diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6e6af53..d1c6ad4 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -19,7 +19,7 @@ repos: - --maxkb=2048 - id: trailing-whitespace - repo: https://github.com/psf/black - rev: 21.8b0 + rev: 22.3.0 hooks: - id: black - repo: https://github.com/pycqa/isort diff --git a/environment.yml b/environment.yml index fe3011d..ebcd47c 100644 --- a/environment.yml +++ b/environment.yml @@ -17,6 +17,7 @@ dependencies: - pytest-cov - pytorch - pyyaml + - osfclient - pip : - git+https://github.com/compSPI/simSPI.git - starfile diff --git a/ioSPI/datasets.py b/ioSPI/datasets.py index fa82093..8ea891b 100644 --- a/ioSPI/datasets.py +++ b/ioSPI/datasets.py @@ -1,36 +1,58 @@ """Module to house methods related to datasets (micrographs, meta-data, etc.).""" +import io import os -import typing -from pathlib import Path +import subprocess -import requests +class OSFProject: + """Class to list, download and upload data in an OSF project. -class Project: - """Class to list, download and upload data from OSF. + It uses osfclient library. Parameters ---------- - username : str + username : str, default = None Username corresponding to an account on OSF. E.g. email address used to create an OSF account. - token : str - Personal token from OSF.io. + token : str, default = None + Personal token from osf.io. See: https://osf.io/settings/tokens - project_id : str, default = "7g42j" + project_id : str, default = "xbr2m" Identifier of the project, found on the OSF project page. - E.g. 7g42j for project at https://osf.io/7g42j/ + E.g. xbr2m for project at https://osf.io/xbr2m/ + storage : str, default = "osfstorage" + Storage provider of the project. + osfclient_path : str, default = None See Also -------- + osfclient: https://github.com/osfclient/osfclient OSF API documentation : https://developer.osf.io/ """ - def __init__(self, username: str, token: str, project_id: str = "7g42j") -> None: + def __init__( + self, + username: str = None, + token: str = None, + project_id: str = "xbr2m", + storage: str = "osfstorage", + osfclient_path: str = None, + ) -> None: + if username is None: + raise TypeError("username must be provided.") self.username = username + + if token is None: + raise TypeError("token must be provided.") self.token = token + self.project_id = project_id + self.storage = storage + self.osfclient_path = osfclient_path + self.osfclient_command = "osf " + if osfclient_path is not None: + self.osfclient_command = self.osfclient_path + self.osfclient_command config_path = os.path.join(".osfcli.config") with open(config_path, "w") as out_file: @@ -43,30 +65,47 @@ def __init__(self, username: str, token: str, project_id: str = "7g42j") -> None def ls(self): """List all files in the project.""" print(f"Listing files from OSF project: {self.project_id}...") - os.system("osf ls") + return subprocess.run( + self.osfclient_command + "ls", + shell=True, + text=True, + check=True, + stdout=subprocess.PIPE, + ).stdout - @staticmethod - def download(remote_path, local_path): - """Download file from osf and save it locally. + def download(self, remote_path: str = None, local_path: str = None): + """Download a file from an OSF project and save it locally. Parameters ---------- - remote_path : str - Remote path of the file on OSF. + remote_path : str, default = None + Remote path of the file in an OSF project, + which will be appended to the project storage name (by default, osfstorage). E.g. osfstorage/ randomrot1D_nodisorder/ 4v6x_randomrot_copy6_defocus3.0_yes_noise.txt - local_path : str + local_path : str, default = None Local path where the file will be saved. E.g. 4v6x_randomrot_copy6_defocus3.0_yes_noise.txt """ - print(f"Downloading {remote_path} to {local_path}...") - os.system(f"osf fetch {remote_path} {local_path}") + if remote_path is None: + raise TypeError("remote_path must be provided.") + if local_path is None: + raise TypeError("local_path must be provided.") + + full_remote_path = self.storage + "/" + remote_path + print(f"Downloading {full_remote_path} to {local_path}...") + subprocess.run( + self.osfclient_command + f"fetch {full_remote_path} {local_path}", + shell=True, + text=True, + check=True, + stdout=subprocess.PIPE, + ) print("Done!") - @staticmethod - def upload(remote_path, local_path): - """Upload file to osf. + def upload(self, local_path: str = None, remote_path: str = None): + """Upload a file to an OSF project. Notes ----- @@ -74,182 +113,55 @@ def upload(remote_path, local_path): Parameters ---------- - remote_path : str - Remote path of the file on OSF. + local_path : str, default = None + Local path where the file will be saved. + E.g. 4v6x_randomrot_copy6_defocus3.0_yes_noise.txt + remote_path : str, default = None + Remote path of the file in an OSF project, + which will be appended to the project storage name (by default, osfstorage). E.g. osfstorage/ randomrot1D_nodisorder/ 4v6x_randomrot_copy6_defocus3.0_yes_noise.txt - local_path : str - Local path where the file will be saved. - E.g. 4v6x_randomrot_copy6_defocus3.0_yes_noise.txt """ - print(f"Uploading {local_path} to {remote_path}...") - os.system(f"osf upload {local_path} {remote_path}") + if local_path is None: + raise TypeError("local_path must be provided.") + if remote_path is None: + raise TypeError("remote_path must be provided.") + + full_remote_path = self.storage + "/" + remote_path + print(f"Uploading {local_path} to {full_remote_path}...") + f = subprocess.run( + self.osfclient_command + f"upload {local_path} " f"{full_remote_path}", + shell=True, + text=True, + check=True, + stdout=subprocess.PIPE, + ).stdout + print(io.StringIO(f).readlines()) print("Done!") - -class OSFUpload: - """Class to upload datasets to OSF.io. - - Parameters - ---------- - token : str - Personal token from OSF.io with access to dataset (e.g. cryoEM, etc). - data_node_guid : str, default = "24htr" - OSF GUID of data node that houses dataset. - - Attributes - ---------- - headers : dict of type str:str - Headers containing authorisation token for requests. - base_url : str - OSF.io API url base. - data_node_guid : str - OSF GUID of data node that houses dataset. - - See Also - -------- - OSF API documentation : https://developer.osf.io/ - """ - - def __init__(self, token: str, data_node_guid: str = "24htr") -> None: - - self.headers = {"Authorization": f"Bearer {token}"} - self.base_url = "https://api.osf.io/v2/" - - requests.get(self.base_url, headers=self.headers).raise_for_status() - - self.data_node_guid = data_node_guid - - def read_structure_guid(self, structure_label: str) -> str: - """Return GUID of OSF node for structures with given label. - - If no existing node is found, returns none. - + def remove(self, remote_path: str = None): + """Remove a file in an OSF project. Parameters ---------- - structure_label:str - Structure ID from PDB or EMDB used for generating data. - - Returns - ------- - GUID of structure node on OSF.io - - See Also - -------- - Protein Data Bank(PDB) : https://www.rcsb.org/ - EM Data Resource(EMDB) : https://www.emdataresource.org/ - """ - existing_structures = self.read_existing_structure_labels() - if structure_label not in existing_structures: - return None - return existing_structures[structure_label] - - def write_child_node( - self, parent_guid: str, title: str, tags: typing.Optional[str] = None - ) -> str: - """Write a new child node in OSF.io. - - Parameters - ---------- - parent_guid:str - GUID of parent node. - title:str - Title of child node. - tags: list[sr], optional - Tags of child node. - - Returns - ------- - str - GUID of newly created child node. - - Raises - ------ - HTTPError - Raised if POST request to OSF.io fails. + remote_path : str, default = None + Remote path of the file to remove in an OSF project, + which will be appended to the project storage name (by default, osfstorage). + E.g. osfstorage/ + randomrot1D_nodisorder/ + 4v6x_randomrot_copy6_defocus3.0_yes_noise.txt """ - request_url = f"{self.base_url}nodes/{parent_guid}/children/" - - request_body = { - "type": "nodes", - "attributes": {"title": title, "category": "data", "public": True}, - } - - if tags is not None: - request_body["attributes"]["tags"] = tags - - response = requests.post( - request_url, headers=self.headers, json={"data": request_body} + if remote_path is None: + raise TypeError("remote_path must be provided.") + + full_remote_path = self.storage + "/" + remote_path + print(f"Removing {full_remote_path} in the project...") + subprocess.run( + self.osfclient_command + f"remove {full_remote_path}", + shell=True, + text=True, + check=True, + stdout=subprocess.PIPE, ) - response.raise_for_status() - return response.json()["data"]["id"] - - def read_existing_structure_labels(self) -> typing.Dict[str, str]: - """Get labels and GUIDs of structural nodes in OSF dataset. - - Returns - ------- - dict of type str : str - Returns dictionary of node labels mapped to node GUIDs. - - Raises - ------ - HTTPError - Raised if GET request to OSF.io fails. - """ - request_url = f"{self.base_url}nodes/{self.data_node_guid}/children/" - response = requests.get(request_url, headers=self.headers) - response.raise_for_status() - dataset_node_children = response.json()["data"] - - existing_structures = { - child["attributes"]["title"]: child["id"] for child in dataset_node_children - } - - return existing_structures - - def write_files(self, dataset_guid: str, file_paths: typing.List[str]): - """Post files to a node in OSF.io. - - Parameters - ---------- - dataset_guid : str - GUID of node where file is to be uploaded. - file_paths : list[str] - File paths of files to be uploaded. - - Returns - ------- - bool - True if all uploads are successful, false otherwise. - """ - files_base_url = "http://files.ca-1.osf.io/v1/resources/" - create_request_url = f"{files_base_url}{dataset_guid}/providers/osfstorage/" - success = True - - for file_path_string in file_paths: - file_path = Path(file_path_string) - - query_parameters = f"?kind=file&name={file_path.name}" - response = requests.put( - create_request_url + query_parameters, headers=self.headers - ) - response.raise_for_status() - - data_upload__url = response.json()["data"]["links"]["upload"] - - with open(file_path, "rb") as file_content: - response = requests.put( - data_upload__url, data=file_content, headers=self.headers - ) - response.raise_for_status() - - if not response.ok: - print(f"Upload {file_path} failed with code {response.status_code}") - success = False - else: - print(f"Uploaded {file_path} ") - - return success + print("Done!") diff --git a/notebooks/download_and_upload_with_osf.ipynb b/notebooks/download_and_upload_with_osf.ipynb index 5d7a49c..ef51b77 100644 --- a/notebooks/download_and_upload_with_osf.ipynb +++ b/notebooks/download_and_upload_with_osf.ipynb @@ -11,15 +11,11 @@ "source": [ "# Download and Upload with OSF\n", "\n", - "This tutorial shows how to download and upload cryo-EM datasets using the `datasets` module from `ioSPI`, that interact with the [Open Science Foundation (OSF)](https://osf.io/) framework.\n", + "This tutorial shows how to download and upload cryo-EM datasets using the `datasets` module from `ioSPI`, which interact with the [Open Science Foundation (OSF)](https://osf.io/) framework. We will also learn how to list and remove files.\n", "\n", "OSF is an initiative that aims to increase the openness, reproducibility and integrity of scientific research. Among other functionalities, it is possible to upload scientific data which can be accessed by an Application Programming Interface (API). \n", "\n", - "``ioSPI`` offers functionalities that allow uploading and accessing cryo-EM data using:\n", - "- either, in order to get started: using the class `Project` that leverages the package `osfclient`\n", - "- or, if the user requires finer control: using the class `OSFUpload` which follows `OSF APIv2`. \n", - "\n", - "This tutorial introduces both options." + "`ioSPI` offers functionalities that allow uploading and accessing cryo-EM data using the class `OSFProject` that leverages the package `osfclient`." ] }, { @@ -31,7 +27,7 @@ } }, "source": [ - "# Set-up" + "# Setup" ] }, { @@ -43,9 +39,9 @@ } }, "source": [ - "First, you will need to get setup with osf.\n", + "First, you will need to get setup with OSF.\n", "\n", - "- Create an account on https://osf.io/ and save the email address you use.\n", + "- Create an account on and save the email address you use.\n", "- On this account, create a personal token in [Settings](https://osf.io/settings/tokens) and save it.\n", "\n", "The email address and the token will be needed to connect to different OSF projects.\n", @@ -55,31 +51,17 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 3, "id": "e74dd634", "metadata": { "pycharm": { "name": "#%%\n" } }, - "outputs": [ - { - "ename": "ModuleNotFoundError", - "evalue": "No module named 'ioSPI'", - "output_type": "error", - "traceback": [ - "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", - "\u001B[0;31mModuleNotFoundError\u001B[0m Traceback (most recent call last)", - "Input \u001B[0;32mIn [1]\u001B[0m, in \u001B[0;36m\u001B[0;34m()\u001B[0m\n\u001B[1;32m 1\u001B[0m \u001B[38;5;66;03m# Temp for non-conda. Remove later.\u001B[39;00m\n\u001B[1;32m 2\u001B[0m \u001B[38;5;66;03m# import sys\u001B[39;00m\n\u001B[1;32m 3\u001B[0m \u001B[38;5;66;03m# sys.path.append('../../')\u001B[39;00m\n\u001B[0;32m----> 6\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mioSPI\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m datasets\n", - "\u001B[0;31mModuleNotFoundError\u001B[0m: No module named 'ioSPI'" - ] - } - ], + "outputs": [], "source": [ - "# Temp for non-conda. Remove later.\n", - "# import sys\n", - "# sys.path.append('../../')\n", - "\n", + "import sys\n", + "sys.path.append('../')\n", "\n", "from ioSPI import datasets" ] @@ -119,14 +101,14 @@ "source": [ "Find the OSF project from which you wish to download your data. \n", "\n", - "In this tutorial, we use a project called \"cryoEM simulated\" which contains simulated images from the 80s human ribosome. This project is on osf at the url: \"https://osf.io/7g42j/\".\n", + "In this tutorial, we use a project called \"simSPI\" which is a dummy project for testing. This project is on OSF at the url: .\n", "\n", "- Save the ID of the project of interest, which appears in the project's url.\n", "\n", - "In our case, the project ID is `7g42j`.\n", + "In our case, the project ID is `xbr2m`.\n", "\n", - "- Create an object from the class `Project` using:\n", - " - your credentials from the set up: email address and token,\n", + "- Create an object from the class `OSFProject` using:\n", + " - your credentials from the setup: email address and token,\n", " - the project ID that you just saved." ] }, @@ -149,10 +131,10 @@ } ], "source": [ - "cryoem_simulated_project = datasets.Project(\n", + "osf_project = datasets.OSFProject(\n", " username=\"ninamio78@gmail.com\", \n", " token=\"HBGGBOJcLYQfadEKIOyXJiLTum3ydXK4nGP3KmbkYUeBuYkZma9LPBSYennQn92gjP2NHn\",\n", - " project_id=\"7g42j\")" + " project_id=\"xbr2m\")" ] }, { @@ -166,14 +148,14 @@ "source": [ "You have successfully set up the configuration of the OSF project!\n", "\n", - "## List Files on the OSF Project\n", + "## List Files in the OSF Project\n", "\n", - "Now you can list the files available on this OSF project. Note that this code can take a few minutes to run." + "Now you can list the files available in this OSF project." ] }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 9, "id": "f4f5b054", "metadata": { "pycharm": { @@ -185,2129 +167,13 @@ "name": "stdout", "output_type": "stream", "text": [ - "Listing files from OSF project: 7g42j...\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy9_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy9_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy6_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy6_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy6_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy9_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy9_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy6_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy9_defocus1.5_yes_noise.h5\n", - 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"osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy3_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy2_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy9_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy3_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy8_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy9_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy9_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy9_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy3_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy9_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy8_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy5_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy4_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy4_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy8_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy6_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy8_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy4_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy8_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy5_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy1_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy8_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy4_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy4_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy8_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy5_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy6_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy8_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy9_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy8_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy8_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy4_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy3_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy4_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy9_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy2_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy9_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy1_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy1_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy1_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy4_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy1_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy3_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy4_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy5_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy9_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy8_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy8_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy4_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy1_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy1_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy4_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy2_defocus2.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy6_defocus2.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy1_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy1_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy1_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy4_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus1.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy8_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy2_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy9_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy6_defocus1.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus1.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus3.0_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus2.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy5_defocus2.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy9_defocus0.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy4_defocus1.5_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy9_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy3_defocus3.0_yes_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus0.5_no_noise.h5\n", - "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy6_defocus1.5_no_noise.h5\n" + "Listing files from OSF project: xbr2m...\n", + "osfstorage/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\n" ] } ], "source": [ - "cryoem_simulated_project.ls()" + "osf_project.ls()" ] }, { @@ -2319,18 +185,18 @@ } }, "source": [ - "We observe that this project contains many files, organized in different folders.\n", + "We observe that this project contains one file in a directory called `osfstorage`. This is a default storage used in an OSF project. We don't have to worry about this for now.\n", "\n", " ## Download Files from the OSF Project\n", "\n", - "We can download one of these files, e.g. choosing from the above list the following txt file:\n", + "We can download one of these files, e.g., choosing from the above list the following txt file:\n", "\n", - "- `osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt`.\n" + "- `4v6x_randomrot_copy0_defocus3.0_yes_noise.txt`.\n" ] }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 10, "id": "6f5270f4", "metadata": { "pycharm": { @@ -2342,7 +208,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Downloading osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt to 4v6x_randomrot_copy0_defocus3.0_yes_noise.txt...\n", + "Downloading osfstorage/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt to 4v6x_randomrot_copy0_defocus3.0_yes_noise.txt...\n", "Done!\n" ] }, @@ -2350,13 +216,13 @@ "name": "stderr", "output_type": "stream", "text": [ - "100%|██████████| 4.22k/4.22k [00:00<00:00, 19.1Mbytes/s]\n" + "100%|██████████| 4.22k/4.22k [00:00<00:00, 18.0Mbytes/s]\n" ] } ], "source": [ - "cryoem_simulated_project.download(\n", - " remote_path=\"osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\", \n", + "osf_project.download(\n", + " remote_path=\"4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\",\n", " local_path=\"4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\")" ] }, @@ -2369,7 +235,9 @@ } }, "source": [ - "## Upload Files to an OSF Project" + "You can check if the file is downloaded in the current working directory.\n", + "\n", + "## Upload Files to the OSF Project" ] }, { @@ -2381,25 +249,23 @@ } }, "source": [ - "Importantly, OSF will not let you upload data to any folder: authorization is requested.\n", + "Importantly, OSF will not let you upload data to any folder: authorization is required.\n", "\n", - "To test this functionality, you can create a new project through osf.io (https://osf.io/myprojects/) by clicking: `Create project`.\n", + "To test this functionality, you can create a new project through osf.io by clicking: `Create Project`.\n", "\n", "This will create a new project page, as the one we are using here.\n", "- Save the project ID of the project you just created!\n", "\n", - "You should then create a new `my_project` object of the class `datasets.Project` with the new project ID.\n", - "\n", - "For the purpose of this tutorial, however, we will stay with our original project cryoEM simulated and use our object `cryoem_simulated_project`.\n", + "You should then create a new `my_project` object of the class `datasets.OSFProject` with the new project ID.\n", "\n", - "We re-upload the file that we just downloaded, renaming it by adding a `new_version` prefix to its name. We will first create a child node inside the parent node which corresponds to our root directory. Then, we will upload the file to ths child node.\n", + "For the purpose of this tutorial, however, we will stay with our original project and use our object `osf_project`.\n", "\n", - "To do this, let's create an instance of ``OSFUpload`` class which takes care of uploading data to ``osf.io``. Provide the personal token and project ID." + "We re-upload the file that we just downloaded, renaming it by adding a `new_version` prefix to its name." ] }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 11, "id": "74c6125e", "metadata": { "pycharm": { @@ -2411,19 +277,19 @@ "name": "stdout", "output_type": "stream", "text": [ - "{'Authorization': 'Bearer HBGGBOJcLYQfadEKIOyXJiLTum3ydXK4nGP3KmbkYUeBuYkZma9LPBSYennQn92gjP2NHn'}\n" + "Uploading 4v6x_randomrot_copy0_defocus3.0_yes_noise.txt to osfstorage/new_version_4v6x_randomrot_copy0_defocus3.0_yes_noise.txt...\n", + "Done!\n" ] } ], "source": [ - "osf = datasets.OSFUpload(token=cryoem_simulated_project.token, data_node_guid=cryoem_simulated_project.project_id)\n", - "print(osf.headers)" + "osf_project.upload(\"4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\", \"new_version_4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\")" ] }, { "cell_type": "markdown", "source": [ - "Now we create a child node inside the parent node, for representing the dataset with 80s ribosome data. We will use the pdb id as the name for this new node, and the function will return its ID. Since the child is also a node, it can be accessed separately from the parent node." + "Let's check if the upload was successful by listing the files in the OSF project." ], "metadata": { "collapsed": false, @@ -2434,20 +300,20 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 12, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "64cx2\n" + "Listing files from OSF project: xbr2m...\n", + "osfstorage/new_version_4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\n", + "osfstorage/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\n" ] } ], "source": [ - "pdb_id = '4v6x'\n", - "child_guid = osf.write_child_node(parent_guid=cryoem_simulated_project.project_id, title= pdb_id)\n", - "print(child_guid)" + "osf_project.ls()" ], "metadata": { "collapsed": false, @@ -2459,38 +325,34 @@ { "cell_type": "markdown", "source": [ - "Now, we finally upload the files related to the 80s ribosome to the child node using ``write_files`` function. Note the ``file_paths`` must be a list, thus ``[]`` is needed around the filepaths." + "You should see the file `new_version_4v6x_randomrot_copy0_defocus3.0_yes_noise.txt` in the list.\n", + "\n", + "## Remove Files in the OSF Project\n", + "\n", + "Finally, let's tidy up the project by removing the file we uploaded.\n" ], "metadata": { "collapsed": false, "pycharm": { "name": "#%% md\n" } - }, - "outputs": [] + } }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 13, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "Uploaded 4v6x_randomrot_copy0_defocus3.0_yes_noise.txt \n" + "Removing osfstorage/new_version_4v6x_randomrot_copy0_defocus3.0_yes_noise.txt in the project...\n", + "Done!\n" ] - }, - { - "data": { - "text/plain": "True" - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" } ], "source": [ - "osf.write_files(child_guid, [\"4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\"])" + "osf_project.remove(\"new_version_4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\")" ], "metadata": { "collapsed": false, @@ -2502,7 +364,7 @@ { "cell_type": "markdown", "source": [ - "We can now check if it was uploaded correctly using the function `read_structure_guid` which will return an ID corresponding to the pdb id passed as a parameter." + "Check if the file was removed." ], "metadata": { "collapsed": false, @@ -2513,19 +375,19 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 14, "outputs": [ { - "data": { - "text/plain": "'ezh4k'" - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" + "name": "stdout", + "output_type": "stream", + "text": [ + "Listing files from OSF project: xbr2m...\n", + "osfstorage/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\n" + ] } ], "source": [ - "osf.read_structure_guid(pdb_id)" + "osf_project.ls()" ], "metadata": { "collapsed": false, @@ -2537,7 +399,9 @@ { "cell_type": "markdown", "source": [ - "Congratulations! You have successfully downloaded and uploaded data from/to OSF." + "You should see that the file was removed from the project.\n", + "\n", + "Brilliant! Now you know how to upload, download, list and remove files in an OSF project!" ], "metadata": { "collapsed": false, @@ -2549,9 +413,9 @@ ], "metadata": { "kernelspec": { - "name": "venv_iospi", + "name": "python3", "language": "python", - "display_name": "venv_iospi" + "display_name": "Python 3 (ipykernel)" }, "language_info": { "codemirror_mode": { diff --git a/tests/test_datasets.py b/tests/test_datasets.py index c0562c1..f69f7e9 100644 --- a/tests/test_datasets.py +++ b/tests/test_datasets.py @@ -1,168 +1,148 @@ -"""Tests for osf_upload.""" +"""Unit tests for listing/uploading/downloading datasets on an OSF project. + +These assume the tests are executed in a Conda environment and GitHub actions +when tested non-locally. +""" + +import io import os import random import string -from pathlib import Path +import subprocess import pytest -import requests from ioSPI import datasets @pytest.fixture(autouse=True, scope="session") -def setup_teardown(): - """Test node creation and clean-up for tests.""" - token = os.environ["TEST_TOKEN"] - request_headers = {"Authorization": f"Bearer {token}"} - base_api_url = "https://api.osf.io/v2/nodes/" - - test_node_label = "test_" + "".join( - random.choice(string.ascii_letters) for i in range(5) +def setup(): + """Set up for tests.""" + print("Creating a test project for dataset") + project = datasets.OSFProject( + username="ninamio78@gmail.com", + token="HBGGBOJcLYQfadEKIOyXJiLTum3ydXK4nGP3KmbkYUeBuYkZma9LPBSYennQn92gjP2NHn", + project_id="xbr2m", + osfclient_path="$CONDA/bin/", ) + yield project - print(f"Creating test node Dataset -> internal -> {test_node_label} ") - - internal_node_guid = "9jwpu" - request_url = f"{base_api_url}{internal_node_guid}/children/" - - request_body = { - "type": "nodes", - "attributes": {"title": test_node_label, "category": "data"}, - } - - response = requests.post( - request_url, headers=request_headers, json={"data": request_body} - ) - response.raise_for_status() - pytest.auth_token = token - pytest.test_node_guid = response.json()["data"]["id"] - pytest.test_node_label = test_node_label - pytest.request_headers = request_headers - pytest.base_api_url = base_api_url - - yield - - print( - f"\nDeleting test node Dataset -> internal -> " - f"{test_node_label} and its sub-components." +@pytest.fixture(autouse=True, scope="session") +def set_file_path(): + """Set up a temporary text file path for upload. + + Set local_testing = True when testing locally, False if on GitHub. + """ + file_path = "tests/data/" + local_testing = False + if not local_testing: + file_path = "/home/runner/work/ioSPI/ioSPI/" + file_path + + file_name = ( + "test_upload-" + + "".join(random.choice(string.ascii_letters) for i in range(5)) + + ".txt" ) - cleanup(pytest.test_node_guid, test_node_label) - - -def cleanup(node_guid, test_node_label): - """Recursively delete nodes and subcomponents.""" - base_node_url = f"{pytest.base_api_url}{node_guid}/" + return file_path, file_name - response = requests.get(f"{base_node_url}children/", headers=pytest.request_headers) - response.raise_for_status() - for node_child in response.json()["data"]: - cleanup(node_child["id"], node_child["attributes"]["title"]) +@pytest.fixture(autouse=True, scope="session") +def create_test_file(set_file_path): + """Create a temporary text file for upload.""" + with open(set_file_path[0] + set_file_path[1], "w") as f: + f.write("Hello World!") - response = requests.delete(base_node_url, headers=pytest.request_headers) - if not response.ok: - print( - f"Failure: {test_node_label} could not be" - f" deleted due to error code {response.status_code}." - ) - print(response.json()["errors"][0]["detail"]) - else: - print(f"Success: {test_node_label} deleted") +def test_constructor_valid(): + """Test the constructor.""" + project = datasets.OSFProject( + username="ninamio78@gmail.com", + token="HBGGBOJcLYQfadEKIOyXJiLTum3ydXK4nGP3KmbkYUeBuYkZma9LPBSYennQn92gjP2NHn", + ) + assert project.username is not None + assert project.token is not None + assert project.project_id is not None + assert project.storage is not None -@pytest.fixture -def mock_osf_upload(): - """Return OSFUpload for testing.""" - return datasets.OSFUpload(pytest.auth_token, pytest.test_node_guid) +def test_constructor_invalid_because_no_username(): + """Test if an error is raised when no username is provided to the constructor.""" + with pytest.raises(TypeError): + datasets.OSFProject(token="token") -@pytest.fixture -def create_upload_file(tmp_path): - """Create temporary text file for upload.""" - file_path = Path(tmp_path, "test_upload_1.txt") - with open(file_path, "w") as f: - f.write("Hello World") - return file_path +def test_constructor_invalid_because_no_token(): + """Test if an error is raised when no token is provided to the constructor.""" + with pytest.raises(TypeError): + datasets.OSFProject(username="username") -def test_constructor(): - """Test constructor populates class attributes.""" - test_class = datasets.OSFUpload(pytest.auth_token) +def test_upload_valid(setup, set_file_path): + """Test the upload method.""" + setup.upload(set_file_path[0] + set_file_path[1], set_file_path[1]) + file_exists = False + file_list = setup.ls() + file_list = io.StringIO(file_list) + line = file_list.readline() + while line: + file_exists = set_file_path[1] == line.split("/")[1].strip() + if file_exists: + break + line = file_list.readline() - assert test_class.headers is not None - assert test_class.base_url is not None - assert test_class.data_node_guid is not None + assert file_exists + subprocess.run(f"rm {set_file_path[0]}{set_file_path[1]}", shell=True, check=True) -def test_write_child_node(mock_osf_upload): - """Test whether nodes are created.""" - test_node_label = "test_write_child_node" + "".join( - random.choice(string.ascii_letters) for i in range(5) - ) - returned_guid = mock_osf_upload.write_child_node( - pytest.test_node_guid, test_node_label - ) - response = requests.get( - f"{pytest.base_api_url}{returned_guid}", headers=pytest.request_headers - ) - assert test_node_label == response.json()["data"]["attributes"]["title"] +def test_upload_invalid_because_no_local_path(setup): + """Test if an error is raised when no local_path is provided.""" + with pytest.raises(TypeError): + setup.upload(remote_path="remote_path") -def test_read_existing_structure_labels(mock_osf_upload): - """Test if uploaded test node is retrieved.""" - request_url = f"{pytest.base_api_url}{pytest.test_node_guid}/children/" - test_node_label = "test_read_existing_structure_labels_" + "".join( - random.choice(string.ascii_letters) for i in range(5) - ) - request_body = { - "type": "nodes", - "attributes": {"title": test_node_label, "category": "data"}, - } +def test_upload_invalid_because_no_remote_path(setup): + """Test if an error is raised when no remote_path is provided.""" + with pytest.raises(TypeError): + setup.upload(local_path="local_path") - requests.post( - request_url, headers=pytest.request_headers, json={"data": request_body} - ).raise_for_status() - assert test_node_label in mock_osf_upload.read_existing_structure_labels() +def test_download_valid(setup, set_file_path): + """Test the download method.""" + setup.download(set_file_path[1], set_file_path[0] + set_file_path[1]) + assert os.path.exists(set_file_path[0] + set_file_path[1]) + subprocess.run(f"rm {set_file_path[0]}{set_file_path[1]}", shell=True, check=True) -def test_read_structure_guid(mock_osf_upload): - """Test if valid guid is returned for a structure's label.""" - test_node_label = "test_read_structure_guid" + "".join( - random.choice(string.ascii_letters) for i in range(5) - ) +def test_download_invalid_because_no_remote_path(setup): + """Test if an error is raised when no remote_path is provided.""" + with pytest.raises(TypeError): + setup.download(local_path="local_path") - returned_guid = mock_osf_upload.read_structure_guid(test_node_label) - assert returned_guid is None - request_url = f"{pytest.base_api_url}{pytest.test_node_guid}/children/" - request_body = { - "type": "nodes", - "attributes": {"title": test_node_label, "category": "data", "public": True}, - } - response = requests.post( - request_url, headers=pytest.request_headers, json={"data": request_body} - ) - response.raise_for_status() +def test_download_invalid_because_no_local_path(setup): + """Test if an error is raised when no local_path is provided.""" + with pytest.raises(TypeError): + setup.download(remote_path="remote_path") - assert response.json()["data"]["id"] == mock_osf_upload.read_structure_guid( - test_node_label - ) +def test_remove_valid(setup, set_file_path): + """Test the remove method.""" + setup.remove(set_file_path[1]) + file_exists = False + file_list = setup.ls() + file_list = io.StringIO(file_list) + line = file_list.readline() + while line: + file_exists = set_file_path[1] == line.split("/")[1].strip() + if file_exists: + break + line = file_list.readline() -def test_write_files(mock_osf_upload, create_upload_file): - """Test whether files are uploaded to OSF.""" - assert mock_osf_upload.write_files(pytest.test_node_guid, [str(create_upload_file)]) - - response = requests.get( - f"{pytest.base_api_url}{pytest.test_node_guid}/files/osfstorage/", - headers=pytest.request_headers, - ) + assert not file_exists - response.raise_for_status() - parsed_response = response.json()["data"][0] - assert Path(create_upload_file).name == parsed_response["attributes"]["name"] +def test_remove_invalid_because_no_remote_path(setup): + """Test if an error is raised when no remote_path is provided.""" + with pytest.raises(TypeError): + setup.remove()