[ENH] add code and test to help create schemas

.gitignore

@@ -1,3 +1,6 @@
+**/tmp
+Pipfile
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

.pre-commit-config.yaml

@@ -8,7 +8,13 @@ repos:
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
+
 -   repo: https://github.com/psf/black
     rev: 22.6.0
     hooks:
     -   id: black
+
+-   repo: https://github.com/asottile/reorder_python_imports
+    rev: "v3.8.2"
+    hooks:
+        - id: reorder-python-imports

.vscode/settings.json

@@ -0,0 +1,6 @@
+{
+    "cSpell.words": [
+        "reproschema"
+    ],
+    "autoDocstring.docstringFormat": "numpy"
+}

pyproject.toml

@@ -0,0 +1,3 @@
+[tool.pytest.ini_options]
+minversion = "4.4.0"
+addopts = "-ra -vv"

reproschema/_version.py

@@ -3,12 +3,9 @@
 # feature). Distribution tarballs (built by setup.py sdist) and build
 # directories (produced by setup.py build) will contain a much shorter file
 # that just contains the computed version number.
-
 # This file is released into the public domain. Generated by
 # versioneer-0.18 (https://github.com/warner/python-versioneer)
-
 """Git implementation of _version.py."""
-
 import errno
 import os
 import re

reproschema/cli.py

@@ -1,8 +1,10 @@
 import os
+
 import click
 
-from . import get_logger, set_logger_level
 from . import __version__
+from . import get_logger
+from . import set_logger_level
 
 lgr = get_logger()
 

reproschema/jsonldutils.py

@@ -1,8 +1,12 @@
-from pyld import jsonld
-from pyshacl import validate as shacl_validate
 import json
 import os
-from .utils import start_server, stop_server, lgr
+
+from pyld import jsonld
+from pyshacl import validate as shacl_validate
+
+from .utils import lgr
+from .utils import start_server
+from .utils import stop_server
 
 
 def load_file(path_or_url, started=False, http_kwargs={}):

reproschema/models/README.md

@@ -0,0 +1,8 @@
+# README
+
+## reproschema file creation
+
+The creation reproschema protocols, activities and items (or Field) are handled
+by 3 python classes with the same names contained in their dedicated modules.
+
+They all inherit from the same base class.

reproschema/models/__init__.py

@@ -1,3 +1,3 @@
-from .protocol import Protocol
 from .activity import Activity
 from .item import Item
+from .protocol import Protocol

reproschema/models/activity.py

@@ -1,67 +1,73 @@
+from pathlib import Path
+from typing import Dict
+from typing import Optional
+from typing import Union
+
+from .base import COMMON_SCHEMA_ORDER
+from .base import DEFAULT_LANG
 from .base import SchemaBase
+from .item import Item
 
 
 class Activity(SchemaBase):
     """
     class to deal with reproschema activities
     """
 
-    schema_type = "reproschema:Activity"
-
-    def __init__(self, version=None):
-        super().__init__(version)
-        self.schema["ui"] = {"shuffle": [], "order": [], "addProperties": []}
-
-    def set_ui_shuffle(self, shuffle=False):
-        self.schema["ui"]["shuffle"] = shuffle
-
-    def set_URI(self, URI):
-        self.URI = URI
-
-    def get_URI(self):
-        return self.URI
-
-    # TODO
-    # preamble
-    # compute
-    # citation
-    # image
-
-    def set_defaults(self, name):
-        self._ReproschemaSchema__set_defaults(name)  # this looks wrong
-        self.set_ui_shuffle(False)
-
-    def update_activity(self, item_info):
-
-        # TODO
-        # - remove the hard coding on visibility and valueRequired
-
-        # update the content of the activity schema with new item
-
-        item_info["URI"] = "items/" + item_info["name"]
-
-        append_to_activity = {
-            "variableName": item_info["name"],
-            "isAbout": item_info["URI"],
-            "isVis": item_info["visibility"],
-            "valueRequired": False,
-        }
-
-        self.schema["ui"]["order"].append(item_info["URI"])
-        self.schema["ui"]["addProperties"].append(append_to_activity)
-
-    def sort(self):
-        schema_order = [
-            "@context",
-            "@type",
-            "@id",
-            "prefLabel",
-            "description",
-            "schemaVersion",
-            "version",
-            "ui",
-        ]
-        self.sort_schema(schema_order)
-
-        ui_order = ["shuffle", "order", "addProperties"]
-        self.sort_ui(ui_order)
+    def __init__(
+        self,
+        name: Optional[str] = "activity",
+        schemaVersion: Optional[str] = None,
+        prefLabel: Optional[str] = "activity",
+        altLabel: Optional[Dict[str, str]] = None,
+        description: Optional[str] = "",
+        preamble: Optional[str] = None,
+        citation: Optional[str] = None,
+        image: Optional[Union[str, Dict[str, str]]] = None,
+        audio: Optional[Union[str, Dict[str, str]]] = None,
+        video: Optional[Union[str, Dict[str, str]]] = None,
+        messages: Optional[Dict[str, str]] = None,
+        suffix: Optional[str] = "_schema",
+        visible: Optional[bool] = True,
+        required: Optional[bool] = False,
+        skippable: Optional[bool] = True,
+        limit: Optional[str] = None,
+        randomMaxDelay: Optional[str] = None,
+        schedule: Optional[str] = None,
+        ext: Optional[str] = ".jsonld",
+        output_dir: Optional[Union[str, Path]] = Path.cwd(),
+        lang: Optional[str] = DEFAULT_LANG(),
+    ):
+
+        schema_order = COMMON_SCHEMA_ORDER() + ["citation", "compute", "messages"]
+
+        super().__init__(
+            at_id=name,
+            schemaVersion=schemaVersion,
+            at_type="reproschema:Activity",
+            prefLabel={lang: prefLabel},
+            altLabel=altLabel,
+            description=description,
+            preamble=preamble,
+            citation=citation,
+            messages=messages,
+            image=image,
+            audio=audio,
+            video=video,
+            schema_order=schema_order,
+            visible=visible,
+            required=required,
+            skippable=skippable,
+            limit=limit,
+            randomMaxDelay=randomMaxDelay,
+            schedule=schedule,
+            suffix=suffix,
+            ext=ext,
+            output_dir=output_dir,
+            lang=lang,
+        )
+        self.ui.shuffle = False
+        self.update()
+
+    def append_item(self, item: Item):
+        self.ui.append(obj=item, variableName=item.get_basename())