cmem-cmemc 24.3.2__py3-none-any.whl → 25.1.0__py3-none-any.whl

cmem_cmemc/completion.py

@@ -3,11 +3,12 @@
 # ruff: noqa: ARG001
 import os
 import pathlib
+from collections import OrderedDict
 from contextlib import suppress
 from typing import Any
 
 import requests.exceptions
-from click import Context
+from click import ClickException, Context
 from click.parser import Argument, split_arg_string
 from click.shell_completion import CompletionItem
 from cmem.cmempy.dp.authorization.conditions import (
@@ -38,7 +39,8 @@ from cmem.cmempy.workspace.search import list_items
 from natsort import natsorted, ns
 
 from cmem_cmemc.constants import NS_ACL, NS_ACTION, NS_GROUP, NS_USER
-from cmem_cmemc.context import CONTEXT
+from cmem_cmemc.context import ApplicationContext
+from cmem_cmemc.placeholder import QueryPlaceholder, get_placeholders_for_query
 from cmem_cmemc.smart_path import SmartPath as Path
 from cmem_cmemc.utils import (
     convert_iri_to_qname,
@@ -47,6 +49,7 @@ from cmem_cmemc.utils import (
     struct_to_table,
 )
 
+NOT_SORTED = -1
 SORT_BY_KEY = 0
 SORT_BY_DESC = 1
 
@@ -66,7 +69,7 @@ def finalize_completion(
     ----
         candidates (list):  completion dictionary to filter
         incomplete (str):   incomplete string at the cursor
-        sort_by (str):      SORT_BY_KEY or SORT_BY_DESC
+        sort_by (str):      SORT_BY_KEY, SORT_BY_DESC or NOT_SORTED
         nat_sort (bool):    if true, uses the natsort package for sorting
         reverse (bool):     if true, sorts in reverse order
 
@@ -76,26 +79,30 @@ def finalize_completion(
 
     Raises:
     ------
-        ValueError in case of wrong sort_by parameter
+        ClickException in case of wrong sort_by parameter
 
     """
-    if sort_by not in (SORT_BY_KEY, SORT_BY_DESC):
-        raise ValueError("sort_by should be 0 or 1.")
+    if sort_by not in (SORT_BY_KEY, SORT_BY_DESC, NOT_SORTED):
+        raise ClickException("sort_by should be -1, 0 or 1.")
     incomplete = incomplete.lower()
     if len(candidates) == 0:
         return candidates
-    # remove duplicates
-    candidates = list(set(candidates))
+    # remove duplicates (preserving the order)
+    candidates = list(OrderedDict.fromkeys(candidates))
+
     if isinstance(candidates[0], str):
         # list of strings filtering and sorting
         filtered_candidates = [
             element for element in candidates if element.lower().find(incomplete) != -1
         ]
+        if sort_by == NOT_SORTED:
+            return filtered_candidates
         if nat_sort:
             return natsorted(seq=filtered_candidates, alg=ns.IGNORECASE, reverse=reverse)
         # this solves that case-insensitive sorting is not stable in ordering
         # of "equal" keys (https://stackoverflow.com/a/57923460)
         return sorted(filtered_candidates, key=lambda x: (str(x).casefold(), x), reverse=reverse)
+
     if isinstance(candidates[0], tuple):
         # list of tuples filtering and sorting
         filtered_candidates = [
@@ -104,7 +111,9 @@ def finalize_completion(
             if str(element[0]).lower().find(incomplete) != -1
             or str(element[1]).lower().find(incomplete) != -1
         ]
-        if nat_sort:
+        if sort_by == NOT_SORTED:
+            sorted_list = filtered_candidates
+        elif nat_sort:
             sorted_list = natsorted(
                 seq=filtered_candidates,
                 key=lambda k: k[sort_by],
@@ -121,7 +130,8 @@ def finalize_completion(
             CompletionItem(value=element[0].replace(":", r"\:"), help=element[1])
             for element in sorted_list
         ]
-    raise ValueError(
+
+    raise ClickException(
         "Candidates should be a list of strings or a list of tuples." f" Got {candidates}"
     )
 
@@ -156,7 +166,7 @@ def add_metadata_parameter(list_: list | None = None) -> list:
 
 def acl_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of access condition identifier"""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     options = []
     acls = fetch_all_acls()
     for access_condition in acls:
@@ -170,7 +180,7 @@ def acl_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionIt
 
 def acl_actions(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of access condition actions"""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     options = []
     results = get_actions().json()
     for _ in results:
@@ -191,7 +201,7 @@ def acl_actions(ctx: Context, param: Argument, incomplete: str) -> list[Completi
 
 def acl_users(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of access condition users"""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     options = []
     try:
         for _ in list_users():
@@ -212,7 +222,7 @@ def acl_users(ctx: Context, param: Argument, incomplete: str) -> list[Completion
 
 def acl_groups(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of access condition groups"""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     options = []
     try:
         for _ in list_groups():
@@ -260,7 +270,7 @@ def add_read_only_and_uri_property_parameters(list_: list | None = None) -> list
 
 def dataset_parameter(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of dataset parameters for a dataset type."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     args = get_completion_args(incomplete)
     incomplete = incomplete.lower()
     # look if cursor is in value position of the -p option and
@@ -310,7 +320,7 @@ def dataset_parameter(ctx: Context, param: Argument, incomplete: str) -> list[Co
 
 def dataset_types(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of dataset types."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     incomplete = incomplete.lower()
     options = []
     plugins = get_task_plugins()
@@ -329,7 +339,7 @@ def dataset_types(ctx: Context, param: Argument, incomplete: str) -> list[Comple
 
 def dataset_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of projectid:datasetid dataset identifier."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     results = list_items(item_type="dataset")
     datasets = results["results"]
     options = [(f"{_['projectId']}:{_['id']}", _["label"]) for _ in datasets]
@@ -368,14 +378,14 @@ def dataset_list_filter(ctx: Context, param: Argument, incomplete: str) -> list[
 
 def resource_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of projectid:resourceid resource identifier."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     options = [_["id"] for _ in get_all_resources()]
     return finalize_completion(candidates=options, incomplete=incomplete, sort_by=SORT_BY_DESC)
 
 
 def scheduler_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of projectid:schedulerid scheduler identifier."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     options = []
     schedulers = list_items(
         item_type="task",
@@ -392,7 +402,7 @@ def vocabularies(
     ctx: Context, param: Argument, incomplete: str, filter_: str = "all"
 ) -> list[CompletionItem]:
     """Prepare a list of vocabulary graphs for auto-completion."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     vocabs = get_vocabularies(filter_=filter_)
     options = []
     for _ in vocabs:
@@ -437,7 +447,7 @@ def file_list(
 
 def workflow_io_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of io workflows."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     options = []
     for _ in get_workflows_io():
         workflow_id = _["projectId"] + ":" + _["id"]
@@ -453,7 +463,7 @@ def replay_files(ctx: Context, param: Argument, incomplete: str) -> list[Complet
 
 def installed_package_names(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of installed packages."""
-    CONTEXT.set_connection_from_args(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     options = [(_["name"], _["version"]) for _ in list_packages()]
     return finalize_completion(candidates=options, incomplete=incomplete, sort_by=SORT_BY_KEY)
 
@@ -617,21 +627,47 @@ def triple_files(ctx: Context, param: Argument, incomplete: str) -> list[Complet
     )
 
 
+def sparql_accept_types(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
+    """Prepare a list of commonly used SPARQL accept content types."""
+    examples = [
+        (
+            "text/csv",
+            "CSV response, used for SELECT queries, omits language tags and datatypes of literals",
+        ),
+        ("application/sparql-results+json", "JSON response, used for SELECT queries"),
+        ("text/turtle", "Turtle response, used for CONSTRUCT queries"),
+        ("application/n-triples", "N-Triples response, used for CONSTRUCT queries"),
+    ]
+    return finalize_completion(candidates=examples, incomplete=incomplete)
+
+
 def placeholder(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of placeholder from the to-be executed queries."""
-    # look if cursor is in value position of the -p option and
-    # return nothing in case it is (values are not completed atm)
     args = get_completion_args(incomplete)
-    if args[len(args) - 2] in ("-p", "--parameter"):
-        return []
     # setup configuration
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     # extract placeholder from given queries in the command line
     options = []
+    placeholders: dict[str, QueryPlaceholder] = {}
+    catalog = QueryCatalog()  # fetch all queries
     for _, arg in enumerate(args):
-        query = QueryCatalog().get_query(arg)
+        query = catalog.get_query(arg)
         if query is not None:
+            # collect all placeholder descriptions of existing queries
+            placeholders = placeholders | get_placeholders_for_query(iri=query.url)
+            # collect all placeholder keys
             options.extend(list(query.get_placeholder_keys()))
+    # look if cursor is in value position of the -p option and
+    # use placeholder value completion, in case it is
+    if args[len(args) - 2] in ("-p", "--parameter"):
+        key = args[len(args) - 1]
+        if key in placeholders:
+            candidates = placeholders[key].complete(incomplete=incomplete)
+            return finalize_completion(
+                candidates=candidates, incomplete=incomplete, sort_by=NOT_SORTED
+            )
+        return []
+
     # look for already given parameter in the arguments and remove them from
     # the available options
     for num, arg in enumerate(args):
@@ -642,7 +678,7 @@ def placeholder(ctx: Context, param: Argument, incomplete: str) -> list[Completi
 
 def remote_queries(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of query URIs."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     options = []
     for query in QueryCatalog().get_queries().values():
         url = query.short_url
@@ -662,7 +698,7 @@ def remote_queries_and_sparql_files(
 
 def workflow_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of projectid:taskid workflow identifier."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     workflows = list_items(item_type="workflow")["results"]
     options = []
     for _ in workflows:
@@ -676,7 +712,7 @@ def workflow_ids(ctx: Context, param: Argument, incomplete: str) -> list[Complet
 
 def marshalling_plugins(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of supported workspace/project import/export plugins."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     options = get_marshalling_plugins()
     if "description" in options[0]:
         final_options = [(_["id"], _["description"]) for _ in options]
@@ -691,7 +727,7 @@ def marshalling_plugins(ctx: Context, param: Argument, incomplete: str) -> list[
 
 def project_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of project IDs for auto-completion."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     projects = get_projects()
     options = []
     for _ in projects:
@@ -712,7 +748,7 @@ def _prepare_graph_options(
     skip_selected_iris: bool = True,
 ) -> list[tuple[str, str]]:
     """Prepare a list of graphs with iri and label"""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     graphs = get_graphs(writeable=writeable, readonly=readonly)
     options = []
     for graph in graphs:
@@ -777,8 +813,8 @@ def graph_uris_with_all_graph_uri(
 def connections(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of config connections for auto-completion."""
     # since ctx does not have an obj here, we re-create the object
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
-    options = CONTEXT.config.sections()
+    app = ApplicationContext.from_params(ctx.find_root().params)
+    options = app.get_config().sections()
     return finalize_completion(candidates=options, incomplete=incomplete)
 
 
@@ -846,7 +882,7 @@ def graph_list_filter(ctx: Context, param: Argument, incomplete: str) -> list[Co
 
 def variable_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of variables IDs for auto-completion."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     variables = get_all_variables()
     options = []
     for _ in variables:
@@ -978,14 +1014,14 @@ def status_keys(ctx: Context, param: Argument, incomplete: str) -> list[Completi
 
 def user_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of username for admin update/delete/password command."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     options = [_["username"] for _ in list_users()]
     return finalize_completion(candidates=options, incomplete=incomplete, sort_by=SORT_BY_DESC)
 
 
 def user_group_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of group name for admin user update --(un)assign-group parameter"""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     if not ctx.args:
         return []
     users = get_user_by_username(username=str(ctx.args[0]))
@@ -1011,24 +1047,15 @@ def user_group_ids(ctx: Context, param: Argument, incomplete: str) -> list[Compl
 
 def client_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of client ids for admin secret and update command."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     options = [_["clientId"] for _ in list_open_id_clients()]
     return finalize_completion(candidates=options, incomplete=incomplete, sort_by=SORT_BY_DESC)
 
 
 def transformation_task_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
     """Prepare a list of projectId:transformation task identifier."""
-    CONTEXT.set_connection_from_params(ctx.find_root().params)
+    ApplicationContext.set_connection_from_params(ctx.find_root().params)
     results = list_items(item_type="transform")
     datasets = results["results"]
     options = [(f"{_['projectId']}:{_['id']}", _["label"]) for _ in datasets]
     return finalize_completion(candidates=options, incomplete=incomplete, sort_by=SORT_BY_DESC)
-
-
-def linking_task_ids(ctx: Context, param: Argument, incomplete: str) -> list[CompletionItem]:
-    """Prepare a list of projectId:linking task identifier."""
-    CONTEXT.set_connection_from_args(ctx.find_root().params)
-    results = list_items(item_type="linking")
-    datasets = results["results"]
-    options = [(_["projectId"] + r"\:" + _["id"], _["label"]) for _ in datasets]
-    return finalize_completion(candidates=options, incomplete=incomplete, sort_by=SORT_BY_DESC)

cmem_cmemc/config_parser.py

@@ -0,0 +1,44 @@
+"""Config parser module with a custom configuration parser."""
+
+import configparser
+
+
+class PureSectionConfigParser(configparser.RawConfigParser):
+    """A configuration parser that retrieves section data without defaults."""
+
+    _defaults: dict
+
+    def options(self, section: str) -> list:
+        """Return a list of option names for the given section, excluding defaults.
+
+        This method temporarily removes default options to ensure only explicitly
+        defined options in the given section are returned.
+
+        Args:
+            section (str): The section name.
+
+        Returns:
+            list: A list of option names in the specified section.
+
+        """
+        _d = self._defaults.copy()
+        try:
+            self._defaults.clear()
+            return super().options(section)
+        finally:
+            self._defaults.update(_d)
+
+    def optionxform(self, option: str) -> str:
+        """Preserve the case of option names.
+
+        By default, `optionxform` in `RawConfigParser` converts option names to lowercase.
+        This overridden method ensures that option names remain unchanged.
+
+        Args:
+            option (str): The option name.
+
+        Returns:
+            str: The unmodified option name.
+
+        """
+        return option