Make web UI dependencies optional

.github/workflows/tests.yml

@@ -17,7 +17,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .[test]
+        pip install .[test,ui]
         python -c "import nltk; nltk.download('punkt'); nltk.download('stopwords')"
         python -m adeft.download
     - name: Tests

.gitignore

@@ -133,3 +133,4 @@ doc/_build/
 benchmarks/data/**
 benchmarks/results/**
 .DS_Store
+test.db

Dockerfile

@@ -4,6 +4,6 @@ RUN python -m pip install --upgrade pip
 
 COPY . /app
 WORKDIR /app
-RUN python -m pip install .
+RUN python -m pip install .[ui]
 RUN python -m gilda.resources
 ENTRYPOINT gilda --port 8001 --host "0.0.0.0"

README.md

@@ -62,7 +62,8 @@ results = gilda.annotate('Calcium is released from the ER.')
 ```
 
 ### Use as a web service
-The REST service accepts POST requests with a JSON header on the /ground
+
+The REST service accepts POST requests with a JSON header on the `/ground`
 endpoint. There is a public REST service running at http://grounding.indra.bio
 but the service can also be run locally as
 
@@ -106,7 +107,7 @@ is an issue, the following options are recommended.
 other processes send requests to.
 
 2. Create a custom Grounder instance that only loads a subset of terms
-approrpiate for a narrow use case.
+appropriate for a narrow use case.
 
 3. Gilda also offers an optional sqlite back-end which significantly decreases
 memory usage and results in minor drop in the number of strings grounder per

gilda/app/app.py

@@ -1,127 +1,12 @@
 from textwrap import dedent
 from typing import Optional
 
-from flask import Blueprint, Flask, abort, jsonify, \
-    render_template, request, current_app
-from flask_bootstrap import Bootstrap
+from flask import Flask, abort, jsonify, redirect, request
 from flask_restx import Api, Resource, fields
-from flask_wtf import FlaskForm
-from werkzeug.local import LocalProxy
-from wtforms import StringField, SubmitField, TextAreaField, \
-    SelectMultipleField
-from wtforms.validators import DataRequired
 
 from gilda import __version__ as version
-from gilda.resources import popular_organisms, organism_labels
 from gilda.grounder import GrounderInput, Grounder
-
-ui_blueprint = Blueprint("ui", __name__, url_prefix="/")
-
-# The way that local proxies work is that when the app gets
-# instantiated, you can stick objects into the `app.config`
-# dictionary, then the local proxy lets you access them through
-# a fake "current_app" object.
-grounder = LocalProxy(lambda: current_app.config["grounder"])
-
-ORGANISMS_FIELD = SelectMultipleField(
-    'Species priority (optional)',
-    choices=[(org, organism_labels[org]) for org in popular_organisms],
-    id='organism-select',
-    description=dedent("""\
-        Optionally select one or more taxonomy
-        species IDs to define a species priority list.  Click
-        <a type="button" href="#" data-toggle="modal" data-target="#species-modal">
-        here <i class="far fa-question-circle">
-        </i></a> for more details.
-    """),
-)
-
-class GroundForm(FlaskForm):
-    text = StringField(
-        'Text',
-        validators=[DataRequired()],
-        description=dedent("""\
-            Input the entity text (e.g., <code>k-ras</code>) to ground."""
-            #Click <a type="button" href="#" data-toggle="modal" data-target="#text-modal">
-            #here <i class="far fa-question-circle">
-            #</i></a> for more information
-        ),
-    )
-    context = TextAreaField(
-        'Context (optional)',
-        description=dedent("""\
-            Optionally provide additional text context to help disambiguation. Click
-            <a type="button" href="#" data-toggle="modal" data-target="#context-modal">
-            here <i class="far fa-question-circle">
-            </i></a> for more details.
-        """)
-    )
-    organisms = ORGANISMS_FIELD
-    submit = SubmitField('Submit')
-
-    def get_matches(self):
-        return grounder.ground(self.text.data, context=self.context.data,
-                               organisms=self.organisms.data)
-
-
-class NERForm(FlaskForm):
-    text = TextAreaField(
-        'Text',
-        validators=[DataRequired()],
-        description=dedent("""\
-            Text from which to identify and ground named entities.
-        """)
-    )
-    organisms = ORGANISMS_FIELD
-    submit = SubmitField('Submit')
-
-    def get_annotations(self):
-        from gilda.ner import annotate
-
-        return annotate(self.text.data, grounder=grounder,
-                        organisms=self.organisms.data)
-
-
-@ui_blueprint.route('/', methods=['GET', 'POST'])
-def home():
-    text = request.args.get('text')
-    if text is not None:
-        context = request.args.get('context')
-        organisms = request.args.getlist('organisms')
-        matches = grounder.ground(text, context=context, organisms=organisms)
-        return render_template('matches.html', matches=matches, version=version,
-                               text=text, context=context)
-
-    form = GroundForm()
-    if form.validate_on_submit():
-        matches = form.get_matches()
-        return render_template(
-            'matches.html',
-            matches=matches,
-            version=version,
-            text=form.text.data,
-            context=form.context.data,
-            # Add a new form that doesn't auto-populate
-            form=GroundForm(formdata=None),
-        )
-    return render_template('home.html', form=form, version=version)
-
-
-@ui_blueprint.route('/ner', methods=['GET', 'POST'])
-def view_ner():
-    form = NERForm()
-    if form.validate_on_submit():
-        annotations = form.get_annotations()
-        return render_template(
-            'ner_matches.html',
-            annotations=annotations,
-            version=version,
-            text=form.text.data,
-            # Add a new form that doesn't auto-populate
-            form=NERForm(formdata=None),
-        )
-    return render_template('ner_home.html', form=form, version=version)
-
+from gilda.app.proxies import grounder
 
 # NOTE: the Flask REST-X API has to be declared here, below the home endpoint
 # otherwise it reserves the / base path.
@@ -363,14 +248,53 @@ def get(self):
         return jsonify(grounder.get_models())
 
 
-def get_app(terms: Optional[GrounderInput] = None) -> Flask:
+def get_app(terms: Optional[GrounderInput] = None, *, ui: bool = True) -> Flask:
     app = Flask(__name__)
     app.config['RESTX_MASK_SWAGGER'] = False
     app.config['WTF_CSRF_ENABLED'] = False
     app.config['SWAGGER_UI_DOC_EXPANSION'] = 'list'
     app.config["grounder"] = Grounder(terms=terms)
-    Bootstrap(app)
-    app.register_blueprint(ui_blueprint, url_prefix="/")
+
+    if not ui:
+        _mount_home_redirect(app)
+    else:
+        try:
+            import importlib.metadata as importlib_metadata
+        except ImportError:
+            import importlib_metadata
+
+        try:
+            from flask_bootstrap import Bootstrap
+
+            bootstrap_version = importlib_metadata.version("flask_bootstrap")
+            if "3.3.7.1" != bootstrap_version:
+                raise ImportError(
+                    dedent(
+                        """\
+                    The wrong flask-bootstrap is installed, therefore the UI
+                    can not be enabled. Please run the following commands in
+                    the shell:
+
+                      pip uninstall flask-bootstrap bootstrap-flask
+                      pip install flask-bootstrap
+                    """
+                    )
+                )
+
+            from gilda.app.ui import ui_blueprint
+        except ImportError:
+            _mount_home_redirect(app)
+        else:
+            Bootstrap(app)
+            app.register_blueprint(ui_blueprint, url_prefix="/")
+
     # has to be put after defining the UI blueprint otherwise it reserves "/"
     api.init_app(app)
     return app
+
+
+def _mount_home_redirect(app):
+    @app.route("/")
+    def home_redirect():
+        """Redirect the home url to the API documentation."""
+        return redirect("/apidocs")

gilda/app/proxies.py

@@ -0,0 +1,13 @@
+from werkzeug.local import LocalProxy
+
+from flask import current_app
+
+__all__ = [
+    "grounder",
+]
+
+# The way that local proxies work is that when the app gets
+# instantiated, you can stick objects into the `app.config`
+# dictionary, then the local proxy lets you access them through
+# a fake "current_app" object.
+grounder = LocalProxy(lambda: current_app.config["grounder"])

gilda/app/ui.py

@@ -0,0 +1,121 @@
+from textwrap import dedent
+
+from flask import Blueprint, render_template, request
+from flask_wtf import FlaskForm
+from wtforms import SelectMultipleField, StringField, SubmitField, TextAreaField
+from wtforms.validators import DataRequired
+
+from gilda.app.proxies import grounder
+from gilda import __version__ as version
+from gilda.resources import organism_labels, popular_organisms
+
+__all__ = [
+    "ui_blueprint",
+]
+
+ORGANISMS_FIELD = SelectMultipleField(
+    "Species priority (optional)",
+    choices=[(org, organism_labels[org]) for org in popular_organisms],
+    id="organism-select",
+    description=dedent(
+        """\
+        Optionally select one or more taxonomy
+        species IDs to define a species priority list.  Click
+        <a type="button" href="#" data-toggle="modal" data-target="#species-modal">
+        here <i class="far fa-question-circle">
+        </i></a> for more details.
+    """
+    ),
+)
+
+
+class GroundForm(FlaskForm):
+    text = StringField(
+        "Text",
+        validators=[DataRequired()],
+        description="Input the entity text (e.g., <code>k-ras</code>) to ground.",
+    )
+    context = TextAreaField(
+        "Context (optional)",
+        description=dedent(
+            """\
+            Optionally provide additional text context to help disambiguation. Click
+            <a type="button" href="#" data-toggle="modal" data-target="#context-modal">
+            here <i class="far fa-question-circle">
+            </i></a> for more details.
+        """
+        ),
+    )
+    organisms = ORGANISMS_FIELD
+    submit = SubmitField("Submit")
+
+    def get_matches(self):
+        return grounder.ground(
+            self.text.data, context=self.context.data, organisms=self.organisms.data
+        )
+
+
+class NERForm(FlaskForm):
+    text = TextAreaField(
+        "Text",
+        validators=[DataRequired()],
+        description=dedent(
+            """\
+            Text from which to identify and ground named entities.
+        """
+        ),
+    )
+    organisms = ORGANISMS_FIELD
+    submit = SubmitField("Submit")
+
+    def get_annotations(self):
+        from gilda.ner import annotate
+
+        return annotate(
+            self.text.data, grounder=grounder, organisms=self.organisms.data
+        )
+
+
+ui_blueprint = Blueprint("ui", __name__, url_prefix="/")
+
+
+@ui_blueprint.route("/", methods=["GET", "POST"])
+def home():
+    text = request.args.get("text")
+    if text is not None:
+        context = request.args.get("context")
+        organisms = request.args.getlist("organisms")
+        matches = grounder.ground(text, context=context, organisms=organisms)
+        return render_template(
+            "matches.html", matches=matches, version=version, text=text, context=context
+        )
+
+    form = GroundForm()
+    if form.validate_on_submit():
+        matches = form.get_matches()
+        return render_template(
+            "matches.html",
+            matches=matches,
+            version=version,
+            text=form.text.data,
+            context=form.context.data,
+            # Add a new form that doesn't auto-populate
+            form=GroundForm(formdata=None),
+        )
+    return render_template("home.html", form=form, version=version)
+
+
+@ui_blueprint.route("/ner", methods=["GET", "POST"])
+def view_ner():
+    form = NERForm()
+    if form.validate_on_submit():
+        annotations = form.get_annotations()
+        return render_template(
+            "ner_matches.html",
+            annotations=annotations,
+            version=version,
+            text=form.text.data,
+            # Add a new form that doesn't auto-populate
+            form=NERForm(formdata=None),
+        )
+    return render_template("ner_home.html", form=form, version=version)