ivoryos 1.0.9__py3-none-any.whl → 1.4.4__py3-none-any.whl

ivoryos/routes/control/templates/control/controllers_new.html

@@ -1,89 +0,0 @@
-{% extends 'base.html' %}
-{% block title %}IvoryOS | New devices{% endblock %}
-
-{% block body %}
-    <div class="row">
-        <div class="col-xl-4 col-lg-4 col-md-6 mb-4 ">
-            <h5>Available Python API</h5>
-            <hr>
-            {% for instrument in api_variables %}
-                <div class="bg-white rounded shadow-sm position-relative">
-                    <h5 class="p-3 controller-card">
-                        <a href="{{ url_for('control.new_controller', instrument=instrument) }}" class="text-dark stretched-link">{{instrument}}</a>
-                    </h5>
-                </div>
-            {% endfor %}
-            <div class="bg-white rounded shadow-sm position-relative">
-                <h5 class="p-3 controller-card">
-                    <a data-bs-toggle="modal" href="#importAPI" class="stretched-link"><i class="bi bi-folder-plus"></i> Import API</a>
-                </h5>
-            </div>
-        </div>
-        <div class="col-xl-5 col-lg-5 col-md-6 mb-4 ">
-            {% if device %}
-                <h5>Connecting</h5><hr>
-                <form role="form" method='POST' name="init" action="{{ url_for('control.new_controller', instrument=instrument) }}">
-                    <div class="form-group">
-                        <div class="input-group mb-3">
-                            <span class="input-group-text" >Name this device</span>
-                            <input class="form-control" type="text" id="device_name" name="device_name" aria-labelledby="nameHelpBlock" placeholder="e.g. {{device.__name__}}_1" >
-                            <div id="nameHelpBlock" class="form-text">
-                                Name your instrument, avoid names that are defined on the right
-                            </div>
-                        </div>
-                        {% for arg in device.__init__.__annotations__ %}
-                            {% if not arg == "return" %}
-                                <div class="input-group mb-3">
-                                    <span class="input-group-text" >{{arg}}</span>
-                                    <input class="form-control"  type="text" id="{{arg}}" name="{{arg}}"
-                                           placeholder="{{device.__init__.__annotations__[arg].__name__}}"
-                                           value="{{args.parameters[arg].default if not args.parameters[arg].default.__name__ == '_empty' else ''}}">
-                                    {% if device.__init__.__annotations__[arg].__module__ is not in ["builtins", "typing"] %}
-                                        <a role="button" href="{{ url_for('control.new_controller', instrument=device.__init__.__annotations__[arg].__name__) }}" class="btn btn-secondary">initialize {{device.__init__.__annotations__[arg].__name__}} first</a>
-                                    {% endif %}
-                                </div>
-                            {% endif %}
-                        {% endfor %}
-                        <button type="submit" class="btn btn-dark">Connect</button>
-                    </div>
-                </form>
-            {% endif %}
-        </div>
-        <div class="col-xl-3 col-lg-3 col-md-6 mb-4">
-            <h5>Defined Instruments</h5><hr>
-            {% if defined_variables %}
-                <ul class="list-group">
-                    {% for instrument in defined_variables %}
-                        <li class="list-group-item">{{instrument}}</li>
-                    {% endfor %}
-                </ul>
-            {% endif %}
-        </div>
-    </div>
-
-
-    <div class="modal fade" id="importAPI" tabindex="-1" aria-labelledby="importModal" aria-hidden="true" >
-        <div class="modal-dialog">
-            <div class="modal-content">
-                <div class="modal-header">
-                    <h1 class="modal-title fs-5" id="importModal">Import API by file path</h1>
-                    <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
-                </div>
-                <form method="POST" action="{{ url_for('control.import_api') }}" enctype="multipart/form-data">
-                    <div class="modal-body">
-                        <h5>input manually</h5>
-                        <div class="input-group mb-3">
-                            <label class="input-group-text" for="filepath">File Path:</label>
-                            <input type="text" class="form-control" name="filepath" id="filepath">
-                        </div>
-                        <div class="modal-footer">
-                            <button type="button" class="btn btn-secondary" data-bs-dismiss="modal"> Close </button>
-                            <button type="submit"  class="btn btn-primary"> Save </button>
-                        </div>
-                    </div>
-                </form>
-            </div>
-        </div>
-    </div>
-
-{% endblock %}

ivoryos/routes/database/database.py

@@ -1,306 +0,0 @@
-from flask import Blueprint, redirect, url_for, flash, request, render_template, session, current_app, jsonify
-from flask_login import login_required
-
-from ivoryos.utils.db_models import Script, db, WorkflowRun, WorkflowStep
-from ivoryos.utils.utils import get_script_file, post_script_file
-
-database = Blueprint('database', __name__, template_folder='templates/database')
-
-
-
-@database.route("/database/scripts/edit/<script_name>")
-@login_required
-def edit_workflow(script_name:str):
-    """
-    .. :quickref: Database; load workflow script to canvas
-
-    load the selected workflow to the design canvas
-
-    .. http:get:: /database/scripts/edit/<script_name>
-
-    :param script_name: script name
-    :type script_name: str
-    :status 302: redirect to :http:get:`/ivoryos/design/script/`
-    """
-    row = Script.query.get(script_name)
-    script = Script(**row.as_dict())
-    post_script_file(script)
-    pseudo_name = session.get("pseudo_deck", "")
-    off_line = current_app.config["OFF_LINE"]
-    if off_line and pseudo_name and not script.deck == pseudo_name:
-        flash(f"Choose the deck with name {script.deck}")
-    if request.accept_mimetypes.best_match(['application/json', 'text/html']) == 'application/json':
-        return jsonify({
-            "script": script.as_dict(),
-            "python_script": script.compile(),
-        })
-    return redirect(url_for('design.experiment_builder'))
-
-
-@database.route("/database/scripts/delete/<script_name>")
-@login_required
-def delete_workflow(script_name: str):
-    """
-    .. :quickref: Database; delete workflow
-
-    delete workflow from database
-
-    .. http:get:: /database/scripts/delete/<script_name>
-
-    :param script_name: workflow name
-    :type script_name: str
-    :status 302: redirect to :http:get:`/ivoryos/database/scripts/`
-
-    """
-    Script.query.filter(Script.name == script_name).delete()
-    db.session.commit()
-    return redirect(url_for('database.load_from_database'))
-
-
-@database.route("/database/scripts/save")
-@login_required
-def publish():
-    """
-    .. :quickref: Database; save workflow to database
-
-    save workflow to database
-
-    .. http:get:: /database/scripts/save
-
-    :status 302: redirect to :http:get:`/ivoryos/experiment/build/`
-    """
-    script = get_script_file()
-    if not script.name or not script.deck:
-        flash("Deck cannot be empty, try to re-submit deck configuration on the left panel")
-    row = Script.query.get(script.name)
-    if row and row.status == "finalized":
-        flash("This is a protected script, use save as to rename.")
-    elif row and not session['user'] == row.author:
-        flash("You are not the author, use save as to rename.")
-    else:
-        db.session.merge(script)
-        db.session.commit()
-        flash("Saved!")
-    return redirect(url_for('design.experiment_builder'))
-
-
-@database.route("/database/scripts/finalize")
-@login_required
-def finalize():
-    """
-    .. :quickref: Database; finalize the workflow
-
-    [protected workflow] prevent saving edited workflow to the same workflow name
-
-    .. http:get:: /finalize
-
-    :status 302: redirect to :http:get:`/ivoryos/experiment/build/`
-
-    """
-    script = get_script_file()
-    script.finalize()
-    if script.name:
-        db.session.merge(script)
-        db.session.commit()
-    post_script_file(script)
-    return redirect(url_for('design.experiment_builder'))
-
-
-@database.route("/database/scripts/", strict_slashes=False)
-@database.route("/database/scripts/<deck_name>")
-@login_required
-def load_from_database(deck_name=None):
-    """
-    .. :quickref: Database; database page
-
-    backend control through http requests
-
-    .. http:get:: /database/scripts/<deck_name>
-
-    :param deck_name: filter for deck name
-    :type deck_name: str
-
-    """
-    session.pop('edit_action', None)  # reset cache
-    query = Script.query
-    search_term = request.args.get("keyword", None)
-    if search_term:
-        query = query.filter(Script.name.like(f'%{search_term}%'))
-    if deck_name is None:
-        temp = Script.query.with_entities(Script.deck).distinct().all()
-        deck_list = [i[0] for i in temp]
-    else:
-        query = query.filter(Script.deck == deck_name)
-        deck_list = ["ALL"]
-    page = request.args.get('page', default=1, type=int)
-    per_page = 10
-
-    scripts = query.paginate(page=page, per_page=per_page, error_out=False)
-    if request.accept_mimetypes.best_match(['application/json', 'text/html']) == 'application/json':
-        scripts = query.all()
-        script_names = [script.name for script in scripts]
-        return jsonify({
-            "workflows": script_names,
-        })
-    else:
-        # return HTML
-        return render_template("scripts_database.html", scripts=scripts, deck_list=deck_list, deck_name=deck_name)
-
-
-@database.route("/database/scripts/rename", methods=['POST'])
-@login_required
-def edit_run_name():
-    """
-    .. :quickref: Database; edit workflow name
-
-    edit the name of the current workflow, won't save to the database
-
-    .. http:post:: database/scripts/rename
-
-    : form run_name: new workflow name
-    :status 302: redirect to :http:get:`/ivoryos/experiment/build/`
-
-    """
-    if request.method == "POST":
-        run_name = request.form.get("run_name")
-        exist_script = Script.query.get(run_name)
-        if not exist_script:
-            script = get_script_file()
-            script.save_as(run_name)
-            post_script_file(script)
-        else:
-            flash("Script name is already exist in database")
-        return redirect(url_for("design.experiment_builder"))
-
-
-@database.route("/database/scripts/save_as", methods=['POST'])
-@login_required
-def save_as():
-    """
-    .. :quickref: Database; save the run name as
-
-    save the current workflow script as
-
-    .. http:post:: /database/scripts/save_as
-
-    : form run_name: new workflow name
-    :status 302: redirect to :http:get:`/ivoryos/experiment/build/`
-
-    """
-    if request.method == "POST":
-        run_name = request.form.get("run_name")
-        register_workflow = request.form.get("register_workflow")
-        exist_script = Script.query.get(run_name)
-        if not exist_script:
-            script = get_script_file()
-            script.save_as(run_name)
-            script.registered = register_workflow == "on"
-            script.author = session.get('user')
-            post_script_file(script)
-            publish()
-        else:
-            flash("Script name is already exist in database")
-        return redirect(url_for("design.experiment_builder"))
-
-
-# -----------------------------------------------------------
-# ------------------  Workflow logs   -----------------------
-# -----------------------------------------------------------
-@database.route('/database/workflows/')
-def list_workflows():
-    """
-    .. :quickref: Database; list all workflow logs
-
-    list all workflow logs
-
-    .. http:get:: /database/workflows/
-
-    """
-    query = WorkflowRun.query.order_by(WorkflowRun.id.desc())
-    search_term = request.args.get("keyword", None)
-    if search_term:
-        query = query.filter(WorkflowRun.name.like(f'%{search_term}%'))
-    page = request.args.get('page', default=1, type=int)
-    per_page = 10
-
-    workflows = query.paginate(page=page, per_page=per_page, error_out=False)
-    if request.accept_mimetypes.best_match(['application/json', 'text/html']) == 'application/json':
-        workflows = query.all()
-        workflow_data = {w.id:{"workflow_name":w.name, "start_time":w.start_time} for w in workflows}
-        return jsonify({
-            "workflow_data": workflow_data,
-        })
-    else:
-        return render_template('workflow_database.html', workflows=workflows)
-
-
-@database.route("/database/workflows/<int:workflow_id>")
-def get_workflow_steps(workflow_id:int):
-    """
-    .. :quickref: Database; list all workflow logs
-
-    list all workflow logs
-
-    .. http:get:: /database/workflows/<int:workflow_id>
-
-    """
-    workflow = db.session.get(WorkflowRun, workflow_id)
-    steps = WorkflowStep.query.filter_by(workflow_id=workflow_id).order_by(WorkflowStep.start_time).all()
-
-    # Use full objects for template rendering
-    grouped = {
-        "prep": [],
-        "script": {},
-        "cleanup": [],
-    }
-
-    # Use dicts for JSON response
-    grouped_json = {
-        "prep": [],
-        "script": {},
-        "cleanup": [],
-    }
-
-    for step in steps:
-        step_dict = step.as_dict()
-
-        if step.phase == "prep":
-            grouped["prep"].append(step)
-            grouped_json["prep"].append(step_dict)
-
-        elif step.phase == "script":
-            grouped["script"].setdefault(step.repeat_index, []).append(step)
-            grouped_json["script"].setdefault(step.repeat_index, []).append(step_dict)
-
-        elif step.phase == "cleanup" or step.method_name == "stop":
-            grouped["cleanup"].append(step)
-            grouped_json["cleanup"].append(step_dict)
-
-    if request.accept_mimetypes.best_match(['application/json', 'text/html']) == 'application/json':
-        return jsonify({
-            "workflow_info": workflow.as_dict(),
-            "steps": grouped_json,
-        })
-    else:
-        return render_template("workflow_view.html", workflow=workflow, grouped=grouped)
-
-
-@database.route("/database/workflows/delete/<int:workflow_id>")
-@login_required
-def delete_workflow_data(workflow_id: int):
-    """
-    .. :quickref: Database; delete experiment data from database
-
-    delete workflow data from database
-
-    .. http:get:: /database/workflows/delete/<int:workflow_id>
-
-    :param workflow_id: workflow id
-    :type workflow_id: int
-    :status 302: redirect to :http:get:`/ivoryos/database/workflows/`
-
-    """
-    run = WorkflowRun.query.get(workflow_id)
-    db.session.delete(run)
-    db.session.commit()
-    return redirect(url_for('database.list_workflows'))

ivoryos/routes/database/templates/database/step_card.html

@@ -1,7 +0,0 @@
-<div class="card mb-2 {{ 'border-danger text-danger bg-light' if step.run_error else 'border-secondary' }}">
-  <div class="card-body p-2">
-    <strong>{{ step.method_name }}</strong>
-    <small>Start: {{ step.start_time }}</small>
-    <small>End: {{ step.end_time }}</small>
-  </div>
-</div>

ivoryos/routes/database/templates/database/workflow_view.html

@@ -1,130 +0,0 @@
-{% extends 'base.html' %}
-
-{% block title %}IvoryOS | Experiment Results{% endblock %}
-
-{% block body %}
-<style>
-  .vis-time-axis .vis-text.vis-minor,
-  .vis-time-axis .vis-text.vis-major {
-    color: #666;
-  }
-  .vis-item.stop {
-    background-color: red;
-    color: white;
-    border: none;
-    font-weight: bold;
-  }
-</style>
-
-<div id="timeline"></div>
-
-<script src="https://unpkg.com/vis-timeline@latest/standalone/umd/vis-timeline-graph2d.min.js"></script>
-<link href="https://unpkg.com/vis-timeline@latest/styles/vis-timeline-graph2d.min.css" rel="stylesheet"/>
-
-<h1>Experiment Step View</h1>
-
-<div id="visualization"></div>
-
-<script type="text/javascript">
-  var container = document.getElementById('visualization');
-
-  const items = [
-    {% if grouped.prep %}
-      {
-        id: 'prep',
-        content: 'Prep Phase',
-        start: '{{ grouped.prep[0].start_time }}',
-        end: '{{ grouped.prep[-1].end_time }}',
-        className: 'prep',
-        group: 'prep'
-      },
-    {% endif %}
-
-    {% for repeat_index, step_list in grouped.script.items()|sort %}
-      {
-        id: 'iter{{ repeat_index }}',
-        content: 'Iteration {{ repeat_index }}',
-        start: '{{ step_list[0].start_time }}',
-        end: '{{ step_list[-1].end_time }}',
-        className: 'script',
-        group: 'iter{{ repeat_index }}'
-      },
-      {% for step in step_list %}
-        {% if step.method_name == "stop" %}
-          {
-            id: 'stop-{{ step.id }}',
-            content: '🛑 Stop',
-            start: '{{ step.start_time }}',
-            type: 'point',
-            className: 'stop',
-            group: 'iter{{ repeat_index }}'
-          },
-        {% endif %}
-      {% endfor %}
-    {% endfor %}
-
-    {% if grouped.cleanup %}
-      {
-        id: 'cleanup',
-        content: 'Cleanup Phase',
-        start: '{{ grouped.cleanup[0].start_time }}',
-        end: '{{ grouped.cleanup[-1].end_time }}',
-        className: 'cleanup',
-        group: 'cleanup'
-
-      },
-    {% endif %}
-  ];
-
-  const groups = [
-      {% if grouped.prep %}{ id: 'prep', content: 'Prep' },{% endif %}
-      {% for repeat_index in grouped.script.keys()|sort %}{ id: 'iter{{ repeat_index }}', content: 'Iteration {{ repeat_index }}' },{% endfor %}
-      {% if grouped.cleanup %}{ id: 'cleanup', content: 'Cleanup' },{% endif %}
-  ];
-
-  var options = {
-      clickToUse: true,
-      stack: false,  // important to keep point within group row
-      horizontalScroll: true,
-      zoomKey: 'ctrlKey'
-  };
-
-  // Initialize your timeline with the sorted groups
-  const timeline = new vis.Timeline(container, items, groups, options);
-
-  timeline.on('select', function (props) {
-    const id = props.items[0];
-    if (id && id.startsWith('iter')) {
-      const card = document.getElementById('card-' + id);
-      if (card) {
-        const yOffset = -80;
-        const y = card.getBoundingClientRect().top + window.pageYOffset + yOffset;
-        window.scrollTo({ top: y, behavior: 'smooth' });
-      }
-    }
-  });
-</script>
-
-<h2>Workflow: {{ workflow.name }}</h2>
-
-{% if grouped.prep %}
-  <h4 class="mt-4">Prep Phase</h4>
-  {% for step in grouped.prep %}
-    {% include "step_card.html" %}
-  {% endfor %}
-{% endif %}
-
-{% for repeat_index, step_list in grouped.script.items()|sort %}
-  <h4 class="mt-4" id="card-iter{{ repeat_index }}">Iteration {{ repeat_index }}</h4>
-  {% for step in step_list %}
-    {% include "step_card.html" %}
-  {% endfor %}
-{% endfor %}
-
-{% if grouped.cleanup %}
-  <h4 class="mt-4">Cleanup Phase</h4>
-  {% for step in grouped.cleanup %}
-    {% include "step_card.html" %}
-  {% endfor %}
-{% endif %}
-{% endblock %}