chore: restructure repository (#632)

pyproject.toml

@@ -77,6 +77,8 @@ check-links = """
 darglint = """
     find . -name "*.py" \
     -not -path "./src/dsp_tools/models/*" \
+    -not -path "./src/dsp_tools/commands/xmlupload/models/*" \
+    -not -path "./src/dsp_tools/commands/project/models/*" \
     -not -path "./.git/*" \
     | xargs poetry run darglint -v 2\
 """
@@ -104,25 +106,24 @@ pythonpath = [".", "src", "test"]
 
 
 [tool.mypy]
-ignore_missing_imports = true                 # TODO: deactivate this
+ignore_missing_imports = true                                       # TODO: deactivate this
 show_column_numbers = true
 strict = true
 exclude = [
-    "src/dsp_tools/import_scripts",           # TODO: activate this
-    "src/dsp_tools/models/group.py",          # TODO: activate this
-    "src/dsp_tools/models/helpers.py ",       # TODO: activate this
-    "src/dsp_tools/models/langstring.py",     # TODO: activate this
-    "src/dsp_tools/models/listnode.py",       # TODO: activate this
-    "src/dsp_tools/models/ontology.py",       # TODO: activate this
-    "src/dsp_tools/models/permission.py",     # TODO: activate this
-    "src/dsp_tools/models/project.py",        # TODO: activate this
-    "src/dsp_tools/models/projectContext.py", # TODO: activate this
-    "src/dsp_tools/models/propertyclass.py",  # TODO: activate this
-    "src/dsp_tools/models/resource.py",       # TODO: activate this
-    "src/dsp_tools/models/resourceclass.py",  # TODO: activate this
-    "src/dsp_tools/models/user.py",           # TODO: activate this
-    "src/dsp_tools/models/value.py",          # TODO: activate this
-    "src/dsp_tools/models/xmlresource.py",    # TODO: activate this
+    "src/dsp_tools/commands/xmlupload/models/value.py",             # TODO: activate this
+    "src/dsp_tools/commands/xmlupload/models/permission.py",        # TODO: activate this
+    "src/dsp_tools/commands/xmlupload/models/xmlresource.py",       # TODO: activate this
+    "src/dsp_tools/models/helpers.py",                              # TODO: activate this
+    "src/dsp_tools/models/langstring.py",                           # TODO: activate this
+    "src/dsp_tools/commands/project/models/group.py",               # TODO: activate this
+    "src/dsp_tools/commands/project/models/listnode.py",            # TODO: activate this
+    "src/dsp_tools/commands/project/models/ontology.py",            # TODO: activate this
+    "src/dsp_tools/commands/project/models/project.py",             # TODO: activate this
+    "src/dsp_tools/models/projectContext.py",                       # TODO: activate this
+    "src/dsp_tools/commands/project/models/propertyclass.py",       # TODO: activate this
+    "src/dsp_tools/commands/project/models/resourceclass.py",       # TODO: activate this
+    "src/dsp_tools/commands/project/models/user.py",                # TODO: activate this
+    "src/dsp_tools/import_scripts",                                 # TODO: activate this
 ]
 
 

src/dsp_tools/__init__.py

@@ -0,0 +1 @@
+from dsp_tools.commands import excel2xml

src/dsp_tools/cli.py

@@ -9,27 +9,27 @@
 
 import regex
 
-from dsp_tools.excel2xml import excel2xml
-from dsp_tools.fast_xmlupload.process_files import process_files
-from dsp_tools.fast_xmlupload.upload_files import upload_files
-from dsp_tools.fast_xmlupload.upload_xml import fast_xmlupload
+from dsp_tools.commands.excel2json.lists import excel2lists, validate_lists_section_with_schema
+from dsp_tools.commands.excel2json.project import excel2json
+from dsp_tools.commands.excel2json.properties import excel2properties
+from dsp_tools.commands.excel2json.resources import excel2resources
+from dsp_tools.commands.excel2xml import excel2xml
+from dsp_tools.commands.fast_xmlupload.process_files import process_files
+from dsp_tools.commands.fast_xmlupload.upload_files import upload_files
+from dsp_tools.commands.fast_xmlupload.upload_xml import fast_xmlupload
+from dsp_tools.commands.id2iri import id2iri
+from dsp_tools.commands.project.create.project_create import create_project
+from dsp_tools.commands.project.create.project_create_lists import create_lists
+from dsp_tools.commands.project.create.project_validate import validate_project
+from dsp_tools.commands.project.get import get_project
+from dsp_tools.commands.rosetta import upload_rosetta
+from dsp_tools.commands.start_stack import StackConfiguration, StackHandler
+from dsp_tools.commands.template import generate_template_repo
+from dsp_tools.commands.xmlupload.upload_config import DiagnosticsConfig, UploadConfig
+from dsp_tools.commands.xmlupload.xmlupload import xmlupload
 from dsp_tools.models.exceptions import UserError
 from dsp_tools.utils.create_logger import get_logger
-from dsp_tools.utils.excel2json.lists import excel2lists, validate_lists_section_with_schema
-from dsp_tools.utils.excel2json.project import excel2json
-from dsp_tools.utils.excel2json.properties import excel2properties
-from dsp_tools.utils.excel2json.resources import excel2resources
-from dsp_tools.utils.generate_templates import generate_template_repo
-from dsp_tools.utils.id2iri import id2iri
-from dsp_tools.utils.project_create import create_project
-from dsp_tools.utils.project_create_lists import create_lists
-from dsp_tools.utils.project_get import get_project
-from dsp_tools.utils.project_validate import validate_project
-from dsp_tools.utils.rosetta import upload_rosetta
 from dsp_tools.utils.shared import validate_xml_against_schema
-from dsp_tools.utils.stack_handling import StackConfiguration, StackHandler
-from dsp_tools.utils.xmlupload.upload_config import DiagnosticsConfig, UploadConfig
-from dsp_tools.utils.xmlupload.xmlupload import xmlupload
 
 logger = get_logger(__name__)
 

src/dsp_tools/commands/__init__.py

@@ -0,0 +1 @@
+from . import excel2xml

src/dsp_tools/utils/excel2json/project.py → src/dsp_tools/commands/excel2json/project.py

@@ -3,10 +3,10 @@
 
 import regex
 
+from dsp_tools.commands.excel2json.lists import excel2lists
+from dsp_tools.commands.excel2json.properties import excel2properties
+from dsp_tools.commands.excel2json.resources import excel2resources
 from dsp_tools.models.exceptions import UserError
-from dsp_tools.utils.excel2json.lists import excel2lists
-from dsp_tools.utils.excel2json.properties import excel2properties
-from dsp_tools.utils.excel2json.resources import excel2resources
 
 
 def excel2json(

src/dsp_tools/utils/excel2json/properties.py → src/dsp_tools/commands/excel2json/properties.py

@@ -9,7 +9,7 @@
 import pandas as pd
 import regex
 
-import dsp_tools.utils.excel2json.utils as utl
+import dsp_tools.commands.excel2json.utils as utl
 from dsp_tools.models.exceptions import UserError
 
 languages = ["en", "de", "fr", "it", "rm"]

src/dsp_tools/utils/excel2json/resources.py → src/dsp_tools/commands/excel2json/resources.py

@@ -8,7 +8,7 @@
 import pandas as pd
 import regex
 
-import dsp_tools.utils.excel2json.utils as utl
+import dsp_tools.commands.excel2json.utils as utl
 from dsp_tools.models.exceptions import UserError
 from dsp_tools.utils.shared import check_notna, prepare_dataframe
 

src/dsp_tools/excel2xml.py → src/dsp_tools/commands/excel2xml.py

@@ -17,6 +17,7 @@
 from lxml import etree
 from lxml.builder import E  # pylint: disable=no-name-in-module
 
+from dsp_tools.commands.xmlupload.models.value import UriValue
 from dsp_tools.models.exceptions import BaseError
 from dsp_tools.models.helpers import DateTimeStamp
 
@@ -25,7 +26,6 @@
 # doing this requires silencing the corresponding pylint warning
 # (see https://pylint.readthedocs.io/en/latest/user_guide/messages/convention/useless-import-alias.html)
 from dsp_tools.models.propertyelement import PropertyElement as PropertyElement  # pylint: disable=useless-import-alias
-from dsp_tools.models.value import UriValue
 from dsp_tools.utils.shared import check_notna as check_notna  # pylint: disable=useless-import-alias
 from dsp_tools.utils.shared import simplify_name as simplify_name  # pylint: disable=useless-import-alias
 from dsp_tools.utils.shared import validate_xml_against_schema

src/dsp_tools/fast_xmlupload/upload_files.py → src/dsp_tools/commands/fast_xmlupload/upload_files.py

@@ -10,8 +10,8 @@
 from regex import regex
 from requests import JSONDecodeError
 
-from dsp_tools.connection.connection import Connection
 from dsp_tools.models.exceptions import UserError
+from dsp_tools.utils.connection import Connection
 from dsp_tools.utils.create_logger import get_logger
 from dsp_tools.utils.shared import login
 

src/dsp_tools/fast_xmlupload/upload_xml.py → src/dsp_tools/commands/fast_xmlupload/upload_xml.py

@@ -5,11 +5,11 @@
 
 from lxml import etree
 
-from dsp_tools.fast_xmlupload.upload_files import get_pkl_files
+from dsp_tools.commands.fast_xmlupload.upload_files import get_pkl_files
+from dsp_tools.commands.xmlupload.upload_config import UploadConfig
+from dsp_tools.commands.xmlupload.xmlupload import xmlupload
 from dsp_tools.models.exceptions import UserError
 from dsp_tools.utils.create_logger import get_logger
-from dsp_tools.utils.xmlupload.upload_config import UploadConfig
-from dsp_tools.utils.xmlupload.xmlupload import xmlupload
 
 logger = get_logger(__name__)
 

src/dsp_tools/utils/project_create.py → src/dsp_tools/commands/project/create/project_create.py

@@ -5,20 +5,20 @@
 
 import regex
 
-from dsp_tools.connection.connection import Connection
+from dsp_tools.commands.excel2json.lists import expand_lists_from_excel
+from dsp_tools.commands.project.create.project_create_lists import create_lists_on_server
+from dsp_tools.commands.project.create.project_validate import validate_project
+from dsp_tools.commands.project.models.group import Group
+from dsp_tools.commands.project.models.ontology import Ontology
+from dsp_tools.commands.project.models.project import Project
+from dsp_tools.commands.project.models.propertyclass import PropertyClass
+from dsp_tools.commands.project.models.resourceclass import ResourceClass
+from dsp_tools.commands.project.models.user import User
 from dsp_tools.models.exceptions import BaseError, UserError
-from dsp_tools.models.group import Group
 from dsp_tools.models.helpers import Cardinality, Context, DateTimeStamp
 from dsp_tools.models.langstring import LangString
-from dsp_tools.models.ontology import Ontology
-from dsp_tools.models.project import Project
-from dsp_tools.models.propertyclass import PropertyClass
-from dsp_tools.models.resourceclass import ResourceClass
-from dsp_tools.models.user import User
+from dsp_tools.utils.connection import Connection
 from dsp_tools.utils.create_logger import get_logger
-from dsp_tools.utils.excel2json.lists import expand_lists_from_excel
-from dsp_tools.utils.project_create_lists import create_lists_on_server
-from dsp_tools.utils.project_validate import validate_project
 from dsp_tools.utils.shared import login, parse_json_input, try_network_action
 
 logger = get_logger(__name__)

src/dsp_tools/utils/project_create_lists.py → src/dsp_tools/commands/project/create/project_create_lists.py

@@ -1,12 +1,12 @@
 from typing import Any, Optional, Union
 
-from dsp_tools.connection.connection import Connection
+from dsp_tools.commands.excel2json.lists import expand_lists_from_excel
+from dsp_tools.commands.project.create.project_validate import validate_project
+from dsp_tools.commands.project.models.listnode import ListNode
+from dsp_tools.commands.project.models.project import Project
 from dsp_tools.models.exceptions import BaseError, UserError
-from dsp_tools.models.listnode import ListNode
-from dsp_tools.models.project import Project
+from dsp_tools.utils.connection import Connection
 from dsp_tools.utils.create_logger import get_logger
-from dsp_tools.utils.excel2json.lists import expand_lists_from_excel
-from dsp_tools.utils.project_validate import validate_project
 from dsp_tools.utils.shared import login, parse_json_input, try_network_action
 
 logger = get_logger(__name__)

src/dsp_tools/utils/project_validate.py → src/dsp_tools/commands/project/create/project_validate.py

@@ -9,8 +9,8 @@
 import networkx as nx
 import regex
 
+from dsp_tools.commands.excel2json.lists import expand_lists_from_excel
 from dsp_tools.models.exceptions import BaseError
-from dsp_tools.utils.excel2json.lists import expand_lists_from_excel
 
 
 def _check_for_duplicate_names(project_definition: dict[str, Any]) -> bool:

src/dsp_tools/utils/project_get.py → src/dsp_tools/commands/project/get.py

@@ -4,13 +4,13 @@
 
 import regex
 
-from dsp_tools.connection.connection_live import ConnectionLive
+from dsp_tools.commands.project.models.group import Group
+from dsp_tools.commands.project.models.listnode import ListNode
+from dsp_tools.commands.project.models.ontology import Ontology
+from dsp_tools.commands.project.models.project import Project
+from dsp_tools.commands.project.models.user import User
 from dsp_tools.models.exceptions import BaseError
-from dsp_tools.models.group import Group
-from dsp_tools.models.listnode import ListNode
-from dsp_tools.models.ontology import Ontology
-from dsp_tools.models.project import Project
-from dsp_tools.models.user import User
+from dsp_tools.utils.connection_live import ConnectionLive
 
 
 def get_project(

src/dsp_tools/models/group.py → src/dsp_tools/commands/project/models/group.py

@@ -29,12 +29,12 @@
 from typing import Any, Optional, Union
 from urllib.parse import quote_plus
 
-from dsp_tools.connection.connection import Connection
+from dsp_tools.commands.project.models.model import Model
+from dsp_tools.commands.project.models.project import Project
 from dsp_tools.models.exceptions import BaseError
 from dsp_tools.models.helpers import Actions
 from dsp_tools.models.langstring import LangString
-from dsp_tools.models.model import Model
-from dsp_tools.models.project import Project
+from dsp_tools.utils.connection import Connection
 
 
 class Group(Model):  # pylint: disable=too-many-instance-attributes

src/dsp_tools/models/listnode.py → src/dsp_tools/commands/project/models/listnode.py

@@ -28,13 +28,13 @@
 from typing import Any, Optional, Union
 from urllib.parse import quote_plus
 
-from dsp_tools.connection.connection import Connection
+from dsp_tools.commands.project.models.model import Model
+from dsp_tools.commands.project.models.project import Project
+from dsp_tools.commands.project.models.set_encoder import SetEncoder
 from dsp_tools.models.exceptions import BaseError
 from dsp_tools.models.helpers import Actions
 from dsp_tools.models.langstring import LangString, Languages
-from dsp_tools.models.model import Model
-from dsp_tools.models.project import Project
-from dsp_tools.models.set_encoder import SetEncoder
+from dsp_tools.utils.connection import Connection
 
 
 def list_creator(con: Connection, project: Project, parent_node: "ListNode", nodes: list[dict]) -> list["ListNode"]:

src/dsp_tools/models/model.py → src/dsp_tools/commands/project/models/model.py

@@ -1,4 +1,4 @@
-from dsp_tools.connection.connection import Connection
+from dsp_tools.utils.connection import Connection
 
 
 class Model:  # pylint: disable=too-few-public-methods

src/dsp_tools/models/ontology.py → src/dsp_tools/commands/project/models/ontology.py

@@ -35,14 +35,14 @@
 
 import regex
 
-from dsp_tools.connection.connection import Connection
+from dsp_tools.commands.project.models.model import Model
+from dsp_tools.commands.project.models.project import Project
+from dsp_tools.commands.project.models.propertyclass import PropertyClass
+from dsp_tools.commands.project.models.resourceclass import ResourceClass
+from dsp_tools.commands.project.models.set_encoder import SetEncoder
 from dsp_tools.models.exceptions import BaseError
 from dsp_tools.models.helpers import Actions, Context, DateTimeStamp, WithId
-from dsp_tools.models.model import Model
-from dsp_tools.models.project import Project
-from dsp_tools.models.propertyclass import PropertyClass
-from dsp_tools.models.resourceclass import ResourceClass
-from dsp_tools.models.set_encoder import SetEncoder
+from dsp_tools.utils.connection import Connection
 
 
 class Ontology(Model):  # pylint: disable=too-many-instance-attributes

src/dsp_tools/models/project.py → src/dsp_tools/commands/project/models/project.py

@@ -30,12 +30,12 @@
 from typing import Any, Optional, Union
 from urllib.parse import quote_plus
 
-from dsp_tools.connection.connection import Connection
+from dsp_tools.commands.project.models.model import Model
+from dsp_tools.commands.project.models.set_encoder import SetEncoder
 from dsp_tools.models.exceptions import BaseError
 from dsp_tools.models.helpers import Actions
 from dsp_tools.models.langstring import LangString, Languages
-from dsp_tools.models.model import Model
-from dsp_tools.models.set_encoder import SetEncoder
+from dsp_tools.utils.connection import Connection
 
 
 class Project(Model):  # pylint: disable=too-many-instance-attributes,too-many-public-methods

src/dsp_tools/models/propertyclass.py → src/dsp_tools/commands/project/models/propertyclass.py

@@ -6,13 +6,13 @@
 
 import regex
 
-from dsp_tools.connection.connection import Connection
+from dsp_tools.commands.project.models.listnode import ListNode
+from dsp_tools.commands.project.models.model import Model
+from dsp_tools.commands.project.models.set_encoder import SetEncoder
 from dsp_tools.models.exceptions import BaseError
 from dsp_tools.models.helpers import Actions, Context, DateTimeStamp, WithId
 from dsp_tools.models.langstring import LangString, Languages
-from dsp_tools.models.listnode import ListNode
-from dsp_tools.models.model import Model
-from dsp_tools.models.set_encoder import SetEncoder
+from dsp_tools.utils.connection import Connection
 
 
 class PropertyClass(Model):  # pylint: disable=too-many-instance-attributes,too-many-public-methods

src/dsp_tools/models/resourceclass.py → src/dsp_tools/commands/project/models/resourceclass.py

@@ -16,12 +16,12 @@
 
 import regex
 
-from dsp_tools.connection.connection import Connection
+from dsp_tools.commands.project.models.model import Model
+from dsp_tools.commands.project.models.set_encoder import SetEncoder
 from dsp_tools.models.exceptions import BaseError
 from dsp_tools.models.helpers import Actions, Cardinality, Context, DateTimeStamp
 from dsp_tools.models.langstring import LangString, Languages
-from dsp_tools.models.model import Model
-from dsp_tools.models.set_encoder import SetEncoder
+from dsp_tools.utils.connection import Connection
 
 
 class HasProperty(Model):

src/dsp_tools/models/user.py → src/dsp_tools/commands/project/models/user.py

@@ -29,13 +29,13 @@
 from typing import Any, Optional, Union
 from urllib.parse import quote_plus
 
-from dsp_tools.connection.connection import Connection
+from dsp_tools.commands.project.models.group import Group
+from dsp_tools.commands.project.models.model import Model
+from dsp_tools.commands.project.models.project import Project
 from dsp_tools.models.exceptions import BaseError
-from dsp_tools.models.group import Group
 from dsp_tools.models.helpers import Actions
 from dsp_tools.models.langstring import Languages
-from dsp_tools.models.model import Model
-from dsp_tools.models.project import Project
+from dsp_tools.utils.connection import Connection
 
 
 class User(Model):  # pylint: disable=too-many-instance-attributes,too-many-public-methods

src/dsp_tools/utils/rosetta.py → src/dsp_tools/commands/rosetta.py

@@ -2,10 +2,10 @@
 import subprocess
 from pathlib import Path
 
+from dsp_tools.commands.project.create.project_create import create_project
+from dsp_tools.commands.xmlupload.upload_config import UploadConfig
+from dsp_tools.commands.xmlupload.xmlupload import xmlupload
 from dsp_tools.models.exceptions import UserError
-from dsp_tools.utils.project_create import create_project
-from dsp_tools.utils.xmlupload.upload_config import UploadConfig
-from dsp_tools.utils.xmlupload.xmlupload import xmlupload
 
 
 def _update_possibly_existing_repo(rosetta_folder: Path) -> bool: