fixing issue497

.github/workflows/buildandtestpython.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: [3.8, 3.9, '3.10', '3.11']
 
     steps:
       - uses: actions/checkout@v2

.github/workflows/pythonpublish.yml

@@ -2,7 +2,7 @@ name: Upload Python Package
 
 on:
   release:
-    types: [created]
+    types: [published]
 
 jobs:
   deploy:

.gitignore

@@ -139,6 +139,8 @@ performances/profiles/*
 .github/workflows/_build.yml
 course/
 bin/
-isa-reports/
+isa-reports/*
 isaRDF/
-venv*/
+venv*/
+instance/*
+instance/

isa-cookbook/content/notebooks/querying-isa-with-graphql-and-sparql.ipynb

@@ -24,7 +24,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 17,
    "outputs": [],
    "source": [
     "# Let's first import all the packages we need"
@@ -35,7 +35,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 18,
    "outputs": [],
    "source": [
     "from os import path\n",
@@ -61,7 +61,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 19,
    "outputs": [],
    "source": [
     "filepath = path.join('json', 'BII-S-3', 'BII-S-3.json')\n",
@@ -90,8 +90,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "outputs": [],
+   "execution_count": 20,
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['sample collection', 'nucleic acid extraction', 'reverse transcription', 'library construction', 'nucleic acid sequencing', 'data transformation']\n"
+     ]
+    }
+   ],
    "source": [
     "query = \"\"\"\n",
     "{\n",
@@ -127,10 +135,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 21,
    "outputs": [],
    "source": [
-    "set_context(new_context='wdt', combine=False, local=False)"
+    "set_context(vocab='wd', local=True, prepend_url='https://example.com', all_in_one=False)"
    ],
    "metadata": {
     "collapsed": false
@@ -139,10 +147,12 @@
   {
    "cell_type": "markdown",
    "source": [
-    "The `set_context()` method takes three parameters:\n",
-    "    - new_context: to choose the vocabulary to use between `sdo`, `obo` and `wdt`\n",
-    "    - combine: if `True`, only one context will be used\n",
-    "    - local: if `True`, uses local files else the GitHub contexts"
+    "The `set_context()` method takes five parameters:\n",
+    "   - vocab: to choose the vocabulary to use between `sdo`, `obo`, `wdt`, `wd` and `sio`\n",
+    "   - local: if `True`, uses local files else the GitHub contexts\n",
+    "   - prepend_url: the url to prepend to the isa identifiers (this is the URL of your SPARQL endpoint)\n",
+    "   - all_in_on: if `True`, all the contexts are pulled from a single file instead of separate context files\n",
+    "   - include_context: if `True`, the context is included in the JSON-LD serialization, else it only contains the URL or local path to the context file."
    ],
    "metadata": {
     "collapsed": false
@@ -159,7 +169,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 22,
    "outputs": [],
    "source": [
     "ld = investigation.to_dict(ld=True)"
@@ -190,22 +200,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 23,
    "outputs": [],
    "source": [
     "# Creating the namespace\n",
-    "WDT = Namespace(\"http://www.wikidata.org/wiki/\")\n",
-    "WDTP = Namespace('https://www.wikidata.org/wiki/Property:')\n",
+    "WD = Namespace(\"http://www.wikidata.org/entity/\")\n",
     "ISA = Namespace('https://isa.org/')\n",
     "\n",
     "ld_string = json.dumps(ld) # Get a string representation of the ld variable\n",
     "graph = Graph() # Create an empty graph\n",
     "graph.parse(data=ld_string, format='json-ld') # Load the data into the graph\n",
     "\n",
     "# Finally, bind the namespaces to the graph\n",
-    "graph.bind('wdt', WDT)\n",
-    "graph.bind('isa', ISA)\n",
-    "graph.bind('wdtp', WDTP)"
+    "graph.bind('wdt', WD)\n",
+    "graph.bind('isa', ISA)"
    ],
    "metadata": {
     "collapsed": false
@@ -222,23 +230,30 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "outputs": [],
+   "execution_count": 24,
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['sample collection', 'nucleic acid extraction', 'reverse transcription', 'library construction', 'nucleic acid sequencing', 'data transformation']\n"
+     ]
+    }
+   ],
    "source": [
     "query = \"\"\"\n",
     "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n",
     "PREFIX owl: <http://www.w3.org/2002/07/owl#>\n",
     "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n",
     "PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n",
-    "PREFIX wdtp: <https://www.wikidata.org/wiki/Property:>\n",
-    "PREFIX wdt: <http://www.wikidata.org/wiki/>\n",
+    "PREFIX wd: <http://www.wikidata.org/entity/>\n",
     "\n",
     "SELECT distinct ?protocolTypeName\n",
     "WHERE {\n",
-    "    ?p rdf:type wdt:Q41689629 . # Is a protocol\n",
-    "    ?p wdtp:P7793 ?protocolType .\n",
-    "    ?protocolType wdtp:P527 ?protocolTypeName . # Get each protocol type name\n",
-    "    FILTER (?protocolTypeName!=\"\"^^wdt:Q1417099) # Filter out empty protocol type name\n",
+    "    ?p rdf:type wd:Q41689629 . # Is a protocol\n",
+    "    ?p wd:P7793 ?protocolType .\n",
+    "    ?protocolType wd:P527 ?protocolTypeName . # Get each protocol type name\n",
+    "    FILTER (?protocolTypeName!=\"\"^^wd:Q1417099) # Filter out empty protocol type name\n",
     "}\n",
     "\"\"\"\n",
     "protocols_sparql = []\n",

isatools/convert/isatab2json.py

@@ -19,7 +19,7 @@
 log = logging.getLogger('isatools')
 
 SCHEMAS_PATH = join(os.path.dirname(os.path.realpath(__file__)),
-                    "../resources/schemas/v1.0.1/")
+                    "..", "resources", "schemas", "isa_model_version_1_0_schemas", "core")
 INVESTIGATION_SCHEMA = "investigation_schema.json"
 
 # REGEXES

isatools/create/connectors.py

@@ -119,9 +119,9 @@ def assay_ordered_dict_to_template(assay_ord_dict):
     :return: dict, can be directly serialized to JSON
     """
     res = dict()
-    res['measurement_type'] = _reverse_map_ontology_annotation(assay_ord_dict['measurement_type'],
+    res['measurement_type'] = _reverse_map_ontology_annotation(assay_ord_dict.get('measurement_type', None),
                                                                compress_strings=True)
-    res['technology_type'] = _reverse_map_ontology_annotation(assay_ord_dict['technology_type'],
+    res['technology_type'] = _reverse_map_ontology_annotation(assay_ord_dict.get('technology_type', None),
                                                               compress_strings=True)
     res['workflow'] = []
     for name, nodes in assay_ord_dict.items():

isatools/create/model.py

@@ -7,7 +7,8 @@
 import itertools
 import json
 import re
-from collections import OrderedDict, Iterable
+from collections import OrderedDict
+from collections.abc import Iterable
 from copy import deepcopy
 import logging
 from numbers import Number

isatools/database/__init__.py

@@ -0,0 +1,17 @@
+"""
+The isatools database package contains the SQLAlchemy models for the ISA tools library.
+It works by dynamically adding methods to the models defined in the isatools.model package.
+
+The database model is highly sensitive to identifiers. We suggest serializing all your ISA-tab files to json
+to enforce the generation of identifiers. This will ensure that the database model can be used to serialize the ISA
+objects in SQLAlchemy.
+
+Authors: D. Batista (@Terazus)
+"""
+
+from isatools.database.utils import app, db
+from isatools.database.models import (
+    Comment, Publication, Investigation, Study, OntologyAnnotation, OntologySource,
+    Parameter, Person, Process, Protocol, Source, Characteristic, Factor, Sample,
+    FactorValue, Material, ParameterValue, Assay, Datafile as DataFile
+)

isatools/database/models/__init__.py

@@ -0,0 +1,92 @@
+from isatools.database.models.comment import (
+    CommentModel as Comment, Comment as CommentTable, make_comment_methods
+)
+from isatools.database.models.publication import (
+    PublicationModel as Publication, Publication as PublicationTable, make_publication_methods
+)
+from isatools.database.models.investigation import (
+    InvestigationModel as Investigation, Investigation as InvestigationTable, make_investigation_methods
+)
+from isatools.database.models.study import (
+    StudyModel as Study, Study as StudyTable, make_study_methods
+)
+from isatools.database.models.ontology_annotation import (
+    OntologyAnnotationModel as OntologyAnnotation, OntologyAnnotation as OntologyAnnotationTable,
+    make_ontology_annotation_methods
+)
+from isatools.database.models.ontology_source import (
+    OntologySourceModel as OntologySource, OntologySource as OntologySourceTable, make_ontology_source_methods
+)
+from isatools.database.models.parameter import (
+    ParameterModel as Parameter, Parameter as ParameterTable, make_parameter_methods
+)
+from isatools.database.models.person import (
+    PersonModel as Person, Person as PersonTable, make_person_methods
+)
+from isatools.database.models.process import (
+    ProcessModel as Process, Process as ProcessTable, make_process_methods
+)
+from isatools.database.models.protocol import (
+    ProtocolModel as Protocol, Protocol as ProtocolTable, make_protocol_methods
+)
+from isatools.database.models.source import (
+    SourceModel as Source, Source as SourceTable, make_source_methods
+)
+from isatools.database.models.characteristic import (
+    CharacteristicModel as Characteristic, Characteristic as CharacteristicTable, make_characteristic_methods
+)
+from isatools.database.models.study_factor import (
+    StudyFactorModel as Factor, StudyFactor as FactorTable, make_study_factor_methods
+)
+from isatools.database.models.sample import (
+    SampleModel as Sample, Sample as SampleTable, make_sample_methods
+)
+from isatools.database.models.factor_value import (
+    FactorValueModel as FactorValue, FactorValue as FactorValueTable, make_factor_value_methods
+)
+from isatools.database.models.material import (
+    MaterialModel as Material, Material as MaterialTable, make_material_methods
+)
+from isatools.database.models.parameter_value import (
+    ParameterValueModel as ParameterValue, ParameterValue as ParameterValueTable, make_parameter_value_methods
+)
+from isatools.database.models.assay import (
+    AssayModel as Assay, Assay as AssayTable, make_assay_methods
+)
+from isatools.database.models.datafile import (
+    DataFileModel as Datafile, Datafile as DatafileTable, make_datafile_methods
+)
+
+
+def __make_methods():
+    # base methods
+    make_comment_methods()
+    make_ontology_source_methods()
+    make_ontology_annotation_methods()
+    make_publication_methods()
+    make_person_methods()
+
+    # studies methods
+    make_parameter_methods()
+    make_parameter_value_methods()
+    make_process_methods()
+    make_protocol_methods()
+    make_study_factor_methods()
+    make_factor_value_methods()
+
+    # materials methods
+    make_characteristic_methods()
+    make_source_methods()
+    make_sample_methods()
+    make_material_methods()
+    make_datafile_methods()
+
+    # assays
+    make_assay_methods()
+
+    # investigation methods
+    make_study_methods()
+    make_investigation_methods()
+
+
+__make_methods()