From e068e76fca3503d127b9ce258d5bcaa47138d65c Mon Sep 17 00:00:00 2001 From: Michael Granitzer Date: Thu, 9 May 2024 09:53:37 +0200 Subject: [PATCH] added duckdb shell --- owi/cli.py | 26 +- owi/core/commands.py | 91 ++- owi/core/datasets.py | 21 +- owi/core/irods.py | 27 +- owi/core/lexis.py | 3 +- poetry.lock | 1724 +----------------------------------------- pyproject.toml | 7 +- 7 files changed, 129 insertions(+), 1770 deletions(-) diff --git a/owi/cli.py b/owi/cli.py index 71db662..5184a21 100644 --- a/owi/cli.py +++ b/owi/cli.py @@ -7,7 +7,7 @@ import owi.plugin import pandas as pd from rich.console import Console from owi.core import OWSProject -from owi.core.commands import show_dataframe, read_config, write_config, resume_logic, DownloadManager +from owi.core.commands import show_dataframe, read_config, write_config, DownloadManager, DirectAccess # TODO add unpack and consider tar.gz when checking for consistency _DOCSTRING = """ @@ -141,12 +141,10 @@ def pull(ctx, specifier, files, no_sync, details): This command is used to download and optionally extract datasets for further local analysis or processing. """ - dm = DownloadManager(ctx.obj['OWI'], **ctx.obj) try: - #dm.pull_logic(specifier, files, no_sync, details, details=details, **ctx.obj) - - results = dm.pull_file_based(specifier, files, no_sync, details, **ctx.obj) + #dm.pull_logic(specifier, files, no_sync, details, details=details) + results = dm.pull_file_based(specifier, files, no_sync, details) _rows= [[r["dataset"]["InternalID"], r["dataset"]["Title"],r["file"]["Path"], r["owilstatus"]["download"], r["owilstatus"]["preparation"]] for r in results] df = pd.DataFrame(_rows, columns=["InternalID", "Title", "Path", "Downloaded", "Prepared"]) @@ -162,10 +160,20 @@ def pull(ctx, specifier, files, no_sync, details): except UserWarning as uw: ctx.obj['CONSOLE'].print("Pull aborted by user") -@click.command(help='Resumes previously initiated downloads and checks if a download from a previous pull is ready') +@click.command(help='gets duckd running over irods and provides a ipython shell (experimental).') +@click.argument('specifier', default="all") +@click.option('--files', default="all", help='Specifier to select specific files within the datasets.') @click.pass_context -def resume(ctx): - resume_logic(ctx.obj['OWI']) +def duckdb(ctx, specifier, files, ): + """ + """ + dm = DirectAccess(ctx.obj['OWI'], **ctx.obj) + try: + #dm.pull_logic(specifier, files, no_sync, details, details=details, **ctx.obj) + results = dm.duckdb_shell(specifier, files) + except UserWarning as uw: + ctx.obj['CONSOLE'].print("Pull aborted by user") + @click.command(help='List all logged events related to dataset management.') @click.pass_context @@ -208,7 +216,7 @@ def remote(ctx, subcmd, args): print(f"Executing command: {subcmd}") print(f"With arguments: {args}") -cmds = [local, stats, ls, pull, events, clean, config, remote, resume] +cmds = [local, stats, ls, pull, events, clean, config, remote, duckdb] for i in cmds: cli.add_command(i) diff --git a/owi/core/commands.py b/owi/core/commands.py index 777ce02..f580c82 100644 --- a/owi/core/commands.py +++ b/owi/core/commands.py @@ -4,20 +4,16 @@ It uses rich ui python library """ import configparser import os -import time -from collections import defaultdict, Counter -from queue import Queue import random +import re +import time +from concurrent.futures import ThreadPoolExecutor, as_completed -from rich.text import Text +from rich.progress import Progress, TextColumn, BarColumn, TimeRemainingColumn from owi.core.render import render_dataframe, ask_yes_no -import re -from rich.progress import Progress, TextColumn, BarColumn, TimeRemainingColumn -import traceback -import json -import os -from concurrent.futures import ThreadPoolExecutor, as_completed + + def show_dataframe(datasets, **kwargs): """ @@ -84,11 +80,6 @@ def show_dataframe(datasets, **kwargs): filtered_df = datasets[excluded_columns] render_dataframe(filtered_df, kwargs["CONSOLE"]) # Render the filtered DataFrame - -def resume_logic(owi): - owi.datasets.transfer_status() - - def read_config(target): """ Reads the configuration from a file located in the specified target directory and returns @@ -152,26 +143,19 @@ def write_config(target, section, option, value): with open(config_path, 'w') as configfile: config.write(configfile) +class BaseCommand: - - -class DownloadManager: - def __init__(self, owi, max_retries=500, sleep=1, n_parallel=4, **kwargs): + def __init__(self, owi, **kwargs): self.owi = owi self.kwargs = kwargs self.console = kwargs["CONSOLE"] self.target = kwargs["TARGET"] self.autoyes = kwargs["AUTOYES"] self.n_parallel = kwargs.get("NPARALLEL", 4) - self.download_queue = Queue() - self.max_retries = max_retries - self.sleep = sleep - self.n_parallel = n_parallel def show_dataframe(self, dataframe): show_dataframe(dataframe, **self.kwargs) - def get_datasets_and_files(self, specifier, file_select, no_sync, details=False, return_files=False): """ Retrieve and analyze datasets based on a specified criteria. @@ -220,7 +204,8 @@ class DownloadManager: progress.update(task, advance=0, description=f"Listing files for {dataset['Title']}") try: # Fetch files from the remote dataset. - files = self.owi.datasets.files(dataset['InternalID'], dataset['Access'], zone=dataset['Zone'], + files = self.owi.datasets.files(dataset['InternalID'], dataset['Access'], + zone=dataset['Zone'], path_filter=file_select) files = files[files["Type"] == "file"] progress.update(task, advance=1, @@ -241,14 +226,14 @@ class DownloadManager: datasets.at[ix, "n_ciff"] = len(df_ciff) datasets.at[ix, "n_groups_parquet"] = df_parquet['Directory'].nunique() datasets.at[ix, "n_groups_ciff"] = df_ciff['Directory'].nunique() - datasets.at[ix, "n_to_sync"] = len(files[files['Local']=="*"]) + datasets.at[ix, "n_to_sync"] = len(files[files['Local'] == "*"]) # If required, collect file details for this dataset. if return_files: if no_sync: _dataset_files[dataset['InternalID']] = files else: - _dataset_files[dataset['InternalID']] = files[files["Local"]=="*"] + _dataset_files[dataset['InternalID']] = files[files["Local"] == "*"] except Exception as e: # Handle exceptions by setting negative counts. self.console.print( @@ -261,6 +246,13 @@ class DownloadManager: return datasets, _dataset_files + +class DownloadManager(BaseCommand): + def __init__(self, owi, max_retries=500, sleep=1, **kwargs): + super().__init__(owi, **kwargs) + self.max_retries = max_retries + self.sleep = sleep + def prepare_and_download_file(self, item, progress, prep_task): try: if "request" not in item or item["request"] is None: @@ -292,7 +284,7 @@ class DownloadManager: "preparation": _req is not None and _req.get("task_state")=="SUCCESS"} return item - def pull_file_based(self, specifier, file_select, no_sync, show_files, **kwargs): + def pull_file_based(self, specifier, file_select, no_sync, show_files): # Get files and datasets and user ok _datasets, _files = self.get_datasets_and_files(specifier, file_select, no_sync, details=True, return_files=True) @@ -313,8 +305,6 @@ class DownloadManager: _file_paths.add(_file["Path"]) _downloads.append({"dataset": _dataset, "file": _file, "request": None}) - - with Progress( TextColumn("[progress.description]{task.description}"), BarColumn(), @@ -354,9 +344,6 @@ class DownloadManager: return results - def __del__(self): - self.download_queue.put(None) # Signal to threads to exit - def _ask_or_raise(self, datasets, _files=None): # print datasets and ask for ok or autook self.console.print("Found the following datasets:") @@ -372,3 +359,41 @@ class DownloadManager: if not accept: raise UserWarning("User Aborted Dataset Download") + + +class DirectAccess(BaseCommand): + """ + the class provides direct access to the irods data (if irods is available) + """ + + def __init__(self, owi, **kwargs): + super().__init__(owi, **kwargs) + if self.owi.datasets.irods is None: + raise IOError("IRODS connection not available. Direct Access is not possible") + + + def duckdb_shell(self, specifier, file_select): + # Get files and datasets and user ok + self.console.print(f"Fetching filenames for {specifier} selectig files for {file_select}") + _datasets = self.owi.datasets.list_irods_datasets() + import duckdb as d + d.register_filesystem(self.owi.datasets.filesystem) + from IPython import embed + for _d in _datasets: + _d["files"] =["irods://"+i for i in self.owi.datasets.filesystem.glob(os.path.join(_d["path"], "**", file_select))] + ds = _datasets + self.console.print("Starting interactive shell. Duckdb is available as 'd' and 'ds' contains " + "available datasets and files. Example would be:\n "+ + """d.sql(f"Select url FROM read_parquet('{ds[-1]['files'][0]}') LIMIT 5").df()""" + ) + c = self.console + embed() + #_file = "irods:///IT4ILexisV2/public/proj862c5962623246664c1fda27b7afb108/5aa5c3dc-dc56-11ee-ad7e-0242c0a87004/metadata_2.parquet" + #parquet = set(_files[_files["Filename"].str.endswith(".parquet")]["Filename"]) + #from = "read_parquet(["+",".join([f"'{f}'" for f in _parquet])+"])" + #select = "Select * " + #self.show_dataframe(duckdb.sql(_select + " FROM " +_from + " LIMIT 5 " ).df()) + #self.show_dataframe(db.sql(f"SELECT url FROM read_parquet({_file}) LIMIT 5 ").df()) + + + diff --git a/owi/core/datasets.py b/owi/core/datasets.py index bffdda1..ce05968 100644 --- a/owi/core/datasets.py +++ b/owi/core/datasets.py @@ -29,14 +29,33 @@ def filter_by_date_range(df, start_date=None, end_date=None): class OWSData: - def __init__(self, project_name, session=None): + def __init__(self, project_name, session=None, lexis_id="proj862c5962623246664c1fda27b7afb108"): self.session =session if session is not None else LexisSession(in_cli=True) self.dscli = OWILexisDataset(self.session) + self.lexis_id = lexis_id self.__project_name = project_name def _to_datetime(self, date: str|datetime): return datetime.strptime(date, "%Y-%m-%d") if isinstance(date,str) else date + @property + def irods(self): + return self.dscli.irods + + @property + def filesystem(self): + return self.irods.filesystem + + def list_irods_datasets(self): + if self.irods is None: return [] + zone = self.irods.zone + datasets = self.irods.filesystem.ls(os.path.join("/", zone,"public",self.lexis_id)) # todo: make configurable + returns = [] + for d in datasets: + do = self.irods.session.collections.get(d) + returns.append({"metadata":{k:v for k,v in do.metadata.items()},"path":d}) + return returns + def ls(self, day: str|datetime|None=None, duration:int = 0, data_center=None, query=None): df = self.dscli.get_all_datasets(content_as_pandas=True) df= df[df["Project"] == self.__project_name] diff --git a/owi/core/irods.py b/owi/core/irods.py index 7571603..654d7de 100644 --- a/owi/core/irods.py +++ b/owi/core/irods.py @@ -7,13 +7,26 @@ from py4lexis.lexis_irods import iRODS class IRODSOWI(iRODS): - def __init__(selfl,session: LexisSession, + def __init__(self,session: LexisSession, suppress_print: bool=True): super().__init__(session, suppress_print) + self._fsspec_fs = None + + @property + def filesystem(self): + """ returns a fsspec filesystem via lazy initialisation""" + if self._fsspec_fs is None: + import fsspec + import irods_fsspec + irods_fsspec.register() + self._fsspec_fs = fsspec.filesystem("irods", session=self.session) + return self._fsspec_fs + + @property + def zone(self): + return self._iRODS__irods.zone + + @property + def session(self): + return self._iRODS__irods - def test(self): - print("in test for irods. unclear whether we can access files directly here") - coll = self._iRODS__irods.collections.get("/IT4ILexisV2/public/proj862c5962623246664c1fda27b7afb108") - for col in coll.subcollections: - print(col) - #self._iRODS__irods.data_objects.get("/IT4ILexisV2/public/proj862c5962623246664c1fda27b7afb108/"+) diff --git a/owi/core/lexis.py b/owi/core/lexis.py index 560e605..af78b6c 100644 --- a/owi/core/lexis.py +++ b/owi/core/lexis.py @@ -26,10 +26,8 @@ class OWILexisDataset(Datasets): self.max_retries = max_retries try: self.irods = IRODSOWI(session) - 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