labii-sdk 1.0__tar.gz

Labii sdk-1.0/LICENSE

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+An SDK for the Labii ELN & LIMS platform (https://www.labii.com)
+that provides interaction with the Labii API.
+Copyright (C) 2022 Labii Inc.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.

Labii sdk-1.0/Labii_SDK.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: Labii-sdk
+Version: 1.0
+Summary: An SDK for the Labii ELN & LIMS platform (https://www.labii.com) that provides interaction with the Labii API.
+Home-page: https://gitlab.com/labii-dev/labii-sdk
+Author: Labii Inc.
+Author-email: developer@labii.com
+License: GNU GPLv3
+Project-URL: Bug Tracker, https://gitlab.com/labii-dev/labii-sdk/-/issues?sort=created_date&state=opened
+Platform: UNKNOWN
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# Labii SDK
+
+An SDK for the [Labii ELN & LIMS platform](https://www.labii.com) that provides interaction with the [Labii API](https://docs.labii.com/api/overview).
+
+![Labii screenshot](https://www.labii.com/media/screenshots/labii-richtext-editor.webp)
+
+This package contains two modules, __api_client__ and __sdk__.
+* Python API clients help you perform Labii API calls, such as authentication, get, patch, post, and delete. Learn more at [APICLIENT.md](./docs/APICLIENT.md)
+* SDK is the toolkit with prebuilt Labii components that developers use to interact with Labii APIs. Learn more at [SDK.md](./docs/SDK.md)
+
+# Install
+```
+pip install labii-sdk
+```
+
+# About Labii
+[Labii](https://www.labii.com) facilitates research and development by providing a user-friendly, customizable Electronic Lab Notebook (ELN) and Laboratory Information Management System (LIMS) to document, manage, and interpret data. Labii ELN & LIMS can be configured for any type of data, and the functions can easily be enhanced and expanded by stand-alone applications. We address the unique needs of each of our customers and are the trusted provider of hundreds of biotech companies and academic labs.
+
+

Labii sdk-1.0/Labii_SDK.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+setup.py
+Labii_SDK.egg-info/PKG-INFO
+Labii_SDK.egg-info/SOURCES.txt
+Labii_SDK.egg-info/dependency_links.txt
+Labii_SDK.egg-info/requires.txt
+Labii_SDK.egg-info/top_level.txt
+Labii_sdk.egg-info/PKG-INFO
+Labii_sdk.egg-info/SOURCES.txt
+Labii_sdk.egg-info/dependency_links.txt
+Labii_sdk.egg-info/requires.txt
+Labii_sdk.egg-info/top_level.txt
+labii_sdk/__init__.py
+labii_sdk/api_client.py
+labii_sdk/files_watch.py
+labii_sdk/sdk.py

Labii sdk-1.0/Labii_SDK.egg-info/dependency_links.txt

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+

Labii sdk-1.0/Labii_SDK.egg-info/requires.txt

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+requests>=2.27.1
+boto3>=1.20.38

Labii sdk-1.0/Labii_SDK.egg-info/top_level.txt

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+labii_sdk

Labii sdk-1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: Labii sdk
+Version: 1.0
+Summary: An SDK for the Labii ELN & LIMS platform (https://www.labii.com) that provides interaction with the Labii API.
+Home-page: https://gitlab.com/labii-dev/labii-sdk
+Author: Labii Inc.
+Author-email: developer@labii.com
+License: GNU GPLv3
+Project-URL: Bug Tracker, https://gitlab.com/labii-dev/labii-sdk/-/issues?sort=created_date&state=opened
+Platform: UNKNOWN
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# Labii SDK
+
+An SDK for the [Labii ELN & LIMS platform](https://www.labii.com) that provides interaction with the [Labii API](https://docs.labii.com/api/overview).
+
+![Labii screenshot](https://www.labii.com/media/screenshots/labii-richtext-editor.webp)
+
+This package contains two modules, __api_client__ and __sdk__.
+* Python API clients help you perform Labii API calls, such as authentication, get, patch, post, and delete. Learn more at [APICLIENT.md](./docs/APICLIENT.md)
+* SDK is the toolkit with prebuilt Labii components that developers use to interact with Labii APIs. Learn more at [SDK.md](./docs/SDK.md)
+
+# Install
+```
+pip install labii-sdk
+```
+
+# About Labii
+[Labii](https://www.labii.com) facilitates research and development by providing a user-friendly, customizable Electronic Lab Notebook (ELN) and Laboratory Information Management System (LIMS) to document, manage, and interpret data. Labii ELN & LIMS can be configured for any type of data, and the functions can easily be enhanced and expanded by stand-alone applications. We address the unique needs of each of our customers and are the trusted provider of hundreds of biotech companies and academic labs.
+
+

Labii sdk-1.0/README.md

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+# Labii SDK
+
+An SDK for the [Labii ELN & LIMS platform](https://www.labii.com) that provides interaction with the [Labii API](https://docs.labii.com/api/overview).
+
+![Labii screenshot](https://www.labii.com/media/screenshots/labii-richtext-editor.webp)
+
+This package contains two modules, __api_client__ and __sdk__.
+* Python API clients help you perform Labii API calls, such as authentication, get, patch, post, and delete. Learn more at [APICLIENT.md](./docs/APICLIENT.md)
+* SDK is the toolkit with prebuilt Labii components that developers use to interact with Labii APIs. Learn more at [SDK.md](./docs/SDK.md)
+
+# Install
+```
+pip install labii-sdk
+```
+
+# About Labii
+[Labii](https://www.labii.com) facilitates research and development by providing a user-friendly, customizable Electronic Lab Notebook (ELN) and Laboratory Information Management System (LIMS) to document, manage, and interpret data. Labii ELN & LIMS can be configured for any type of data, and the functions can easily be enhanced and expanded by stand-alone applications. We address the unique needs of each of our customers and are the trusted provider of hundreds of biotech companies and academic labs.

Labii sdk-1.0/labii_sdk/api_client.py

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+""" api related functions """
+import requests
+import json
+import getpass
+
+class APIObject:
+    base_url = "https://www.labii.dev"
+    email = None
+    password = None
+    token = None
+    organization__sid = None
+    user = None
+
+    def __init__(self, base_url="https://www.labii.dev", email=None, password=None, token=None, organization__sid=None, user=None):
+        self.base_url = base_url
+        self.email = email
+        self.password = password
+        self.token = token
+        self.organization__sid = organization__sid
+        self.user = user
+
+    ######
+    # url
+    def get_list_url(self, app, object, level="organization", sid=None, serializer='list', query=""):
+        """ return the list url """
+        if sid is None:
+            sid = self.organization__sid
+        return f"/{app}/{object}/list/{level}/{sid}/{serializer}/{'' if query == '' else '?'}{query}"
+
+    def get_detail_url(self, app, object, sid, query=""):
+        """ return the detail url """
+        return f"/{app}/{object}/detail/{sid}/{'' if query == '' else '?'}{query}"
+
+    ######
+    # auth
+    def get_headers(self, is_authorized=True):
+        """Return necessary headers for API functions
+
+        Returns:
+            dict: header objects
+        """
+        headers = {
+            "X-Forwarded-For": "batch",
+            "Content-Type": "application/json"
+        }
+        if is_authorized and self.token != None:
+            headers["Authorization"] = f"Token {self.token}"
+        return headers
+
+    def login(self, email="", password=""):
+        """Get authentication token based on user input
+        - self.login()
+            - login with saved email/password
+            - get email/password if not saved
+        - self.login(email=xxx, password=xxx): login with new email/password
+
+        Args:
+            email (str): email to use to login
+            password (str): password to use to login
+        """
+        # get email or password
+        if email != "" and password != "":
+            self.email = email
+            self.password = password
+        else:
+            if self.email is None or self.password is None:
+                self.email = input("Email: ")
+                self.password = getpass.getpass('Password: ')
+        # get token
+        data = {
+            "username": self.email,
+            "password": self.password
+        }
+        response = self.post("/accounts/auth/", data, is_authorized=False)
+        if "token" in response:
+            self.token = response["token"]
+        elif "secret" in response:# two step authentication
+            # use email to verify
+            self.post("/accounts/mfa/code/", {"option": "email", "secret": j["secret"]}, is_authorized=False)
+            code = input("MFA enabled for the account. Please check your email and provide authentication code: ")
+            data = self.post("/accounts/mfa/verify/", {"code": code, "secret": response["secret"]}, is_authorized=False)
+            if "token" in data:
+                self.token = data["token"]
+                self.user = data
+            else:
+                raise RuntimeError(data)
+        else:
+            raise RuntimeError(response)
+
+    def check_token(self):
+        """Check if the exist token is valid. If not valid, it will genereate a new token
+            Labii token expires after 30 minutes of no activity. If your program take more than 30 minutes to run. Use this function to get a new token.
+        """
+        data = self.get("/accounts/checktoken/")
+        if data["detail"] != "Valid token.":
+            self.login()
+
+    ######
+    # api post
+    def post(self, url, data, is_authorized=True):
+        """A function to do POST for labii api
+
+        Args:
+            url (str): API URL
+            data (dict): data to POST, see API documentation (https://docs.labii.com/api/overview) for the format
+            is_authorized (bool): should use the authrized token
+
+        Returns:
+            dict: created object
+        """
+        response = requests.post(url=f"{self.base_url}{url}", data=json.dumps(data, separators=(',',':')), headers=self.get_headers(is_authorized))
+        try:
+            data = json.loads(response.text)
+            return data
+        except:
+            raise RuntimeError(response)
+
+    def patch(self, url, data, is_authorized=True):
+        """A function to do PATCH for labii api
+
+        Args:
+            url (str): API URL
+            data (dict): data to update, see API documentation (https://docs.labii.com/api/overview) for the format
+            is_authorized (bool): should use the authrized token
+
+        Returns:
+            dict: return of the api
+        """
+        response = requests.patch(url=f"{self.base_url}{url}", data=json.dumps(data, separators=(',',':')), headers=self.get_headers(is_authorized))
+        try:
+            data = json.loads(response.text)
+            return data
+        except:
+            raise RuntimeError(response)
+
+    def get(self, url, all=False, is_authorized=True):
+        """A function to do GET for labii api
+
+        Args:
+            url (str): API URL
+            all (bool): should download all
+            is_authorized (bool): should use the authrized token
+
+        Returns:
+            dict: result of the url
+        """
+        if all is False:
+            response = requests.get(url=f"{self.base_url}{url}", headers=self.get_headers(is_authorized))
+            try:
+                data = json.loads(response.text)
+                return data
+            except:
+                raise RuntimeError(response)
+        else:
+            page = 1
+            page_size = 10
+            # update url
+            if "page" in url or "page_size" in url:
+                query = url.split("?")[1].split("&")
+                query_updated = []
+                for item in query:
+                    if not "page" in item and not "page_size" in item:
+                        query_updated.append(item)
+                if len(query_updated) > 0:
+                    url = f"{url.split('?')[0]}?{'&'.join(query_updated)}"
+                else:
+                    url = url.split("?")[0]
+            if "?" in url:
+                url_with_page = f"{url}&page={page}&page_size={page_size}"
+            else:
+                url_with_page = f"{url}?page={page}&page_size={page_size}"
+            response = requests.get(url=f"{self.base_url}{url_with_page}", headers=self.get_headers(is_authorized))
+            data = json.loads(response.text)
+            count = data["count"]
+            results = data["results"]
+            print(f"Total records: {count}")
+            print("Downloading page 1...")
+            while len(results) < count:
+                page += 1
+                print(f"Downloading page {page}...")
+                if "?" in url:
+                    url_with_page = f"{url}&page={page}&page_size={page_size}"
+                else:
+                    url_with_page = f"{url}?page={page}&page_size={page_size}"
+                response = requests.get(url=f"{self.base_url}{url_with_page}", headers=self.get_headers(is_authorized))
+                results = results + json.loads(response.text)["results"]
+            data["results"] = data
+            return data
+
+    def delete(self, url, is_authorized=True):
+        """A function to do delete for labii api
+
+        Args:
+            url (str): API URL
+            is_authorized (bool): should use the authrized token
+
+        Returns:
+            dict: result of the url
+        """
+        response = requests.delete(url=f"{self.base_url}{url}", headers=self.get_headers(is_authorized))
+        if response.status_code != 200:
+            raise RuntimeError(response.text)
+
+#
+# def labii_update_row(token, organization__sid, table__sid, data, base_url=base_url):
+#     """Get or update a row.
+#     - if 'sid' is provided, the row will be updated
+#     - if 'sid' is not provied, a new row will be created
+#
+#     Args:
+#         token (str): the authentification token
+#         organization__sid (str): the sid of your organization
+#         table__sid (str): the sid of the table
+#         data (dict): other attributions, in json format
+#         base_url (str): the base_url
+#
+#     Returns:
+#         dict: the row object.
+#     """
+#     if "sid" in data:# update the row
+#         sid = str(data["sid"])
+#         url = f"/tables/row/detail/{sid}/"
+#         data.pop("sid")
+#         return labii_patch(url, data, token, base_url)
+#     elif "name" in data:
+#         rows = labii_get(f"/tables/row/list/organization/{organization__sid}/name/?table__sid={table__sid}&name={data['name']}", token, base_url)
+#         if rows["count"] == 0: # if not exists
+#             url = f"/tables/row/list/organization/{organization__sid}/detail/?table__sid={table__sid}"
+#             return labii_post(url, data, token, base_url)
+#         else:
+#             url = f"/tables/row/detail/{rows['results'][0]['sid']}/"
+#             return labii_patch(url, data, token, base_url)
+#     else:
+#         raise ValueError("Error: sid or name is required!")
+#
+# def labii_update_cell(token, organization__sid, row__sid, column__sid, data, base_url=base_url):
+#     """update the data for a cell, create the cell if not exists
+#
+#     Args:
+#         token (str): authentication token
+#         organization__sid (str): the sid of the organization
+#         row__sid (str): the sid of the row
+#         column__sid (str): the sid of the column
+#         data (dict): data for the cell, example: {"data": "xxx"}
+#         base_url (str): the base_url
+#
+#     Returns:
+#         dict: the cell data
+#     """
+#     cells = labii_get(f"/tables/cell/list/organization/{organization__sid}/name/?row__sid={row__sid}&column__sid={column__sid}", token, base_url)
+#     if cells["count"] == 0: # if not exists
+#         url = f"/tables/cell/list/organization/{organization__sid}/detail/?row__sid={row__sid}&column__sid={column__sid}"
+#         labii_post(url, data, token, base_url)
+#     else:
+#         url = f"/tables/cell/detail/{cells['results'][0]['sid']}/"
+#         labii_patch(url, data, token, base_url)
+#
+# def labii_update_section(token, organization__sid, row__sid, widget__sid, data, base_url=base_url):
+#     """update the data for a section, create the section if not exists
+#
+#     Args:
+#         token (str): authentication token
+#         organization__sid (str): sid of a organization
+#         row__sid (str): the sid of a row
+#         widget__sid (str): the sid of widget
+#         data (dict): the section data
+#         base_url (str): the base_url
+#
+#     Returns:
+#         dict: the section object
+#     """
+#     sections = labii_get(f"/tables/section/list/organization/{organization__sid}/name/?row__sid={row__sid}&name={data['name'].replace('&', ' ')}", token, base_url)
+#     if "count" in sections:
+#         if sections["count"] == 0: # if not exists
+#             url = f"/tables/section/list/organization/{organization__sid}/detail/?row__sid={row__sid}&widget__sid={widget__sid}"
+#             labii_post(url, data, token, base_url)
+#         else:
+#             url = f"/tables/section/detail/{sections['results'][0]['sid']}/"
+#             labii_patch(url, data, token, base_url)
+#     else:
+#         raise ValueError("Error in updating section")
+#
+# def labii_json_list_to_tsv(results):
+#     """conver the list result in json format into tsv format
+#
+#     Args:
+#         results (array): the results from response
+#
+#     Returns:
+#         string: tsv data
+#     """
+#     if len(results) > 0:
+#         should_collect_title = True
+#         titles = [] # collect list of titles
+#         data = [] # the data of all
+#         for r in results:
+#             d = [] # the data of one row
+#             for field in r:
+#                 if field == "column_set":
+#                     for f in r["column_set"]:
+#                         d.append(str(f["data"]).replace("\n","").replace("\r",""))
+#                         if should_collect_title:
+#                             titles.append(f["column"]["name"])
+#                 elif field != "section_set":
+#                     d.append(str(r[field]).replace("\n","").replace("\r",""))
+#                     if should_collect_title:
+#                         titles.append(field)
+#             if should_collect_title:
+#                 data.append("\t".join(titles))
+#                 should_collect_title = False
+#             data.append("\t".join(d))
+#         return "\n".join(data)
+#     else:
+#         return "";

Labii sdk-1.0/labii_sdk/files_watch.py

@@ -0,0 +1,27 @@
+from api import *
+import os, json
+
+def files_watch(configuration_file="configuration.json"):
+    """
+    """
+    # collect configuration
+    configuration = collect_configuration(configuration_file)
+    
+
+def collect_configuration(configuration_file):
+    """
+    """
+    # read configuration.json
+    configuration = {}
+    if os.path.isfile(configuration_file):
+        with open(configuration_file) as json_file:
+            configuration = json.load(json_file)
+    # collect email and password
+    for i in ["email", "password"]:
+        if not i in configuration:
+            v = input(f"{i.title()}: ")
+            configuration[i] = v
+    # update the configuration
+    with open(configuration_file, 'w') as outfile:
+        json.dump(d, outfile)
+    return configuration

Labii sdk-1.0/labii_sdk/sdk.py

@@ -0,0 +1,90 @@
+""" python api functions """
+#from api import *
+import requests
+import json
+import getpass
+from labii_sdk.api_client import APIObject
+
+class LabiiObject:
+    api = None
+
+    def __init__(self,
+        organization__sid,
+        base_url="https://www.labii.dev",
+        email=None,
+        password=None,
+        token=None,
+        user=None
+    ):
+        self.api = APIObject(base_url=base_url, email=email, password=password, token=token, organization__sid=organization__sid, user=user)
+        self.Organization = self.APIResource(self, "organizations", "organization")
+        self.People = self.APIResource(self, "organizations", "personnel")
+        self.Team = self.APIResource(self, "organizations", "team")
+        self.SAML = self.APIResource(self, "organizations", "saml")
+        self.Project = self.APIResource(self, "projects", "project")
+        self.ProjectMember = self.APIResource(self, "projects", "member")
+        self.Table = self.APIResource(self, "tables", "table")
+        self.Column = self.APIResource(self, "tables", "column")
+        self.Section = self.APIResource(self, "tables", "section")
+        self.Row = self.APIResource(self, "tables", "row")
+        self.Cell = self.APIResource(self, "tables", "cell")
+        self.Version = self.APIResource(self, "tables", "version")
+        self.Visitor = self.APIResource(self, "tables", "visitor")
+
+    class APIResource:
+        """ abstract class """
+        app = None
+        object = None
+
+        class Meta:
+            abstract = True
+
+        def __init__(self, instance, app, object):
+            """
+                - instance, the outer instance
+            """
+            self.instance = instance
+            self.app = app
+            self.object = object
+
+        def create(self, data={}):
+            """ Create a object """
+            return self.instance.api.post(self.instance.api.get_list_url(self.app, self.object, serializer="detail"))
+
+        def retrieve(self, sid):
+            """ Return an object """
+            return self.instance.api.get(self.instance.api.get_detail_url(self.app, self.object, sid=sid))
+
+        def list(self, page=1, page_size=10, all=False, level="organization", serializer="list", query=""):
+            """ Return list of objects """
+            if all is True:
+                url = self.instance.api.get_list_url(
+                    self.app,
+                    self.object,
+                    sid=self.instance.api.organization__sid,
+                    level=level,
+                    serializer=serializer,
+                    query=query
+                )
+                return self.instance.api.get(url, True)
+            else:
+                url = self.instance.api.get_list_url(
+                    self.app,
+                    self.object,
+                    sid=self.instance.api.organization__sid,
+                    level=level,
+                    serializer=serializer,
+                    query=f"page={page}&page_size={page_size}{'' if query == '' else '&'}{query}"
+                )
+                return self.instance.api.get(url)
+
+        def modify(self, sid, data={}):
+            """ Change one object """
+            if self.can_patch:
+                return self.instance.api.patch(self.instance.api.get_detail_url(self.app, self.object, sid=sid), data)
+            else:
+                print("Method not supported!")
+
+        def delete(self, sid):
+            """ Delete a object """
+            self.instance.api.delete(self.instance.api.get_detail_url(self.app, self.object, sid=sid))

Labii sdk-1.0/pyproject.toml

@@ -0,0 +1,6 @@
+[build-system]
+requires = [
+    "setuptools>=42",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"

Labii sdk-1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

Labii sdk-1.0/setup.py

@@ -0,0 +1,25 @@
+import setuptools
+
+long_description = open("README.md").read()
+required = ["requests>=2.27.1", "boto3>=1.20.38"] # Comma seperated dependent libraries name
+
+setuptools.setup(
+    name="Labii sdk",
+    version="1.0", # eg:1.0.0
+    author="Labii Inc.",
+    author_email="developer@labii.com",
+    license="GNU GPLv3",
+    description="An SDK for the Labii ELN & LIMS platform (https://www.labii.com) that provides interaction with the Labii API.",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://gitlab.com/labii-dev/labii-sdk",
+    packages = ['labii_sdk'],
+    # project_urls is optional
+    project_urls={
+        "Bug Tracker": "https://gitlab.com/labii-dev/labii-sdk/-/issues?sort=created_date&state=opened",
+    },
+    key_words="Labii, Labii ELN & LIMS, ELN, LIMS, SDK, Electronic Lab Notebook, Laboratory Information Management System",
+    install_requires=required,
+    #packages=setuptools.find_packages(where="labii"),
+    python_requires=">=3.8",
+)