped",  f"[dim]{results['skip']}[/]")
+    console.print()
+    console.rule(style="dim")
+    console.print(tbl)
+    console.rule(style="dim")
+    console.print()
+
+    if results["fail"]:
+        console.print("[red]Some files failed to upload. Check errors above.[/]\n")
+    elif results["ok"]:
+        console.print("[green]All files uploaded successfully.[/]\n")
+    else:
+        console.print("[yellow]No files were uploaded.[/]\n")
+
+
+# ── Argument parser ───────────────────────────────────────────────────────────
+
+def build_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(
+        prog="abcupload",
+        description="ABCOMICS Genomic Data Upload Tool",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""\
+examples:
+  abcupload -u abc-000001 -p PRJAB00001 -d sample_R1.fastq.gz
+  abcupload -u abc-000001 -p PRJAB00001 -d '*.fastq.gz'
+  abcupload -u abc-000001 -p PRJAB00001 -d file1.bam,file2.bam -o
+  abcupload -u abc-000001 -p PRJAB00001 -d /path/to/data/ -t
+
+environment variable:
+  ABCOMICS_API_KEY   your API key (alternative to -k)
+  export ABCOMICS_API_KEY=your_key_here
+""",
+        add_help=False,
+    )
+
+    req = parser.add_argument_group("required")
+    req.add_argument(
+        "-u", dest="username", metavar="USERNAME", required=True,
+        help="ABCOMICS username",
+    )
+    req.add_argument(
+        "-p", dest="project_id", metavar="PROJECT_ID", required=True,
+        help="project ID  (e.g. PRJAB00001)",
+    )
+    req.add_argument(
+        "-d", dest="data", metavar="DATA", required=True,
+        help="file(s): single file | comma-list | glob pattern | directory",
+    )
+
+    opt = parser.add_argument_group("options")
+    opt.add_argument(
+        "-k", dest="api_key", metavar="API_KEY",
+        default=os.environ.get("ABCOMICS_API_KEY", ""),
+        help="API key  (or: export ABCOMICS_API_KEY=...)",
+    )
+    opt.add_argument("-t", dest="test",      action="store_true", help="test mode — files deleted after 24 h")
+    opt.add_argument("-o", dest="overwrite", action="store_true", help="overwrite existing files without asking")
+    opt.add_argument("-h", "--help",    action="help",    help="show this help and exit")
+    opt.add_argument("-V", "--version", action="version", version=f"%(prog)s {__version__}")
+
+    return parser
+
+
+# ── Entry point ───────────────────────────────────────────────────────────────
+
+def main() -> None:
+    parser = build_parser()
+    args   = parser.parse_args()
+
+    if not args.api_key:
+        err_console.print(
+            "[red]Error:[/] API key required.\n"
+            "  Use [bold]-k KEY[/] or set [bold]ABCOMICS_API_KEY[/] environment variable.\n"
+            "  Contact [bold]contact@abcomics.org[/] if you have not received your key."
+        )
+        sys.exit(1)
+
+    if not re.match(r"^PRJAB\d+$", args.project_id):
+        err_console.print(
+            "[red]Error:[/] PROJECT_ID must start with [bold]PRJAB[/] followed by digits "
+            "(e.g. [bold]PRJAB00001[/])."
+        )
+        sys.exit(1)
+
+    files = resolve_files(args.data)
+    if not files:
+        err_console.print(f"[red]Error:[/] No valid files found in: [bold]{args.data}[/]")
+        sys.exit(1)
+
+    print_banner(args.username, args.project_id, args.test)
+    console.print(f"  Found [bold]{len(files)}[/] file(s) to upload:\n")
+
+    results = {"ok": 0, "fail": 0, "skip": 0}
+
+    for i, fp in enumerate(files, 1):
+        outcome = upload_one(
+            file_path  = fp,
+            username   = args.username,
+            project_id = args.project_id,
+            api_key    = args.api_key,
+            test_mode  = args.test,
+            overwrite  = args.overwrite,
+            index      = i,
+            total      = len(files),
+        )
+        results[outcome] += 1
+        console.print()
+
+    print_summary(results)
+    sys.exit(1 if results["fail"] > 0 else 0)

abcupload-1.0.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: abcupload
+Version: 1.0.0
+Summary: ABCOMICS Genomic Data Upload Tool — upload sequencing files to ABCOMICS
+Author-email: Khadim Gueye <bioinformatics.acegid@run.edu.ng>
+License: MIT
+Project-URL: Homepage, https://abcomics.org
+Project-URL: Repository, https://github.com/african-bioinformatics-center/ABCOMICS_site
+Project-URL: Issues, https://github.com/african-bioinformatics-center/ABCOMICS_site/issues
+Keywords: bioinformatics,genomics,upload,ABCOMICS,fastq,bam,vcf
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Utilities
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests>=2.28
+Requires-Dist: rich>=13.0
+Dynamic: license-file
+
+# abcupload
+
+**ABCOMICS Genomic Data Upload Tool**
+
+A command-line tool to upload sequencing and genomic data files to the
+[ABCOMICS](https://abcomics.org) platform. It handles the full two-step
+upload process automatically: requesting a signed URL from the API, then
+streaming the file directly to secure cloud storage with a live progress bar.
+
+---
+
+## Installation
+
+```bash
+pip install abcupload
+```
+
+Requires Python 3.8 or later. Dependencies (`requests`, `rich`) are installed
+automatically.
+
+---
+
+## Quick start
+
+```bash
+# Set your API key once (contact contact@abcomics.org to receive it)
+export ABCOMICS_API_KEY=your_key_here
+
+# Upload a single file
+abcupload -u abc-000001 -p PRJAB00001 -d sample_R1.fastq.gz
+
+# Upload all FASTQ files in the current directory
+abcupload -u abc-000001 -p PRJAB00001 -d '*.fastq.gz'
+
+# Upload an entire directory (scans for all accepted formats)
+abcupload -u abc-000001 -p PRJAB00001 -d /data/project/
+
+# Upload multiple specific files
+abcupload -u abc-000001 -p PRJAB00001 -d file1.bam,file2.bam
+
+# Test mode — files are deleted after 24 hours
+abcupload -u abc-000001 -p PRJAB00001 -d '*.fastq.gz' -t
+```
+
+---
+
+## Usage
+
+```
+abcupload -u USERNAME -p PROJECT_ID -d DATA [OPTIONS]
+
+required:
+  -u USERNAME     ABCOMICS username          (e.g. abc-000001)
+  -p PROJECT_ID   Project ID                 (e.g. PRJAB00001)
+  -d DATA         What to upload:
+                    single file  :  -d sample.fastq.gz
+                    comma list   :  -d file1.fastq.gz,file2.bam
+                    glob pattern :  -d '*.fastq.gz'
+                    directory    :  -d /path/to/data/
+
+options:
+  -k API_KEY      API key  (alternative to ABCOMICS_API_KEY env var)
+  -t              Test mode — files deleted after 24 h
+  -o              Overwrite existing files without asking
+  -h, --help      Show this help and exit
+  -V, --version   Show version and exit
+```
+
+---
+
+## Environment variable
+
+Set your API key as an environment variable so you do not have to pass `-k`
+on every command:
+
+```bash
+# Add to ~/.bashrc or ~/.zshrc for persistence
+export ABCOMICS_API_KEY=your_key_here
+```
+
+---
+
+## Accepted file formats
+
+| Format  | Extensions |
+|---------|------------|
+| FASTQ   | `.fastq`, `.fq`, `.fastq.gz`, `.fq.gz`, `.fastq.bz2`, `.fq.bz2` |
+| FASTA   | `.fasta`, `.fa`, `.fna`, `.faa`, `.ffn`, `.frn`, `.fasta.gz`, `.fa.gz`, `.fna.gz`, `.faa.gz` |
+| BAM / SAM / CRAM | `.bam`, `.sam`, `.cram` |
+| Index files | `.bai`, `.crai`, `.csi`, `.tbi` |
+| VCF / BCF | `.vcf`, `.vcf.gz`, `.bcf`, `.bcf.gz` |
+| Annotation | `.gff`, `.gff3`, `.gtf`, `.bed` (and `.gz` variants) |
+| Tabular | `.csv`, `.tsv` |
+
+Maximum file size: **500 GB**.
+
+---
+
+## What happens under the hood
+
+1. For each file, `abcupload` sends a POST request to the ABCOMICS API with
+   your username, project ID, and filename.
+2. The API validates the request and returns a time-limited signed URL pointing
+   directly to the ABCOMICS cloud storage bucket.
+3. `abcupload` streams the file to that URL with a live progress bar showing
+   speed, percentage, and estimated time remaining.
+4. If a file with the same name already exists, you are asked whether to
+   overwrite it or skip it (or use `-o` to always overwrite).
+
+---
+
+## Development install
+
+```bash
+git clone https://github.com/african-bioinformatics-center/ABCOMICS_site.git
+cd ABCOMICS_site/abcupload
+pip install -e .
+```
+
+Build a distribution:
+
+```bash
+pip install build
+python -m build
+# output: dist/abcupload-1.0.0.tar.gz  and  dist/abcupload-1.0.0-py3-none-any.whl
+```
+
+---
+
+## Author
+
+**Khadim Gueye** — African Bioinformatics Center (ABCOMICS)  
+Contact: [contact@abcomics.org](mailto:contact@abcomics.org)
+
+---
+
+## License
+
+[MIT](LICENSE)

abcupload-1.0.0.dist-info/RECORD

@@ -0,0 +1,9 @@
+abcupload/__init__.py,sha256=LODdOrmnvJLNCAHeXrR7Fd-a2TBaX3RJwqJeUU-nl8Y,92
+abcupload/__main__.py,sha256=-kKzqu70ZvQr-NSQIQ4wWCALPyrBw7tCevUcb-MT2OE,38
+abcupload/cli.py,sha256=BCY1NECN9Ejby8gVbAhvAY4fpxKED0nJwRG650bhnWs,13463
+abcupload-1.0.0.dist-info/licenses/LICENSE,sha256=FRoGDhpexnax_On5SpHuBMT077owLqriXqLDG16EA2g,1113
+abcupload-1.0.0.dist-info/METADATA,sha256=lAiTUksV5Z240NILYmZoQZy2NXrabPcHLevcPuiERto,4994
+abcupload-1.0.0.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+abcupload-1.0.0.dist-info/entry_points.txt,sha256=lsNOS67j1vY7UL_VkH0KFwwIVPgiA5fCrLxu0Uc2yDk,49
+abcupload-1.0.0.dist-info/top_level.txt,sha256=H5cLjT6Wy7RUtBQrNIjzRW_ghg4WSw28suQH3dbDYT4,10
+abcupload-1.0.0.dist-info/RECORD,,

abcupload-1.0.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

abcupload-1.0.0.dist-info/entry_points.txt

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+[console_scripts]
+abcupload = abcupload.cli:main

abcupload-1.0.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Khadim Gueye — African Bioinformatics Center (ABCOMICS)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

abcupload-1.0.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+abcupload