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_REGISTER_TIMEOUT_S = 15 REGISTRATION_REASON_MESSAGES = { - "invalid_key": ( - "Registration key not recognized. Generate a fresh key from " - "Settings → RIA Agents on the hub." - ), - "expired": ( - "This registration key has expired. Generate a new one from " - "Settings → RIA Agents on the hub." - ), - "revoked": ( - "This registration key was revoked. Generate a new one from " - "Settings → RIA Agents on the hub." - ), + "invalid_key": ("Registration key not recognized. Generate a fresh key from " "Settings → RIA Agents on the hub."), + "expired": ("This registration key has expired. Generate a new one from " "Settings → RIA Agents on the hub."), + "revoked": ("This registration key was revoked. Generate a new one from " "Settings → RIA Agents on the hub."), "already_consumed": ( "This single-use registration key has already been used. " "Generate a new one, or mint a reusable key instead." @@ -226,7 +219,7 @@ def main() -> None: sub.add_parser("detect", help="List available SDR drivers") p_reg = sub.add_parser("register", help="Register agent with RIA Hub and save credentials") - p_reg.add_argument("--hub", required=True, help="RIA Hub URL (e.g. http://whitehorse:3005)") + p_reg.add_argument("--hub", default=DEFAULT_HUB_URL, help=f"RIA Hub URL (default: {DEFAULT_HUB_URL})") p_reg.add_argument( "--api-key", dest="api_key", diff --git a/src/ria_toolkit_oss/annotations/annotation_transforms.py b/src/ria_toolkit_oss/annotations/annotation_transforms.py index 822a75a..bb165b6 100644 --- a/src/ria_toolkit_oss/annotations/annotation_transforms.py +++ b/src/ria_toolkit_oss/annotations/annotation_transforms.py @@ -45,7 +45,14 @@ def is_annotation_contained(inner: Annotation, outer: Annotation) -> bool: outer_sample_stop = outer.sample_start + outer.sample_count if inner.sample_start > outer.sample_start and inner_sample_stop < outer_sample_stop: - if inner.freq_lower_edge > outer.freq_lower_edge and inner.freq_upper_edge < outer.freq_upper_edge: + if ( + inner.freq_lower_edge is not None + and inner.freq_upper_edge is not None + and outer.freq_lower_edge is not None + and outer.freq_upper_edge is not None + and inner.freq_lower_edge > outer.freq_lower_edge + and inner.freq_upper_edge < outer.freq_upper_edge + ): return True return False diff --git a/src/ria_toolkit_oss/data/annotation.py b/src/ria_toolkit_oss/data/annotation.py index d565e17..fe55f97 100644 --- a/src/ria_toolkit_oss/data/annotation.py +++ b/src/ria_toolkit_oss/data/annotation.py @@ -17,10 +17,10 @@ class Annotation: :type sample_start: int :param sample_count: The index of the ending sample of the annotation, inclusive. :type sample_count: int - :param freq_lower_edge: The lower frequency of the annotation. - :type freq_lower_edge: float - :param freq_upper_edge: The upper frequency of the annotation. - :type freq_upper_edge: float + :param freq_lower_edge: The lower frequency of the annotation. Optional; None if not specified in source. + :type freq_lower_edge: float, optional + :param freq_upper_edge: The upper frequency of the annotation. Optional; None if not specified in source. + :type freq_upper_edge: float, optional :param label: The label that will be displayed with the bounding box in compatible viewers including IQEngine. Defaults to an emtpy string. :type label: str, optional @@ -34,8 +34,8 @@ class Annotation: self, sample_start: int, sample_count: int, - freq_lower_edge: float, - freq_upper_edge: float, + freq_lower_edge: Optional[float] = None, + freq_upper_edge: Optional[float] = None, label: Optional[str] = "", comment: Optional[str] = "", detail: Optional[dict] = None, @@ -43,8 +43,8 @@ class Annotation: """Initialize a new Annotation instance.""" self.sample_start = int(sample_start) self.sample_count = int(sample_count) - self.freq_lower_edge = float(freq_lower_edge) - self.freq_upper_edge = float(freq_upper_edge) + self.freq_lower_edge = float(freq_lower_edge) if freq_lower_edge is not None else None + self.freq_upper_edge = float(freq_upper_edge) if freq_upper_edge is not None else None self.label = str(label) self.comment = str(comment) @@ -62,6 +62,8 @@ class Annotation: :returns: True if valid, False if not. """ + if self.freq_lower_edge is None or self.freq_upper_edge is None: + return self.sample_count > 0 return self.sample_count > 0 and self.freq_lower_edge < self.freq_upper_edge def overlap(self, other): @@ -73,6 +75,14 @@ class Annotation: :returns: The area of the overlap in samples*frequency, or 0 if they do not overlap.""" + if ( + self.freq_lower_edge is None + or self.freq_upper_edge is None + or other.freq_lower_edge is None + or other.freq_upper_edge is None + ): + return 0 + sample_overlap_start = max(self.sample_start, other.sample_start) sample_overlap_end = min(self.sample_start + self.sample_count, other.sample_start + other.sample_count) @@ -91,6 +101,8 @@ class Annotation: :returns: sample length multiplied by bandwidth.""" + if self.freq_lower_edge is None or self.freq_upper_edge is None: + return 0 return self.sample_count * (self.freq_upper_edge - self.freq_lower_edge) def __eq__(self, other: Annotation) -> bool: @@ -103,13 +115,16 @@ class Annotation: annotation_dict = {SigMFFile.START_INDEX_KEY: self.sample_start, SigMFFile.LENGTH_INDEX_KEY: self.sample_count} - annotation_dict["metadata"] = { + metadata = { SigMFFile.LABEL_KEY: self.label, SigMFFile.COMMENT_KEY: self.comment, - SigMFFile.FHI_KEY: self.freq_upper_edge, - SigMFFile.FLO_KEY: self.freq_lower_edge, "ria:detail": self.detail, } + if self.freq_upper_edge is not None: + metadata[SigMFFile.FHI_KEY] = self.freq_upper_edge + if self.freq_lower_edge is not None: + metadata[SigMFFile.FLO_KEY] = self.freq_lower_edge + annotation_dict["metadata"] = metadata if _is_jsonable(annotation_dict): return annotation_dict diff --git a/src/ria_toolkit_oss/view/view_signal.py b/src/ria_toolkit_oss/view/view_signal.py index 628bb0e..875df85 100644 --- a/src/ria_toolkit_oss/view/view_signal.py +++ b/src/ria_toolkit_oss/view/view_signal.py @@ -81,6 +81,8 @@ def view_annotations( return 0 for annotation in sorted(annotations, key=_threshold_sort_key, reverse=True): + if annotation.freq_lower_edge is None or annotation.freq_upper_edge is None: + continue t_start = annotation.sample_start / sample_rate t_width = annotation.sample_count / sample_rate f_start = annotation.freq_lower_edge diff --git a/src/ria_toolkit_oss_cli/cli.py b/src/ria_toolkit_oss_cli/cli.py index bf97dfa..a1d92a5 100644 --- a/src/ria_toolkit_oss_cli/cli.py +++ b/src/ria_toolkit_oss_cli/cli.py @@ -2,15 +2,57 @@ This module contains the main group for the ria toolkit oss CLI. """ -import click +import subprocess +import sys +import warnings -from ria_toolkit_oss_cli.ria_toolkit_oss import commands +warnings.filterwarnings( + "ignore", + message="Unable to import Axes3D", + category=UserWarning, + module="matplotlib", +) + +import click # noqa: E402 + +from ria_toolkit_oss_cli.ria_toolkit_oss import commands # noqa: E402 -@click.group() +def _git_lfs_installed() -> bool: + """Return True if git-lfs is available on PATH.""" + try: + return ( + subprocess.run( + ["git", "lfs", "version"], + capture_output=True, + ).returncode + == 0 + ) + except FileNotFoundError: + return False + + +@click.group(invoke_without_command=True) @click.option("-v", "--verbose", is_flag=True, type=bool, help="Increase verbosity, especially useful for debugging.") -def cli(verbose): - pass +@click.pass_context +def cli(ctx, verbose): + lfs_missing = not _git_lfs_installed() + if lfs_missing: + click.echo( + "Warning: git-lfs is not installed. RIA Hub projects require git-lfs to\n" + "track large binary files (models, recordings, datasets).\n" + "\n" + " Linux: sudo apt-get install git-lfs\n" + " macOS: brew install git-lfs\n" + " Other platforms: https://git-lfs.com\n" + "\n" + "After installing, run: git lfs install", + err=True, + ) + if ctx.invoked_subcommand is None: + if lfs_missing and sys.stdin.isatty(): + click.pause(info="\nPress Enter to continue...", err=True) + click.echo(ctx.get_help()) # Loop through project commands, binding them all to the CLI. diff --git a/src/ria_toolkit_oss_cli/ria_toolkit_oss/_hub_auth.py b/src/ria_toolkit_oss_cli/ria_toolkit_oss/_hub_auth.py new file mode 100644 index 0000000..5b62635 --- /dev/null +++ b/src/ria_toolkit_oss_cli/ria_toolkit_oss/_hub_auth.py @@ -0,0 +1,97 @@ +"""Shared authentication and security helpers for RIA Hub API calls.""" + +import base64 +import subprocess +import urllib.error +import urllib.parse +import urllib.request + +import click + +DEFAULT_HUB = "https://riahub.ai" + + +class _NoRedirectHandler(urllib.request.HTTPRedirectHandler): + """Block redirects on authenticated requests to prevent credential exfiltration. + + urllib re-sends the Authorization header on same-host redirects by default. + A malicious server could redirect a POST to a different host to harvest + credentials. We refuse all redirects — API clients should not encounter them + in normal operation. + """ + + def redirect_request(self, req, fp, code, msg, headers, newurl): + raise urllib.error.URLError(f"Unexpected redirect ({code}) to {newurl} — aborting to protect credentials") + + +def hub_opener() -> urllib.request.OpenerDirector: + """Return a urllib opener that blocks redirects.""" + return urllib.request.build_opener(_NoRedirectHandler) + + +def warn_if_insecure(hub: str) -> None: + """Warn when credentials would be sent over plain HTTP to a non-localhost host.""" + parsed = urllib.parse.urlparse(hub) + if parsed.scheme == "http": + host = parsed.hostname or "" + if host not in ("localhost", "127.0.0.1", "::1"): + click.echo( + f"Warning: sending credentials over plain HTTP to {host}. " "Use HTTPS in production.", + err=True, + ) + + +def basic_auth(username: str, password: str) -> str: + return "Basic " + base64.b64encode(f"{username}:{password}".encode()).decode() + + +def get_stored_credentials(hub_url: str) -> tuple[str | None, str | None]: + """Ask git credential fill for stored creds. Returns (username, password) or (None, None).""" + parsed = urllib.parse.urlparse(hub_url) + payload = f"protocol={parsed.scheme}\nhost={parsed.netloc}\n\n" + try: + result = subprocess.run( + ["git", "credential", "fill"], + input=payload, + capture_output=True, + text=True, + timeout=5, + ) + creds = {} + for line in result.stdout.splitlines(): + # Partition on the FIRST '=' only so passwords containing '=' are preserved. + k, sep, v = line.partition("=") + if sep: + creds[k.strip()] = v # keep value verbatim + return creds.get("username"), creds.get("password") + except Exception: + return None, None + + +def store_credentials(hub_url: str, username: str, password: str) -> None: + """Cache credentials via git credential approve (uses the system keychain/store).""" + parsed = urllib.parse.urlparse(hub_url) + payload = ( + f"protocol={parsed.scheme}\n" f"host={parsed.netloc}\n" f"username={username}\n" f"password={password}\n\n" + ) + try: + subprocess.run( + ["git", "credential", "approve"], + input=payload, + capture_output=True, + text=True, + timeout=5, + ) + except Exception: + pass # non-fatal — next push just prompts again + + +def resolve_credentials(hub: str) -> tuple[str, str]: + """Return (username, password), prompting interactively if not cached.""" + username, password = get_stored_credentials(hub) + if username and password: + return username, password + click.echo(f"No stored credentials found for {hub}.") + username = click.prompt("RIA Hub username") + password = click.prompt("Password / personal access token", hide_input=True) + return username, password diff --git a/src/ria_toolkit_oss_cli/ria_toolkit_oss/annotate.py b/src/ria_toolkit_oss_cli/ria_toolkit_oss/annotate.py index 6477d40..b4c8a95 100644 --- a/src/ria_toolkit_oss_cli/ria_toolkit_oss/annotate.py +++ b/src/ria_toolkit_oss_cli/ria_toolkit_oss/annotate.py @@ -86,9 +86,7 @@ def save_recording_auto(recording, output_path, input_path, quiet=False, overwri input_path = Path(input_path) fmt = detect_input_format(input_path) - output_path = determine_output_path( - input_path=input_path, output_path=output_path, fmt=fmt, overwrite=overwrite - ) + output_path = determine_output_path(input_path=input_path, output_path=output_path, fmt=fmt, overwrite=overwrite) if not quiet: if fmt == "sigmf": @@ -258,7 +256,11 @@ def list(input, verbose): user_comment = ann.comment or "" # Basic info - freq_range = f"{format_frequency(ann.freq_lower_edge)} - {format_frequency(ann.freq_upper_edge)}" + freq_range = ( + f"{format_frequency(ann.freq_lower_edge)} - {format_frequency(ann.freq_upper_edge)}" + if ann.freq_lower_edge is not None and ann.freq_upper_edge is not None + else "N/A" + ) click.echo( f" [{i}] Samples {format_sample_count(ann.sample_start)}-" f"{format_sample_count(ann.sample_start + ann.sample_count)}: {ann.label}" @@ -502,8 +504,7 @@ def clear(input, output, overwrite, force, quiet): help="Annotation type", ) @click.option( - "--sample-rate", type=float, default=None, - help="Sample rate in Hz (overrides metadata; required if not in file)" + "--sample-rate", type=float, default=None, help="Sample rate in Hz (overrides metadata; required if not in file)" ) @click.option("--output", "-o", type=click.Path(), help="Output file path") @click.option("--overwrite", is_flag=True, help="Overwrite input file (non-SigMF only)") @@ -617,8 +618,7 @@ def energy( help="Annotation type", ) @click.option( - "--sample-rate", type=float, default=None, - help="Sample rate in Hz (overrides metadata; required if not in file)" + "--sample-rate", type=float, default=None, help="Sample rate in Hz (overrides metadata; required if not in file)" ) @click.option("--output", "-o", type=click.Path(), help="Output file path") @click.option("--overwrite", is_flag=True, help="Overwrite input file (non-SigMF only)") @@ -707,8 +707,7 @@ def cusum(input, label, min_duration, window_size, tolerance, annotation_type, s ) @click.option("--channel", type=int, default=0, help="Channel index to annotate (default: 0)") @click.option( - "--sample-rate", type=float, default=None, - help="Sample rate in Hz (overrides metadata; required if not in file)" + "--sample-rate", type=float, default=None, help="Sample rate in Hz (overrides metadata; required if not in file)" ) @click.option("--output", "-o", type=click.Path(), help="Output file path") @click.option("--overwrite", is_flag=True, help="Overwrite input file (non-SigMF only)") @@ -787,8 +786,7 @@ def threshold(input, threshold, label, window_size, annotation_type, channel, sa @click.option("--noise-threshold-db", type=float, help="Noise floor threshold in dB (auto-estimated if not specified)") @click.option("--min-component-bw", type=float, default=50e3, help="Min component bandwidth in Hz") @click.option( - "--sample-rate", type=float, default=None, - help="Sample rate in Hz (overrides metadata; required if not in file)" + "--sample-rate", type=float, default=None, help="Sample rate in Hz (overrides metadata; required if not in file)" ) @click.option("--output", "-o", type=click.Path(), help="Output file path") @click.option("--overwrite", is_flag=True, help="Overwrite input file (non-SigMF only)") @@ -809,7 +807,8 @@ def _log_separate_start(quiet, recording, indices_list, nfft, noise_threshold_db def separate( - input, indices, nfft, noise_threshold_db, min_component_bw, sample_rate, output, overwrite, quiet, verbose): + input, indices, nfft, noise_threshold_db, min_component_bw, sample_rate, output, overwrite, quiet, verbose +): """ Auto-detect parallel frequency-offset signals and split into sub-bands. @@ -883,7 +882,11 @@ def separate( click.echo("\n Details:") for i in range(initial_count, final_count): ann = recording.annotations[i] - freq_range = f"{format_frequency(ann.freq_lower_edge)} - {format_frequency(ann.freq_upper_edge)}" + freq_range = ( + f"{format_frequency(ann.freq_lower_edge)} - {format_frequency(ann.freq_upper_edge)}" + if ann.freq_lower_edge is not None and ann.freq_upper_edge is not None + else "N/A" + ) click.echo( f" [{i}] samples {format_sample_count(ann.sample_start)}-" f"{format_sample_count(ann.sample_start + ann.sample_count)}: {freq_range}" diff --git a/src/ria_toolkit_oss_cli/ria_toolkit_oss/commands.py b/src/ria_toolkit_oss_cli/ria_toolkit_oss/commands.py index 174a5f4..7587f58 100644 --- a/src/ria_toolkit_oss_cli/ria_toolkit_oss/commands.py +++ b/src/ria_toolkit_oss_cli/ria_toolkit_oss/commands.py @@ -16,9 +16,11 @@ from .generate import generate # from .generate import generate from .init import init from .serve import serve +from .setup_repo import setup_repo from .split import split from .transform import transform from .transmit import transmit +from .upload import upload from .view import view # Aliases diff --git a/src/ria_toolkit_oss_cli/ria_toolkit_oss/setup_repo.py b/src/ria_toolkit_oss_cli/ria_toolkit_oss/setup_repo.py new file mode 100644 index 0000000..b826ec3 --- /dev/null +++ b/src/ria_toolkit_oss_cli/ria_toolkit_oss/setup_repo.py @@ -0,0 +1,401 @@ +"""ria setup_repo — create and configure a RIA Hub Project repo.""" + +import json +import os +import re +import subprocess +import sys +import urllib.error +import urllib.parse +import urllib.request + +import click + +from ._hub_auth import ( + DEFAULT_HUB, + _NoRedirectHandler, + basic_auth, + resolve_credentials, + store_credentials, + warn_if_insecure, +) + +RIA_LFS_RULES = [ + ("*.pt", "filter=lfs diff=lfs merge=lfs -text"), + ("*.pth", "filter=lfs diff=lfs merge=lfs -text"), + ("*.onnx", "filter=lfs diff=lfs merge=lfs -text"), + ("*.sigmf", "filter=lfs diff=lfs merge=lfs -text"), + ("*.sigmf-data", "filter=lfs diff=lfs merge=lfs -text"), + ("*.sigmf-meta", "filter=lfs diff=lfs merge=lfs -text"), + ("*.npy", "filter=lfs diff=lfs merge=lfs -text"), + ("*.npz", "filter=lfs diff=lfs merge=lfs -text"), + ("*.h5", "filter=lfs diff=lfs merge=lfs -text"), + ("*.hdf5", "filter=lfs diff=lfs merge=lfs -text"), + ("*.bin", "filter=lfs diff=lfs merge=lfs -text"), + ("*.pkl", "filter=lfs diff=lfs merge=lfs -text"), +] + +# Repo names must be safe directory names and valid git remote path components. +_SAFE_NAME_RE = re.compile(r"^[A-Za-z0-9._-]{1,100}$") + + +# --------------------------------------------------------------------------- +# API helpers +# --------------------------------------------------------------------------- + + +def _api_request( + hub: str, + path: str, + method: str, + username: str, + password: str, + body: dict | None = None, +) -> tuple[dict, int]: + """ + Make an authenticated request to the RIA Hub API. + Returns (parsed_response_body, http_status_code). + Status 0 means a network/connection error. + Credentials are sent as HTTP Basic auth — safe over HTTPS and localhost HTTP. + Redirects are blocked to prevent credential exfiltration. + """ + url = f"{hub.rstrip('/')}/api/v1{path}" + data = json.dumps(body).encode() if body is not None else None + req = urllib.request.Request(url, data=data, method=method) + req.add_header("Content-Type", "application/json") + req.add_header("Authorization", basic_auth(username, password)) + + opener = urllib.request.build_opener(_NoRedirectHandler) + try: + with opener.open(req, timeout=15) as resp: + return json.loads(resp.read() or b"{}"), resp.status + except urllib.error.HTTPError as e: + try: + resp_body = json.loads(e.read() or b"{}") + except Exception: + resp_body = {} + return resp_body, e.code + except urllib.error.URLError as e: + return {"message": str(e.reason)}, 0 + + +def _get_authenticated_username(hub: str, username: str, password: str) -> str | None: + """Return the login name of the authenticated user from GET /api/v1/user. + + This is the canonical username for URL construction — it may differ from + git config user.name which is a display name, not a login. + """ + body, status = _api_request(hub, "/user", "GET", username, password) + if status == 200: + return body.get("login") + return None + + +def _repo_exists(hub: str, owner: str, name: str, username: str, password: str) -> bool: + body, status = _api_request( + hub, + f"/repos/{urllib.parse.quote(owner, safe='')}/{urllib.parse.quote(name, safe='')}", + "GET", + username, + password, + ) + return status == 200 + + +def _create_repo_on_hub(hub: str, name: str, username: str, password: str, private: bool) -> bool: + """Create an RIA Hub Project repo via API. + + Returns True if the repo was freshly created (server seeded README.md and + .gitattributes via auto_init + is_ria), False if the hub was unreachable + (local fallback needed). Exits on fatal errors (auth, quota, name taken). + """ + body, status = _api_request( + hub, + "/user/repos", + "POST", + username, + password, + { + "name": name, + "auto_init": True, + "is_ria": True, + "private": private, + "default_branch": "main", + }, + ) + + if status == 201: + click.echo(f"Repository '{name}' created on RIA Hub.") + return True + + if status == 0: + click.echo( + f"Warning: could not reach RIA Hub at {hub}: {body.get('message', 'connection failed')}", + err=True, + ) + click.echo("Continuing with local setup only — create the repo manually on RIA Hub.", err=True) + return False + + msg = body.get("message", "") + + if status == 401: + click.echo("Error: authentication failed — check your username/password.", err=True) + sys.exit(1) + + if status in (403, 413) or "quota" in msg.lower() or "limit" in msg.lower(): + click.echo("Error: cannot create repository — storage quota or account limit reached.", err=True) + if msg: + click.echo(f" Server message: {msg}", err=True) + sys.exit(1) + + if status == 422 or "already exist" in msg.lower(): + click.echo(f"Repository '{name}' already exists on RIA Hub.") + return False + + click.echo(f"Error creating repository (HTTP {status}): {msg}", err=True) + sys.exit(1) + + +# --------------------------------------------------------------------------- +# Local git helpers +# --------------------------------------------------------------------------- + + +def _tracked_patterns(ga_path: str) -> set: + if not os.path.exists(ga_path): + return set() + patterns = set() + with open(ga_path, encoding="utf-8") as f: + for line in f: + line = line.strip() + if not line or line.startswith("#"): + continue + m = re.match(r"^(\S+)\s+", line) + if m: + patterns.add(m.group(1)) + return patterns + + +def _write_local_ria_files(repo_path: str, repo_name: str) -> None: + """Seed README.md and .gitattributes locally (used when hub is unreachable or --no-remote).""" + # README + for candidate in ("README.md", "README.rst", "README.txt", "README"): + if os.path.exists(os.path.join(repo_path, candidate)): + click.echo(f"README: {candidate} already exists, skipping") + break + else: + with open(os.path.join(repo_path, "README.md"), "w", encoding="utf-8") as f: + f.write( + f"# {repo_name}\n" + "\n" + "A RIA Hub project.\n" + "\n" + "## Description\n" + "\n" + "\n" + "\n" + "## Contents\n" + "\n" + "\n" + ) + click.echo("README.md: created") + + # .gitattributes + ga_path = os.path.join(repo_path, ".gitattributes") + existing = _tracked_patterns(ga_path) + new_rules = [(p, a) for p, a in RIA_LFS_RULES if p not in existing] + + if new_rules: + existing_content = "" + if os.path.exists(ga_path): + with open(ga_path, encoding="utf-8") as f: + existing_content = f.read() + + separator = "" if (not existing_content or existing_content.endswith("\n")) else "\n" + addition = separator + "".join(f"{pattern} {attrs}\n" for pattern, attrs in new_rules) + + with open(ga_path, "a", encoding="utf-8") as f: + f.write(addition) + click.echo(f".gitattributes: {len(new_rules)} rule(s) added") + else: + click.echo(".gitattributes: all RIA Hub rules are already present") + + +def _git(repo_path: str, *args: str, check: bool = True) -> subprocess.CompletedProcess: + return subprocess.run( + ["git", "-C", repo_path, *args], + capture_output=True, + text=True, + check=check, + ) + + +def _resolve_path_and_name(name: str | None, local_path: str | None) -> tuple[str, str]: + if local_path: + repo_path = os.path.abspath(local_path) + repo_name = name or os.path.basename(repo_path) + elif name: + repo_path = os.path.abspath(name) + repo_name = name + else: + repo_path = os.path.abspath(".") + repo_name = os.path.basename(repo_path) + return repo_path, repo_name + + +def _resolve_owner(hub: str, username: str | None, password: str | None, owner: str | None) -> str: + if not owner and username and password: + api_login = _get_authenticated_username(hub, username, password) + owner = api_login or username + return owner or "unknown" + + +def _git_init(repo_path: str) -> None: + if os.path.isdir(os.path.join(repo_path, ".git")): + return + result = _git(repo_path, "init", "-b", "main", check=False) + if result.returncode != 0: + # Older git (< 2.28) doesn't support -b; fall back and rename. + _git(repo_path, "init") + _git(repo_path, "symbolic-ref", "HEAD", "refs/heads/main") + click.echo("git init: done (branch: main)") + + +def _configure_remote( + repo_path: str, hub: str, resolved_owner: str, repo_name: str, username: str | None, no_remote: bool +) -> None: + if no_remote or not username: + click.echo( + f"Skipped remote setup. Add it manually:\n" + f" git -C {repo_path} remote add origin " + f"{hub.rstrip('/')}/{resolved_owner}/{repo_name}.git" + ) + return + remote_url = f"{hub.rstrip('/')}/{resolved_owner}/{repo_name}.git" + existing = _git(repo_path, "remote", "get-url", "origin", check=False) + if existing.returncode == 0: + existing_url = existing.stdout.strip() + if existing_url == remote_url: + click.echo(f"remote origin: {remote_url} (already set)") + else: + click.echo( + f"remote 'origin' already points to {existing_url}.\n" + f" To update: git remote set-url origin {remote_url}" + ) + else: + _git(repo_path, "remote", "add", "origin", remote_url) + click.echo(f"remote origin: {remote_url}") + + +# --------------------------------------------------------------------------- +# Command +# --------------------------------------------------------------------------- + + +@click.command("setup_repo") +@click.argument("name", required=False) +@click.option( + "--path", "local_path", default=None, help="Local directory (default: current dir, or created from NAME)." +) +@click.option("--hub", default=DEFAULT_HUB, show_default=True, metavar="URL", help="RIA Hub base URL.") +@click.option( + "--owner", + default=None, + metavar="USER", + help="RIA Hub login username (default: looked up from the API using your credentials).", +) +@click.option("--private", is_flag=True, default=False, help="Create the repository as private.") +@click.option( + "--no-remote", is_flag=True, default=False, help="Skip creating the repository on RIA Hub (local setup only)." +) +def setup_repo( + name: str | None, + local_path: str | None, + hub: str, + owner: str | None, + private: bool, + no_remote: bool, +) -> None: + """Create and configure a RIA Hub Project repo. + + NAME is the repository name. If the local directory does not exist or is + not a git repo, it will be initialised automatically. Credentials are + retrieved from git's credential store — no token setup required if you + have used RIA Hub with git before. + + \b + Examples: + ria setup_repo my-dataset + ria setup_repo my-dataset --hub https://riahub.example.com + ria setup_repo --path ./existing-dir + ria setup_repo my-dataset --private + """ + repo_path, repo_name = _resolve_path_and_name(name, local_path) + + if not _SAFE_NAME_RE.match(repo_name): + click.echo( + f"Error: '{repo_name}' is not a valid repository name.\n" + "Use only letters, numbers, hyphens, underscores, and dots (max 100 chars).", + err=True, + ) + sys.exit(1) + + if not no_remote: + warn_if_insecure(hub) + + username, password = (None, None) if no_remote else resolve_credentials(hub) + resolved_owner = _resolve_owner(hub, username, password, owner) + + # newly_created=True means the server ran auto_init+is_ria and seeded + # README.md + .gitattributes in the initial commit; local setup pulls + # those files via fetch rather than writing them from scratch. + newly_created = False + if not no_remote and username and password: + if _repo_exists(hub, resolved_owner, repo_name, username, password): + click.echo(f"Repository '{resolved_owner}/{repo_name}' already exists on RIA Hub.") + else: + newly_created = _create_repo_on_hub(hub, repo_name, username, password, private) + store_credentials(hub, username, password) + + if not os.path.exists(repo_path): + os.makedirs(repo_path) + click.echo(f"Created directory: {repo_path}") + + _git_init(repo_path) + + if subprocess.run(["git", "lfs", "version"], capture_output=True).returncode != 0: + click.echo( + "Error: git-lfs is not installed.\n" + " Linux: sudo apt-get install git-lfs\n" + " macOS: brew install git-lfs\n" + " Other platforms: https://git-lfs.com", + err=True, + ) + sys.exit(1) + + _git(repo_path, "lfs", "install", "--local") + click.echo("git lfs install --local: done") + + _configure_remote(repo_path, hub, resolved_owner, repo_name, username, no_remote) + + if newly_created: + fetch = _git(repo_path, "fetch", "origin", check=False) + if fetch.returncode == 0: + _git(repo_path, "reset", "--hard", "origin/main") + click.echo("Pulled initial commit from RIA Hub (README.md + .gitattributes)") + else: + click.echo("Warning: fetch failed — falling back to local file setup.", err=True) + _write_local_ria_files(repo_path, repo_name) + else: + _write_local_ria_files(repo_path, repo_name) + + if newly_created: + click.echo(f"\nRepo is ready. Push your work:\n cd {repo_path}\n git push -u origin main") + else: + click.echo( + f"\nRepo is ready. Commit and push:\n" + f" cd {repo_path}\n" + f" git add README.md .gitattributes\n" + f" git commit -m 'chore: initialise RIA Hub project'\n" + f" git push -u origin main" + ) diff --git a/src/ria_toolkit_oss_cli/ria_toolkit_oss/upload.py b/src/ria_toolkit_oss_cli/ria_toolkit_oss/upload.py new file mode 100644 index 0000000..10f04c7 --- /dev/null +++ b/src/ria_toolkit_oss_cli/ria_toolkit_oss/upload.py @@ -0,0 +1,392 @@ +"""ria upload — stream large files to a RIA Hub Project via the LFS API. + +How it works +------------ +1. The file is hashed locally (SHA-256 + size) — this is the LFS object ID. +2. A single POST to the repo's LFS batch endpoint returns an upload URL + (and headers) for any object the server does not already have. +3. The file is streamed to that URL in fixed-size chunks — nothing is ever + fully loaded into memory, so files of any size work. +4. A commit is created via the Gitea contents API that records the LFS + pointer (a small text file) so the file appears in the repo tree. + +No server-side changes are required — this uses the same authenticated LFS +protocol that `git lfs push` uses internally. +""" + +import base64 +import hashlib +import http.client +import json +import math +import os +import sys +import urllib.error +import urllib.parse +import urllib.request + +import click + +from ._hub_auth import ( + DEFAULT_HUB, + basic_auth, + hub_opener, + resolve_credentials, + warn_if_insecure, +) + +# Read buffer for hashing and streaming — 8 MB keeps memory use flat +# for arbitrarily large files. +_CHUNK = 8 * 1024 * 1024 + +LFS_MEDIA_TYPE = "application/vnd.git-lfs+json" + + +# --------------------------------------------------------------------------- +# File helpers +# --------------------------------------------------------------------------- + + +def _hash_file(path: str) -> tuple[str, int]: + """Return (sha256_hex, byte_size) by streaming the file.""" + h = hashlib.sha256() + size = 0 + with open(path, "rb") as f: + while True: + chunk = f.read(_CHUNK) + if not chunk: + break + h.update(chunk) + size += len(chunk) + return h.hexdigest(), size + + +def _lfs_pointer_text(oid: str, size: int) -> str: + return f"version https://git-lfs.github.com/spec/v1\noid sha256:{oid}\nsize {size}\n" + + +# --------------------------------------------------------------------------- +# LFS batch API +# --------------------------------------------------------------------------- + + +def _lfs_batch( + hub: str, + owner: str, + repo: str, + objects: list[dict], + username: str, + password: str, +) -> dict: + """ + POST to /{owner}/{repo}.git/info/lfs/objects/batch. + Returns the parsed JSON response. + Raises on HTTP error or JSON decode failure. + """ + url = ( + f"{hub.rstrip('/')}" + f"/{urllib.parse.quote(owner, safe='')}" + f"/{urllib.parse.quote(repo, safe='')}" + f".git/info/lfs/objects/batch" + ) + body = json.dumps( + { + "operation": "upload", + "transfers": ["basic"], + "objects": objects, + } + ).encode() + + req = urllib.request.Request(url, data=body, method="POST") + req.add_header("Content-Type", LFS_MEDIA_TYPE) + req.add_header("Accept", LFS_MEDIA_TYPE) + req.add_header("Authorization", basic_auth(username, password)) + + opener = hub_opener() + try: + with opener.open(req, timeout=30) as resp: + return json.loads(resp.read()) + except urllib.error.HTTPError as e: + body_text = e.read().decode(errors="replace") + raise RuntimeError(f"LFS batch request failed (HTTP {e.code}): {body_text}") from e + + +# --------------------------------------------------------------------------- +# Gitea contents API — create / update a file to record the LFS pointer +# --------------------------------------------------------------------------- + + +def _get_file_sha( + hub: str, + owner: str, + repo: str, + path: str, + branch: str, + username: str, + password: str, +) -> str | None: + """Return the blob SHA of an existing file, or None if it doesn't exist.""" + url = ( + f"{hub.rstrip('/')}/api/v1" + f"/repos/{urllib.parse.quote(owner, safe='')}/{urllib.parse.quote(repo, safe='')}" + f"/contents/{urllib.parse.quote(path)}" + f"?ref={urllib.parse.quote(branch)}" + ) + req = urllib.request.Request(url) + req.add_header("Authorization", basic_auth(username, password)) + try: + with hub_opener().open(req, timeout=15) as resp: + return json.loads(resp.read()).get("sha") + except urllib.error.HTTPError as e: + if e.code == 404: + return None + raise + + +def _commit_lfs_pointer( + hub: str, + owner: str, + repo: str, + remote_path: str, + pointer_text: str, + branch: str, + message: str, + username: str, + password: str, +) -> None: + """Create or update a file in the repo containing the LFS pointer.""" + url = ( + f"{hub.rstrip('/')}/api/v1" + f"/repos/{urllib.parse.quote(owner, safe='')}/{urllib.parse.quote(repo, safe='')}" + f"/contents/{urllib.parse.quote(remote_path)}" + ) + + existing_sha = _get_file_sha(hub, owner, repo, remote_path, branch, username, password) + + body: dict = { + "message": message, + "content": base64.b64encode(pointer_text.encode()).decode(), + "branch": branch, + } + if existing_sha: + body["sha"] = existing_sha + + method = "PUT" if existing_sha else "POST" + req = urllib.request.Request(url, data=json.dumps(body).encode(), method=method) + req.add_header("Content-Type", "application/json") + req.add_header("Authorization", basic_auth(username, password)) + + try: + with hub_opener().open(req, timeout=30) as resp: + resp.read() + except urllib.error.HTTPError as e: + body_text = e.read().decode(errors="replace") + raise RuntimeError(f"Failed to commit LFS pointer for '{remote_path}' (HTTP {e.code}): {body_text}") from e + + +# --------------------------------------------------------------------------- +# Per-file upload logic +# --------------------------------------------------------------------------- + + +def _upload_single_file( + hub: str, + owner: str, + repo_name: str, + username: str, + password: str, + file_path: str, + remote_dir: str, + message: str | None, + branch: str, +) -> None: + """Hash, upload (if needed), and commit the LFS pointer for one file.""" + filename = os.path.basename(file_path) + file_size = os.path.getsize(file_path) + size_mb = file_size / (1024 * 1024) + + click.echo(f"\n {filename} ({size_mb:.1f} MB)") + + click.echo(" Hashing...", nl=False) + oid, size = _hash_file(file_path) + click.echo(f" sha256:{oid[:12]}...") + + try: + batch = _lfs_batch(hub, owner, repo_name, [{"oid": oid, "size": size}], username, password) + except RuntimeError as e: + click.echo(f"\n Error: {e}", err=True) + sys.exit(1) + + objects = batch.get("objects", []) + if not objects: + click.echo(" Already in LFS — skipping upload.") + else: + obj = objects[0] + if "error" in obj: + err_msg = obj["error"].get("message", "unknown error") + err_code = obj["error"].get("code", 0) + if err_code == 413 or "quota" in err_msg.lower() or "limit" in err_msg.lower(): + click.echo( + f"\n Error: storage quota exceeded for this repo.\n Server: {err_msg}", + err=True, + ) + else: + click.echo(f"\n Error from server: {err_msg}", err=True) + sys.exit(1) + + upload_action = obj.get("actions", {}).get("upload") + if not upload_action: + click.echo(" Already in LFS — skipping upload.") + else: + href = upload_action["href"] + up_headers = upload_action.get("header", {}) + chunks = math.ceil(size / _CHUNK) + click.echo(f" Uploading ({size_mb:.1f} MB, {chunks} chunk{'s' if chunks != 1 else ''})...") + try: + _stream_upload_progress(href, up_headers, file_path, size) + except RuntimeError as e: + click.echo(f"\n Upload failed: {e}", err=True) + sys.exit(1) + click.echo(" Upload complete.") + + verify_action = obj.get("actions", {}).get("verify") + if verify_action: + try: + vreq = urllib.request.Request( + verify_action["href"], + data=json.dumps({"oid": oid, "size": size}).encode(), + method="POST", + ) + vreq.add_header("Content-Type", LFS_MEDIA_TYPE) + vreq.add_header("Accept", LFS_MEDIA_TYPE) + for k, v in verify_action.get("header", {}).items(): + vreq.add_header(k, v) + with urllib.request.urlopen(vreq, timeout=15): + pass + except Exception: + pass # verify is optional; non-fatal on failure + + pointer = _lfs_pointer_text(oid, size) + remote_path = (f"{remote_dir.rstrip('/')}/{filename}").lstrip("/") if remote_dir else filename + commit_msg = message or f"chore: upload {filename} via ria" + + click.echo(f" Committing pointer → {remote_path}...", nl=False) + try: + _commit_lfs_pointer(hub, owner, repo_name, remote_path, pointer, branch, commit_msg, username, password) + click.echo(" done.") + except RuntimeError as e: + click.echo(f"\n Error: {e}", err=True) + sys.exit(1) + + +def _stream_upload_progress(href: str, headers: dict, file_path: str, size: int) -> None: + """Stream file_path to href with a click progress bar.""" + parsed = urllib.parse.urlparse(href) + host = parsed.netloc + path_q = parsed.path + (f"?{parsed.query}" if parsed.query else "") + + if parsed.scheme == "https": + conn = http.client.HTTPSConnection(host, timeout=300) + else: + conn = http.client.HTTPConnection(host, timeout=300) + + all_headers = dict(headers) + all_headers.setdefault("Content-Type", "application/octet-stream") + all_headers["Content-Length"] = str(size) + + try: + conn.connect() + conn.putrequest("PUT", path_q) + for k, v in all_headers.items(): + conn.putheader(k, v) + conn.endheaders() + + with click.progressbar( + length=size, + label=" ", + width=40, + show_eta=True, + show_percent=True, + fill_char="█", + empty_char="░", + ) as bar: + with open(file_path, "rb") as f: + while True: + chunk = f.read(_CHUNK) + if not chunk: + break + conn.send(chunk) + bar.update(len(chunk)) + + resp = conn.getresponse() + resp.read() + if resp.status not in (200, 201): + raise RuntimeError(f"HTTP {resp.status}") + finally: + conn.close() + + +# --------------------------------------------------------------------------- +# Command +# --------------------------------------------------------------------------- + + +@click.command("upload") +@click.argument("files", nargs=-1, required=True) +@click.option( + "--repo", required=True, metavar="OWNER/NAME", help="Target repository on RIA Hub (e.g. benchinnery/my-dataset)." +) +@click.option("--hub", default=DEFAULT_HUB, show_default=True, metavar="URL", help="RIA Hub base URL.") +@click.option("--branch", default="main", show_default=True, help="Branch to commit the files to.") +@click.option( + "--path", + "remote_dir", + default="", + metavar="DIR", + help="Remote directory path inside the repo (default: repo root).", +) +@click.option("--message", "-m", default=None, help="Commit message (default: 'chore: upload via ria').") +def upload( + files: tuple[str], + repo: str, + hub: str, + branch: str, + remote_dir: str, + message: str | None, +) -> None: + """Upload large files to a RIA Hub Project via Git LFS. + + Files are streamed directly to the repo's LFS object store — nothing is + buffered into memory, so files of any size work. Each file creates one + commit recording the LFS pointer. + + \b + Examples: + ria upload recording.sigmf-data --repo benchinnery/my-recordings + ria upload *.npy --repo benchinnery/my-recordings --branch main + ria upload big.pt --repo benchinnery/models --path weights/ + """ + # Validate repo argument + if "/" not in repo: + click.echo("Error: --repo must be in the form OWNER/NAME.", err=True) + sys.exit(1) + owner, repo_name = repo.split("/", 1) + + # Expand and validate files + resolved = [] + for pattern in files: + if not os.path.isfile(pattern): + click.echo(f"Error: '{pattern}' is not a file or does not exist.", err=True) + sys.exit(1) + resolved.append(os.path.abspath(pattern)) + + hub = hub.rstrip("/") + warn_if_insecure(hub) + username, password = resolve_credentials(hub) + + click.echo(f"Uploading {len(resolved)} file(s) to {owner}/{repo_name} on {hub}...") + + for file_path in resolved: + _upload_single_file(hub, owner, repo_name, username, password, file_path, remote_dir, message, branch) + + click.echo(f"\nAll done. {len(resolved)} file(s) uploaded to {owner}/{repo_name}.") diff --git a/tests/agent/test_cli_register_errors.py b/tests/agent/test_cli_register_errors.py index 657dfb0..3448ffc 100644 --- a/tests/agent/test_cli_register_errors.py +++ b/tests/agent/test_cli_register_errors.py @@ -79,9 +79,9 @@ def test_user_agent_is_set_and_not_python_default(): """ ua = agent_cli._user_agent() assert ua, "User-Agent must not be empty" - assert not ua.lower().startswith("python-urllib"), ( - f"User-Agent must not be Python's default (got {ua!r}) — Cloudflare blocks it" - ) + assert not ua.lower().startswith( + "python-urllib" + ), f"User-Agent must not be Python's default (got {ua!r}) — Cloudflare blocks it" assert ua.startswith("ria-agent/") @@ -96,7 +96,10 @@ def test_register_request_carries_explicit_user_agent(tmp_path): captured["api_key"] = req.get_header("X-api-key") captured["timeout"] = kwargs.get("timeout") raise urllib.error.HTTPError( - url=req.full_url, code=403, msg="", hdrs=None, # type: ignore[arg-type] + url=req.full_url, + code=403, + msg="", + hdrs=None, # type: ignore[arg-type] fp=BytesIO(_structured("invalid_key")), ) diff --git a/tests/datatypes/test_annotation.py b/tests/datatypes/test_annotation.py index 5dfdeb5..033ef6a 100644 --- a/tests/datatypes/test_annotation.py +++ b/tests/datatypes/test_annotation.py @@ -199,3 +199,44 @@ def test_annotation_to_sigmf_format_values(): values = list(result.values()) assert 50 in values or ann.sample_start in values assert 100 in values or ann.sample_count in values + + +# --------------------------------------------------------------------------- +# None freq-edge regression tests (SigMF optional fields) +# --------------------------------------------------------------------------- + + +def test_annotation_no_freq_edges(): + ann = Annotation(sample_start=0, sample_count=10, label="burst") + assert ann.freq_lower_edge is None + assert ann.freq_upper_edge is None + + +def test_annotation_is_valid_no_freq_edges(): + ann = Annotation(sample_start=0, sample_count=10, label="burst") + assert ann.is_valid() is True + + ann_zero = Annotation(sample_start=0, sample_count=0, label="burst") + assert ann_zero.is_valid() is False + + +def test_annotation_overlap_none_edges_returns_zero(): + ann1 = Annotation(sample_start=0, sample_count=10) + ann2 = Annotation(sample_start=0, sample_count=10, freq_lower_edge=0, freq_upper_edge=100) + assert ann1.overlap(ann2) == 0 + assert ann2.overlap(ann1) == 0 + + +def test_annotation_area_none_edges_returns_zero(): + ann = Annotation(sample_start=0, sample_count=10, label="burst") + assert ann.area() == 0 + + +def test_annotation_to_sigmf_omits_freq_keys_when_none(): + from sigmf import SigMFFile + + ann = Annotation(sample_start=0, sample_count=10, label="burst") + result = ann.to_sigmf_format() + metadata = result["metadata"] + assert SigMFFile.FLO_KEY not in metadata + assert SigMFFile.FHI_KEY not in metadata diff --git a/tests/io/test_recording_io.py b/tests/io/test_recording_io.py index 16383c2..81ff1cc 100644 --- a/tests/io/test_recording_io.py +++ b/tests/io/test_recording_io.py @@ -189,3 +189,21 @@ def test_sigmf_3(tmp_path): to_sigmf(recording=recording1, path=tmp_path, filename=filename.name) except IOError as e: assert str(e) == "File already exists" + + +def test_sigmf_annotation_without_freq_edges(tmp_path): + # Regression: annotations that omit the optional SigMF freq edge fields must + # load without error; edges should be None and the annotation still valid. + ann = Annotation(sample_start=0, sample_count=5, label="burst") + recording1 = Recording(data=complex_data_1, metadata=sample_metadata, annotations=[ann]) + + filename = tmp_path / "test" + to_sigmf(recording=recording1, path=tmp_path, filename=filename.name, overwrite=True) + recording2 = from_sigmf(filename) + + assert len(recording2.annotations) == 1 + loaded = recording2.annotations[0] + assert loaded.freq_lower_edge is None + assert loaded.freq_upper_edge is None + assert loaded.is_valid() is True + assert loaded.label == "burst"