Delivery to the Bucket

.github/workflows/Sync-dev-with-main.yml

@@ -0,0 +1,48 @@
+name: Rebase main and dev and add .dev to version
+
+on:
+  workflow_run:
+    workflows: ["Tag and Release"]
+    types:
+      - completed
+  workflow_dispatch:
+
+jobs:
+  rebase:
+    runs-on: ubuntu-latest
+    if: ${{ github.event.workflow_run.conclusion == 'success' || github.event_name == 'workflow_dispatch' }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+          fetch-depth: 0
+          token: ${{ secrets.BOT_ACCESS_TOKEN }}
+
+      - name: Setup Git
+        run: |
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git config user.name "github-actions[bot]"
+
+      - name: Fetch all branches
+        run: git fetch --all
+
+      - name: Rebase dev with main
+        run: |
+          git checkout dev
+          git rebase origin/main
+
+      - name: Update the version to <latest>.dev
+        id: update_version
+        run: |
+          version_file="genpipes/__version__.py"
+          version_number=$(sed -n "s/__version__ = '\([^']*\)'/\1/p" $version_file)
+          if [[ "$version_number" != *.dev ]]; then
+            echo "__version__ = '${version_number}.dev'" > $version_file
+          fi
+
+      - name: Commit changes
+        run: |
+          git add genpipes/__version__.py
+          git commit -m "Dev Version update"
+          git push --force-with-lease

.gitignore

@@ -8,6 +8,7 @@ venv
 __pycache__/
 .DS_Store
 .pdm*
+pdm*
 dist/
 
 # Tests

pt_cli/cli.py

@@ -25,7 +25,9 @@
         UnDelete,
         Deprecate,
         UnDeprecate,
-        Curate
+        Curate,
+        GetID,
+        Location,
         )
 
 from .__version__ import __version__
@@ -170,6 +172,9 @@ def projects(parsed_local):
     UnDeprecate(connection_obj=connector_session, subparser=subparser)
     Curate(connection_obj=connector_session, subparser=subparser)
 
+    getid_subparser = GetID(subparser).subparser
+    Location(connection_obj=connector_session, subparser=getid_subparser)
+
     shtab.add_argument_to(parser, ["-s", "--print-completion"])
 
 

pt_cli/connect.py

@@ -10,7 +10,6 @@
 
 import requests
 import bs4
-import lxml
 
 logger = logging.getLogger(__name__)
 
@@ -128,7 +127,7 @@ def maybe_json(self, data):
             return loads
         except json.decoder.JSONDecodeError:
             if isinstance(data, str):
-                soup = bs4.BeautifulSoup(data, features="lxml")
+                soup = bs4.BeautifulSoup(data, features="html5lib")
                 if soup.get_text().startswith("----------"):
                     sys.stdout.write(soup.get_text())
                 elif soup.get_text().startswith("Welcome"):

pt_cli/tools.py

@@ -465,7 +465,7 @@ def json_to_unanalyzed(self):
         unanalyzed = self.unanalyzed
         if not self.output_file:
             if isinstance(unanalyzed, str):
-                soup = bs4.BeautifulSoup(unanalyzed, features="lxml")
+                soup = bs4.BeautifulSoup(unanalyzed, features="html5lib")
                 return sys.stdout.write(soup.get_text())
             # else case, not explicitely written
             return sys.stdout.write(json.dumps(unanalyzed))
@@ -489,6 +489,20 @@ def func(self, parsed_args):
         self.output_file = parsed_args.output
         self.json_to_unanalyzed()
 
+class Undelivered(AddCMD):
+    """
+    Undelivered is a sub-command of Digest subparser using base AddCMD class
+    """
+    __tool_name__ = 'undelivered'
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.parsed_input = None
+        self.output_file = None
+
+    def help(self):
+        return "Will return undelivered Samples name/ID or Readsets name/ID"
+
+
 class Delivery(AddCMD):
     """
     Delivery is a sub-command of Digest subparser using base AddCMD class
@@ -509,10 +523,9 @@ def arguments(self):
         self.parser.add_argument('--specimen_id', help='Specimen ID to be selected', nargs='+')
         self.parser.add_argument('--sample_id', help='Sample ID to be selected', nargs='+')
         self.parser.add_argument('--readset_id', help='Readset ID to be selected', nargs='+')
-        self.parser.add_argument('--experiment_nucleic_acid_type', help="Experiment nucleic_acid_type characterizing the Samples/Readsets (RNA or DNA)", required=False)
+        self.parser.add_argument('--experiment_nucleic_acid_type', help="Experiment nucleic_acid_type characterizing the Samples/Readsets (RNA or DNA)", required=True)
         self.parser.add_argument('--endpoint', help="Endpoint in which data is located", required=True)
         self.parser.add_argument('--output', '-o', help="Name of output file (Default: terminal), formatted as Json file with sample/readset and endpoint")
-        # self.parser.add_argument('--input-json', help="Json file with all parameters")
 
     @property
     def delivery(self):
@@ -564,14 +577,14 @@ def json_to_delivery(self):
         delivery = self.delivery
         if not self.output_file:
             if isinstance(delivery, str):
-                soup = bs4.BeautifulSoup(delivery, features="lxml")
+                soup = bs4.BeautifulSoup(delivery, features="html5lib")
                 return sys.stdout.write(soup.get_text())
             # else case, not explicitely written
-            return sys.stdout.write(json.dumps(delivery))
+            return sys.stdout.write(json.dumps(delivery["DB_ACTION_OUTPUT"]))
         if not delivery:
             raise EmptyGetError
         with open(self.output_file, "w", encoding="utf-8") as out_pair_file:
-            json.dump(delivery, out_pair_file, ensure_ascii=False, indent=4)
+            json.dump(delivery["DB_ACTION_OUTPUT"], out_pair_file, ensure_ascii=False, indent=4)
             logger.info(f"Delivery file written to {self.output_file}")
 
     def func(self, parsed_args):
@@ -950,3 +963,73 @@ def func(self, parsed_args):
             pass
         else:
             sys.stdout.write("\n".join(response["DB_ACTION_OUTPUT"]))
+
+class GetID:
+    """
+    GetID is a subparser of the client in which you can query per table entries to get their IDs
+    """
+    __tool_name__ = 'getid'
+
+    def __init__(self, subparser=argparse.ArgumentParser().add_subparsers()):
+        self.subparser = subparser.add_parser(self.__tool_name__, help=self.help(), add_help=True).add_subparsers()
+
+    def help(self):
+        """
+        :return: the tool help string
+        """
+        return f"All {self.__tool_name__} sub commands, those encapsulate all tables from the database to be queried and get the ID. Use 'pt_cli {self.__tool_name__} --help' to see more details."
+
+
+class Location(AddCMD):
+    """
+    Location is a sub-command of GetID subparser using base AddCMD class
+    """
+    __tool_name__ = 'location'
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.parsed_input = None
+        self.output_file = None
+
+    def help(self):
+        return "Will return location ID based on location endpoint and file name"
+
+    def arguments(self):
+        self.parser.add_argument('--endpoint', help='Endpoint in which data is located', required=True)
+        self.parser.add_argument('--file_name', help='File Name linked to the location', required=True)
+
+    @property
+    def get_location(self):
+        '''
+        Returns a list of location IDs of GenPipes of the API call for get_location
+        :return:
+        '''
+        return self.post('project/get_location', data=self.parsed_input)
+
+    def jsonify_input(self, parsed_args):
+        '''
+        :return: jsonified input args
+        '''
+        json = {
+            "location_endpoint": parsed_args.endpoint,
+            "file_name": parsed_args.file_name
+        }
+
+        return json
+
+
+    def func(self, parsed_args):
+        super().func(parsed_args)
+        # Dev case when using --data-file
+        self.parsed_input = self.data()
+
+        # When --data-file is empty
+        if not self.parsed_input:
+            self.parsed_input = json.dumps(self.jsonify_input(parsed_args), ensure_ascii=False, indent=4)
+        if not self.parsed_input:
+            raise BadArgumentError
+
+        get_location = self.get_location
+        if isinstance(get_location, str):
+            soup = bs4.BeautifulSoup(get_location, features="html5lib")
+            return sys.stdout.write(soup.get_text())
+        return sys.stdout.write(''.join(get_location["DB_ACTION_OUTPUT"]))

pyproject.toml

@@ -21,7 +21,7 @@ dependencies = [
     "pyyaml>=6.0",
     "requests>=2.28",
     "beautifulsoup4>=4.12",
-    "lxml",
+    "html5lib",
     "shtab",
 ]