Merge pull request #40 from pepkit/dev

Release 0.4.2

Author: khoroshevskyi

docs/changelog.md

@@ -2,6 +2,11 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.4.2] - 2024-04-16
+### Updated
+- View creation, by adding description and no_fail flag
+
+
 ## [0.4.1] - 2024-03-07
 ### Fixed
 - Expired token error handling  ([#17](https://github.com/pepkit/pephubclient/issues/17))

docs/templates/usage.template

@@ -0,0 +1,6 @@
+# Usage reference
+
+pephubclient is a command line tool that can be used to interact with the PEPhub API.
+It can be used to create, update, delete PEPs in the PEPhub database.
+
+Below are usage examples for the different commands that can be used with pephubclient.

docs/usage.md

@@ -4,7 +4,7 @@
 import coloredlogs
 
 __app_name__ = "pephubclient"
-__version__ = "0.4.1"
+__version__ = "0.4.2"
 __author__ = "Oleksandr Khoroshevskyi, Rafal Stepien"
 
 

pephubclient/__init__.py

@@ -35,7 +35,7 @@ def send_request(
         headers: Optional[dict] = None,
         cookies: Optional[dict] = None,
         params: Optional[dict] = None,
-        json: Optional[dict] = None,
+        json: Optional[Union[dict, list]] = None,
     ) -> requests.Response:
         request_return = requests.request(
             method=method,

pephubclient/helpers.py

@@ -71,17 +71,25 @@ def create(
         name: str,
         tag: str,
         view_name: str,
+        description: str = None,
         sample_list: list = None,
+        no_fail: bool = False,
     ):
         """
         Create view in project in PEPhub.
 
         :param namespace: namespace of project
         :param name: name of project
         :param tag: tag of project
+        :param description: description of the view
         :param view_name: name of the view
         :param sample_list: list of sample names
+        :param no_fail: whether to raise an error if view was not added to the project
         """
+
+        if not sample_list or not isinstance(sample_list, list):
+            raise ValueError("Sample list must be a list of sample names.")
+
         url = self._build_view_request_url(
             namespace=namespace, name=name, view_name=view_name
         )
@@ -92,6 +100,7 @@ def create(
             method="POST",
             url=url,
             headers=self.parse_header(self.__jwt_data),
+            params={"description": description, "no_fail": no_fail},
             json=sample_list,
         )
         if response.status_code == ResponseStatusCodes.ACCEPTED:

pephubclient/modules/view.py

@@ -8,4 +8,4 @@ coveralls
 pytest-cov
 pre-commit
 coverage
-smokeshow
+smokeshow

requirements/requirements-test.txt

@@ -0,0 +1,21 @@
+#!/bin/bash
+cp ../docs/templates/usage.template usage.template
+
+for cmd in "--help" "pull --help" "push --help"; do
+	echo $cmd
+	echo -e "## \`phc $cmd\`" > USAGE_header.temp
+	phc $cmd --help > USAGE.temp 2>&1
+	# sed -i 's/^/\t/' USAGE.temp
+	sed -i.bak '1s;^;\`\`\`console\
+;' USAGE.temp
+#	sed -i '1s/^/\n\`\`\`console\n/' USAGE.temp
+	echo -e "\`\`\`\n" >> USAGE.temp
+	#sed -i -e "/\`looper $cmd\`/r USAGE.temp" -e '$G' usage.template  # for -in place inserts
+	cat USAGE_header.temp USAGE.temp >> usage.template # to append to the end
+done
+rm USAGE.temp
+rm USAGE_header.temp
+rm USAGE.temp.bak
+mv usage.template ../docs/usage.md
+#cat usage.template
+# rm USAGE.temp