ChemShell QM/MM workflow (#13)

Author: BTSpeake

main.ipynb

@@ -29,6 +29,7 @@
    },
    "outputs": [],
    "source": [
+    "%%capture\n",
     "from aiida import load_profile \n",
     "load_profile();"
    ]

src/aiidalab_alc/common/__init__.py

@@ -0,0 +1 @@
+"""Package for general common components."""

src/aiidalab_alc/common/database.py

@@ -0,0 +1,171 @@
+"""Module for components relating to AiiDA database management."""
+
+import datetime
+
+import ipywidgets as ipw
+import traitlets as tl
+from aiida.orm import (
+    CalcFunctionNode,
+    CalcJobNode,
+    Data,
+    Node,
+    QueryBuilder,
+    WorkChainNode,
+)
+
+
+class AiiDADatabaseWidget(ipw.VBox, tl.HasTraits):
+    """Widget for AiiDA database querying."""
+
+    data_object = tl.Instance(Data, allow_none=True)
+
+    def __init__(self, title: str = "", query: list = None):
+        if query is None:
+            query = []
+        self.title = title
+        self.query_type = tuple(query)
+
+        qbuilder = QueryBuilder().append((CalcJobNode, WorkChainNode), project="label")
+
+        self.drop_down = ipw.Dropdown(
+            options=sorted({"All"}.union({i[0] for i in qbuilder.iterall() if i[0]})),
+            value="All",
+            description="Process Label",
+            disabled=True,
+            style={"description_width": "120px"},
+            layout={"width": "50%"},
+        )
+        self.drop_down.observe(self.search, names="value")
+
+        # Disable process labels selection if we are not looking for the calculated
+        # structures.
+        def disable_drop_down(change):
+            self.drop_down.disabled = not change["new"] == "calculated"
+
+        # Select structures kind.
+        self.mode = ipw.RadioButtons(
+            options=["all", "uploaded", "calculated"], layout={"width": "25%"}
+        )
+        self.mode.observe(self.search, names="value")
+        self.mode.observe(disable_drop_down, names="value")
+
+        # Date range.
+        # Note: there is Date picker widget, but it currently does not work in Safari:
+        # https://ipywidgets.readthedocs.io/en/latest/examples/Widget%20List.html#Date-picker
+        date_text = ipw.HTML(value="<p>Select the date range:</p>")
+        self.start_date_widget = ipw.Text(
+            value="", description="From: ", style={"description_width": "120px"}
+        )
+        self.end_date_widget = ipw.Text(value="", description="To: ")
+
+        # Search button.
+        btn_search = ipw.Button(
+            description="Search",
+            button_style="info",
+            layout={"width": "initial", "margin": "2px 0 0 2em"},
+        )
+        btn_search.on_click(self.search)
+
+        age_selection = ipw.VBox(
+            [
+                date_text,
+                ipw.HBox([self.start_date_widget, self.end_date_widget, btn_search]),
+            ],
+            layout={"border": "1px solid #fafafa", "padding": "1em"},
+        )
+
+        h_line = ipw.HTML("<hr>")
+        box = ipw.VBox([age_selection, h_line, ipw.HBox([self.mode, self.drop_down])])
+
+        self.results = ipw.Dropdown(layout={"width": "900px"})
+        self.results.observe(self._on_select_structure, names="value")
+        self.search()
+        super().__init__([box, h_line, self.results])
+
+    def search(self, _=None) -> None:
+        """Search structures in the AiiDA database."""
+        qbuild = QueryBuilder()
+
+        # If the date range is valid, use it for the search
+        try:
+            start_date = datetime.datetime.strptime(
+                self.start_date_widget.value, "%Y-%m-%d"
+            )
+            end_date = datetime.datetime.strptime(
+                self.end_date_widget.value, "%Y-%m-%d"
+            ) + datetime.timedelta(hours=24)
+
+        # Otherwise revert to the standard (i.e. last 7 days)
+        except ValueError:
+            start_date = datetime.datetime.now() - datetime.timedelta(days=7)
+            end_date = datetime.datetime.now() + datetime.timedelta(hours=24)
+
+            self.start_date_widget.value = start_date.strftime("%Y-%m-%d")
+            self.end_date_widget.value = end_date.strftime("%Y-%m-%d")
+
+        filters = {}
+        filters["ctime"] = {"and": [{">": start_date}, {"<=": end_date}]}
+
+        if self.mode.value == "uploaded":
+            qbuild2 = (
+                QueryBuilder()
+                .append(self.query_type, project=["id"], tag="structures")
+                .append(Node, with_outgoing="structures")
+            )
+            processed_nodes = [n[0] for n in qbuild2.all()]
+            if processed_nodes:
+                filters["id"] = {"!in": processed_nodes}
+            qbuild.append(self.query_type, filters=filters)
+
+        elif self.mode.value == "calculated":
+            if self.drop_down.value == "All":
+                qbuild.append((CalcJobNode, WorkChainNode), tag="calcjobworkchain")
+            else:
+                qbuild.append(
+                    (CalcJobNode, WorkChainNode),
+                    filters={"label": self.drop_down.value},
+                    tag="calcjobworkchain",
+                )
+            qbuild.append(
+                self.query_type,
+                with_incoming="calcjobworkchain",
+                filters=filters,
+            )
+
+        elif self.mode.value == "edited":
+            qbuild.append(CalcFunctionNode)
+            qbuild.append(
+                self.query_type,
+                with_incoming=CalcFunctionNode,
+                filters=filters,
+            )
+
+        elif self.mode.value == "all":
+            qbuild.append(self.query_type, filters=filters)
+
+        qbuild.order_by({self.query_type: {"ctime": "desc"}})
+        matches = {n[0] for n in qbuild.iterall()}
+        matches = sorted(matches, reverse=True, key=lambda n: n.ctime)
+
+        options = [(f"Select a Structure ({len(matches)} found)", False)]
+        for mch in matches:
+            label = f"PK: {mch.pk}"
+            label += " | " + mch.ctime.strftime("%Y-%m-%d %H:%M")
+            label += " | " + mch.base.extras.get("formula", "")
+            label += " | " + mch.node_type.split(".")[-2]
+            label += " | " + mch.label
+            label += " | " + mch.description
+            options.append((label, mch))
+
+        self.results.options = options
+        return
+
+    def _on_select_structure(self, _) -> None:
+        self.data_object = self.results.value or None
+        return
+
+    def disable(self, val: bool) -> None:
+        """Disable the widget."""
+        self.results.disabled = True
+        # self.
+        return

src/aiidalab_alc/common/file_handling.py

@@ -0,0 +1,89 @@
+"""Module for providing functionality to deal with files."""
+
+from io import BytesIO
+
+import traitlets as tl
+from aiida.orm import SinglefileData
+from ipywidgets import FileUpload, HBox, Text
+
+
+class FileUploadWidget(HBox, tl.HasTraits):
+    """A widget for uploading files."""
+
+    file = tl.Instance(SinglefileData, allow_none=True)
+
+    def __init__(self, description: str = "File: ", **kwargs):
+        """
+        FileUploadWidget constructor.
+
+        Parameters
+        ----------
+        **kwargs :
+            Keyword arguments passed to the parent class's constructor.
+        """
+        super().__init__(**kwargs)
+        self.file_dict = None
+
+        self.file_upload = FileUpload(
+            accept="",
+            multiple=False,
+            description="Upload",
+            layout={"width": "20%"},
+        )
+        self.file_handle = Text(
+            value="",
+            placeholder="",
+            description=description,
+            disabled=True,
+            layout={"width": "70%"},
+        )
+        self.children = [self.file_handle, self.file_upload]
+
+        self.file_upload.observe(self._on_file_upload, names="value")
+
+        return
+
+    @property
+    def has_file(self) -> bool:
+        """True if a file has been uploaded."""
+        return self.file is not None
+
+    def _on_file_upload(self, _):
+        """Handle file upload events."""
+        if self.file_upload.value:
+            self.file_dict = self.file_upload.value[
+                list(self.file_upload.value.keys())[0]
+            ]
+            self.file_handle.value = self.file_dict["metadata"]["name"]
+            self.file = self.get_aiida_file_object()
+        else:
+            self.file_handle.value = ""
+        return
+
+    def get_file_contents(self) -> BytesIO | None:
+        """Get the contents of the uploaded file as a BytesIO object."""
+        if self.file_dict is not None:
+            return BytesIO(self.file_dict["content"])
+        return None
+
+    def filename(self) -> str:
+        """Get the name of the uploaded file."""
+        if self.file_dict is not None:
+            return self.file_dict["metadata"]["name"]
+        return ""
+
+    def get_aiida_file_object(self):
+        """Get the uploaded file as an AiiDA SinglefileData object."""
+        if self.file_dict is not None:
+            return SinglefileData(
+                file=self.get_file_contents(),
+                filename=self.filename(),
+                label=self.filename(),
+                description=self.file_handle.description,
+            )
+        return None
+
+    def disable(self, val: bool) -> None:
+        """Disable the file upload widget."""
+        self.file_upload.disabled = val
+        return

src/aiidalab_alc/common/navigation.py

@@ -0,0 +1,74 @@
+"""Module handling navigation controls within the app."""
+
+from functools import partial
+
+import ipywidgets as ipw
+
+from aiidalab_alc.utils import open_link_in_new_tab
+
+
+class QuickAccessButtons(ipw.HBox):
+    """Quick access buttons present in the apps header and start banner."""
+
+    def __init__(self, **kwargs):
+        """
+        QuickAccessButtons constructor.
+
+        Parameters
+        ----------
+        **kwargs :
+            Keyword arguments passed to the `ipywidgets.HBox.__init__()`.
+        """
+        self.new_calc_link = ipw.Button(
+            description="New Calculation",
+            disabled=False,
+            button_style="success",
+            tooltip="Start a new calculation",
+            icon="plus",
+        )
+        self.new_calc_link.on_click(
+            partial(open_link_in_new_tab, "../alc-ux/main.ipynb")
+        )
+
+        self.history_link = ipw.Button(
+            description="History",
+            disabled=False,
+            button_style="primary",
+            tooltip="View Calculation History",
+            icon="history",
+        )
+        self.history_link.on_click(
+            partial(open_link_in_new_tab, "../alc-ux/history.ipynb")
+        )
+
+        self.resource_setup_link = ipw.Button(
+            description="Setup Resources",
+            disabled=False,
+            button_style="primary",
+            tooltip="Configure Computational Resources",
+            icon="cogs",
+            # on_click=partial(onLinkClickt get_app_dir() / "../home/code_setup.ipynb"),
+        )
+        self.resource_setup_link.on_click(
+            partial(open_link_in_new_tab, "../home/code_setup.ipynb")
+        )
+
+        self.docs_link = ipw.Button(
+            description="Documentation",
+            disabled=False,
+            button_style="info",
+            tooltip="Open Documentation",
+            icon="book",
+        )
+        self.docs_link.on_click(
+            partial(open_link_in_new_tab, "https://github.com/stfc/alc-ux")
+        )
+
+        children = [
+            self.new_calc_link,
+            self.history_link,
+            self.resource_setup_link,
+            self.docs_link,
+        ]
+        super().__init__(children=children, layout={"margin": "auto"}, **kwargs)
+        return