seer-pas-sdk 0.1.2__tar.gz → 0.2.1__tar.gz

{seer_pas_sdk-0.1.2 → seer_pas_sdk-0.2.1}/.github/workflows/lint.yml

@@ -7,11 +7,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.8
+      - name: Set up Python
         uses: actions/setup-python@v2
         with:
           python-version: "3.8"
-      - uses: psf/black@stable
+      - uses: psf/black@24.8.0  # last release that supports 3.8
       - name: Install dependencies
         run: pip install . flake8
       - name: Lint with flake8
@@ -20,3 +20,9 @@ jobs:
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Run Bandit
+        uses: tj-actions/bandit@v5.5
+        with:
+          targets: "./seer_pas_sdk/"
+          options: "-r --severity-level=high"
+        

{seer_pas_sdk-0.1.2 → seer_pas_sdk-0.2.1}/.github/workflows/publish.yml

@@ -41,8 +41,7 @@ jobs:
         uses: quarto-dev/quarto-actions/setup@v2
       - name: Set up QuartoDoc + Jupyter
 
-        # TODO: remove upper bound on quartodoc and griffe after fix for machow/quartodoc#357 is released
-        run: pip install 'quartodoc>=0.7.0,<=0.7.5' 'griffe<1.0.0' jupyter
+        run: pip install 'quartodoc>=0.7.6' jupyter
 
       - name: Install seer-pas-sdk
         run: pip install .  # Install SDK libs so quartodoc can find them

{seer_pas_sdk-0.1.2 → seer_pas_sdk-0.2.1}/.gitignore

@@ -80,6 +80,7 @@ docs/_build/
 doc/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook

seer_pas_sdk-0.2.1/PKG-INFO

@@ -0,0 +1,230 @@
+Metadata-Version: 2.4
+Name: seer-pas-sdk
+Version: 0.2.1
+Summary: SDK for Seer Proteograph Analysis Suite (PAS)
+Author-email: Ryan Sun <rsun@seer.bio>
+License: 
+                                         Apache License
+                                   Version 2.0, January 2004
+                                http://www.apache.org/licenses/
+        
+           TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+        
+           1. Definitions.
+        
+              "License" shall mean the terms and conditions for use, reproduction,
+              and distribution as defined by Sections 1 through 9 of this document.
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+              direction or management of such entity, whether by contract or
+              otherwise, or (ii) ownership of fifty percent (50%) or more of the
+              outstanding shares, or (iii) beneficial ownership of such entity.
+        
+              "You" (or "Your") shall mean an individual or Legal Entity
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+        
+           2. Grant of Copyright License. Subject to the terms and conditions of
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+              the conditions stated in this License.
+        
+           5. Submission of Contributions. Unless You explicitly state otherwise,
+              any Contribution intentionally submitted for inclusion in the Work
+              by You to the Licensor shall be under the terms and conditions of
+              this License, without any additional terms or conditions.
+              Notwithstanding the above, nothing herein shall supersede or modify
+              the terms of any separate license agreement you may have executed
+              with Licensor regarding such Contributions.
+        
+           6. Trademarks. This License does not grant permission to use the trade
+              names, trademarks, service marks, or product names of the Licensor,
+              except as required for reasonable and customary use in describing the
+              origin of the Work and reproducing the content of the NOTICE file.
+        
+           7. Disclaimer of Warranty. Unless required by applicable law or
+              agreed to in writing, Licensor provides the Work (and each
+              Contributor provides its Contributions) on an "AS IS" BASIS,
+              WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
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+              PARTICULAR PURPOSE. You are solely responsible for determining the
+              appropriateness of using or redistributing the Work and assume any
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+        
+           8. Limitation of Liability. In no event and under no legal theory,
+              whether in tort (including negligence), contract, or otherwise,
+              unless required by applicable law (such as deliberate and grossly
+              negligent acts) or agreed to in writing, shall any Contributor be
+              liable to You for damages, including any direct, indirect, special,
+              incidental, or consequential damages of any character arising as a
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+              Work (including but not limited to damages for loss of goodwill,
+              work stoppage, computer failure or malfunction, or any and all
+              other commercial damages or losses), even if such Contributor
+              has been advised of the possibility of such damages.
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+           9. Accepting Warranty or Additional Liability. While redistributing
+              the Work or Derivative Works thereof, You may choose to offer,
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+              on Your own behalf and on Your sole responsibility, not on behalf
+              of any other Contributor, and only if You agree to indemnify,
+              defend, and hold each Contributor harmless for any liability
+              incurred by, or claims asserted against, such Contributor by reason
+              of your accepting any such warranty or additional liability.
+        
+           END OF TERMS AND CONDITIONS
+        
+Project-URL: Issues, https://github.com/seerbio/seer-pas-sdk/issues
+Keywords: seer,sdk,pas,mass spectrometry,proteomics
+Classifier: Development Status :: 4 - Beta
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: boto3>=1.26.152
+Requires-Dist: botocore>=1.29.152
+Requires-Dist: pandas>=2.0.1
+Requires-Dist: numpy<2.0.0,>=1.5.3
+Requires-Dist: PyJWT>=2.8.0
+Requires-Dist: python-dotenv>=1.0.0
+Requires-Dist: Requests>=2.31.0
+Requires-Dist: tqdm>=4.65.0
+Dynamic: license-file
+
+# Seer PAS Python SDK
+
+[![Test](https://github.com/seerbio/seer-pas-sdk/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/seerbio/seer-pas-sdk/actions/workflows/test.yml)
+[![Lint](https://github.com/seerbio/seer-pas-sdk/actions/workflows/lint.yml/badge.svg?branch=main)](https://github.com/seerbio/seer-pas-sdk/actions/workflows/lint.yml)
+
+This SDK permits interaction with the Seer Proteograph Analysis Suite using Python.
+
+## Installation
+
+```shell
+pip install seer-pas-sdk
+```
+
+## Usage
+
+To import and set up the SDK:
+
+```python
+from seer_pas_sdk import SeerSDK
+
+# Instantiate an SDK object with your credentials:
+sdk = SeerSDK(USERNAME, PASSWORD)
+```
+
+You can then use the SDK's methods to create, query, or retrieve projects, plates, samples, and analyses.
+
+For complete documentation of this SDK, visit [https://seerbio.github.io/seer-pas-sdk/](https://seerbio.github.io/seer-pas-sdk/ "Documentation").

{seer_pas_sdk-0.1.2 → seer_pas_sdk-0.2.1}/README.md

@@ -22,6 +22,6 @@ from seer_pas_sdk import SeerSDK
 sdk = SeerSDK(USERNAME, PASSWORD)
 ```
 
-You can then use the SDK's functions to create, query, or retrieve projects, plates, samples, and analyses.
+You can then use the SDK's methods to create, query, or retrieve projects, plates, samples, and analyses.
 
 For complete documentation of this SDK, visit [https://seerbio.github.io/seer-pas-sdk/](https://seerbio.github.io/seer-pas-sdk/ "Documentation").

{seer_pas_sdk-0.1.2 → seer_pas_sdk-0.2.1}/docs/index.qmd

@@ -49,11 +49,53 @@ sdk = SeerSDK(USERNAME, PASSWORD, INSTANCE)
 #| output: true
 print(f"User '{USERNAME}' logged in.")
 ```
+You can then use the SDK's methods to create, query, or retrieve projects, plates, samples, and analyses.
+Full documentation can be found [here](https://seerbio.github.io/seer-pas-sdk/reference/SeerSDK.html).
+Additional information and examples can also be found below.
 
+### Multi Tenant Management 
+Introduced in version 0.2.0
+
+By default, you will be active in your home tenant upon log in. The home tenant is defined as the organization account that issued the original invitation for the user to join PAS.
+The optional 'tenant' parameter is available in the SeerSDK constructor to navigate directly to a desired tenant.
+A notification message will display upon login.
+
+
+The following tools are available to navigate between tenants:
+```{python}
+#| eval: false
+from seer_pas_sdk import SeerSDK
+
+sdk = SeerSDK(USERNAME, PASSWORD, INSTANCE, tenant='My Active Tenant')
+
+# Retrieve value of current active tenant
+print(sdk.get_active_tenant())
+
+# List available tenants
+print(sdk.list_user_tenants())
+
+# Switch active tenant
+pas.switch_tenant('My Next Tenant')
+
+```
+
+```{python}
+#| echo: false
+#| output: true
+print(f"User '{USERNAME}' logged in.")
+print("You are now active in My Active Tenant")
+print("My Active Tenant")
+print(
+    {'My Active Tenant' : 'abc1234abc1234',
+    'My Next Tenant' : 'abc1234abc1232'
+    }
+)
+print("You are now active in My Next Tenant")
+```
 
 ### `PlateMap` Object
 
-The PAS Python SDK would allow users to make plate maps file from within the SDK using the `PlateMap` object located in the `objects` module. This module is imported by default within the SDK. The interface of the plate map file contains the following parameters, all of which need to be passed in as lists:
+The PAS Python SDK would allow users to make plate maps file from within the SDK using the `PlateMap` class. The interface of the plate map file contains the following parameters, all of which need to be passed in as lists:
 
 * MS file name as `ms_file_name` 
 * Sample name as `sample_name`
@@ -540,33 +582,6 @@ The file will be stored in `downloads/` in the user-specified path under the uni
 <hr>
 
 
-### Add Project
-Creates a new project with a given `project_name` and a list containing `project_id` strings.
-
-###### <u>Params</u>
-* `project_name`: (`str`) Name of the project.
-* `plate_ids`: (`list[str]`) List of the plate ids to be added to the project.
-* `description`: (`str`, optional) Description of the project.
-* `notes`: (`str`, optional) Notes for the project.
-* `space`: (`str`, optional) Space where the object is contained. Defaults to the space of the user who is creating the project (or `None`).
-<br>
-
-###### <u>Returns</u>
-`res`: (`dict`) A dictionary containing the status of the request if succeeded.
-
-###### <u>Example</u>
-```{python}
-#| eval: false
-project_name = "test_project"
-plate_ids = ["9872e3f0-544e-11ea-ad9e-1991e0725494", "5b05d440-6610-11ea-96e3-d5a4dab4ebf6"]
-log(sdk.add_project(project_name, plate_ids))
-```
-```
-{'status': 'Project started with id = 12a987d0-87d8-11ee-b03f-27a54e8c1798'}
-```
-
-<hr>
-
 ### Analysis Complete
 Returns the status of the analysis with the given `analysis_id`.
 
@@ -588,218 +603,6 @@ log(sdk.analysis_complete(analysis_id))
 
 <hr>
 
-### Add Plate
-Add a plate given a list of `ms_data_files`, `plate_map_file`, `plate_id`, `plate_name`, `sample_description_file` and `space`.
-
-###### <u>Params</u>
-* `ms_data_files`: (`list[str]`) List of MS Data files.
-* `plate_map_file`: (`str` or `PlateMap` object) The plate map file path or `PlateMap` object. 
-* `plate_id`: (`str`) The plate ID. Must be unique.
-* `plate_name`: (`str`) The plate name.
-* `sample_description_file`: (`str`, optional) Path to the sample description file which adds more detail to samples.
-* `space`: (`str`, optional) Space where the plate is contained. Defaults to the space of the user who is creating the project (or `None`).
-<br>
-
-###### <u>Returns</u>
-`res`: (`dict`) A dictionary containing the status of the request if succeeded.
-
-###### <u>Example</u>
-```{python}
-#| eval: false
-data_file_locations = ["testing/AgamSDKTest1.raw", "testing/AgamSDKTest2.raw"]
-plate_map_location = "testing/AgamSDKPlateMapATest.csv"
-sample_plate_id= "unique223id"
-sample_plate_name = "some_plate_name" 
-
-log(sdk.add_plate(data_file_locations, plate_map_location, sample_plate_id, sample_plate_name))
-```
-```
-{'message': "Plate generated with id: '147a7740-87d8-11ee-b03f-27a54e8c1798'"}
-```
-
-Alternatively, instead of the `plate_map_location`, we could use the `PlateMap` object:
-
-```{python}
-#| eval: false
-generated_plate_map_file = PlateMap(
-    ms_file_name =["AgamSDKTest1.raw", "AgamSDKTest2.raw"],
-    sample_name = ["A111", "A112"], 
-    sample_id = ["A111", "A112"], 
-    well_location = ["C11", "D11"], 
-    nanoparticle = ["NONE"], 
-    nanoparticle_id = ["NONE"], 
-    control = ["MPE Control"], 
-    control_id = ["MPE Control"], 
-    sample_volume = [20], 
-    peptide_concentration = [59.514], 
-    peptide_mass_sample = [8.57], 
-    dilution_factor = [1], 
-    plate_id = ["A11", "A11"], 
-    plate_name = ["A11", "A11"] 
-)
-
-log(sdk.add_plate(data_file_locations, generated_plate_map_file, sample_plate_id, sample_plate_name))
-```
-```
-{'message': "Plate generated with id: '1f40cc10-87d8-11ee-b03f-27a54e8c1798'"}
-```
-
-Similarly, you could specify a `sample_description_file` that would specify more parameters for all samples uploaded.
-
-```{python}
-#| eval: false
-data_file_locations = ["testing/AgamSDKTest1.raw", "testing/AgamSDKTest2.raw"]
-plate_map_location = "testing/AgamSDKPlateMapATest.csv"
-sample_description_file = "testing/AgamSDKSampleDesc.csv"
-sample_plate_id= "unique2123id"
-sample_plate_name = "some_plate_name" 
-
-log(sdk.add_plate(data_file_locations, plate_map_location, sample_plate_id, sample_plate_name, sample_description_file))
-```
-```
-{'message': "Plate generated with id: '147a7740-87d8-11ee-b03f-27a54e8c1798'"}
-```
-<hr>
-
-### Upload MS Data Files
-Upload MS data files to the PAS backend.
-
-###### <u>Params</u>
-* `ms_data_files`: (`list[str]`) List of MS Data files.
-* `path`: (`str`, optional) Path to upload the files to in the S3, defaulted to an empty string. Should <b>not</b> contain trailing slashes.
-* `space`: (`str`, optional) ID of the user group to which the files belongs, defaulted to None.
-<br>
-
-###### <u>Returns</u>
-`res`: (`dict`) Contains message whether the files were uploaded or not.
-
-###### <u>Example</u>
-```{python}
-#| eval: false
-data_file_locations = ["testing/AgamSDKTest1.raw", "testing/AgamSDKTest2.raw"]
-
-log(sdk.upload_ms_data_files(data_file_locations))
-```
-```
-{'message': 'Files uploaded successfully.'}
-```
-
-<hr>
-
-### Download Analysis Files
-Download a specific analysis file from the backend given an `analysis_id` to the specified `download_path`.
-
-If no `download_path` is specified or the `download_path` is invalid, the file will be downloaded to the current working directory. 
-
-If no `file_name` is specified, all files for the analysis will be downloaded.
-
-###### <u>Params</u>
-* `analysis_id` : (`str`) ID of the analysis to download.
-* `download_path` : (`str`, optional) Path to download the analysis file to, defaulted to current working directory.
-* file_name : (`str`, optional) Name of the analysis file to download, defaulted to None.
-
-###### <u>Returns</u>
-(`dict`) Message containing whether the file was downloaded or not.
-
-###### <u>Example</u>
-```{python}
-#| eval: false
-analysis_id = "dd4314d0-22b5-11ee-b604-61b98afbb084"
-download_path = "agamjolly/something"
-
-log(sdk.download_analysis_files(analysis_id, download_path=download_path))
-```
-```
-The path "agamjolly/something" you specified does not exist, was either invalid or not absolute.
-
-Downloading files to "/Users/ajolly/Desktop/seer-sdk/downloads/dd4314d0-22b5-11ee-b604-61b98afbb084"
-
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-
-Downloading EXP20004_2020ms0007X11_A.mzML.quant
-Finished downloading EXP20004_2020ms0007X11_A.mzML.quant
-
-Downloading EXP20004_2020ms0007X11_A/0714-diann181-libfree-mbr.json
-Finished downloading 0714-diann181-libfree-mbr.json
-
-Downloading EXP20004_2020ms0007X11_A/diann.log
-Finished downloading diann.log
-
-{'message': 'Files downloaded successfully to /Users/ajolly/Desktop/seer-sdk/downloads/dd4314d0-22b5-11ee-b604-61b98afbb084'}
-```
-
-<hr>
-
 ### List MS Data Files
 Lists all the MS data files in the given folder as long as the folder path passed in the params is valid.
 
@@ -866,34 +669,6 @@ Finished downloading AgamSDKTest2.raw
 
 <hr>
 
-### Link Plate
-Links existing MS data files to user uploaded files to create a new plate. Functionally, this acts the same way as `add_plate`, except this takes in files that already exist on the backend.
-
-###### <u>Params</u>
-* `ms_data_files`: (`list[str]`) Path to MS data files on the PAS backend or the S3 bucket.
-* `plate_map_file`: (`str` or `PlateMap` object) Path to the plate map file, or `PlateMap` object to be linked.
-* `plate_id`: (`str`) The plate ID. Must be unique.
-* `plate_name`: (`str`) The plate name.
-* `sample_description_file`: (`str`, optional) Path to the sample description file which adds more detail to samples.
-* `space`: (`str`, optional) Space where the plate is contained. Defaults to the space of the user who is creating the project (or `None`).
-<br>
-
-###### <u>Returns</u>
-(`dict`) Contains the message whether the plate was linked or not.
-
-###### <u>Example</u>
-```{python}
-#| eval: false
-ms_data_file_locations = ["147a7740-87d8-11ee-b03f-27a54e8c1798/20231120190742420/AgamSDKTest1.raw", "147a7740-87d8-11ee-b03f-27a54e8c1798/20231120190742420/AgamSDKTest2.raw"]
-plate_map_location = "testing/AgamSDKPlateMapATest.csv"
-sample_plate_id= "some_unique_id23"
-sample_plate_name = "linked_plate_name" 
-
-log(sdk.link_plate(ms_data_file_locations, plate_map_location, sample_plate_id, sample_plate_name))
-```
-
-<hr>
-
 ### Group Analysis Results
 Returns the group analysis data for given `analysis_id` (provided it is valid and the group analysis has been successful) and `box_plot` config info.