Release/1.1.0

aiidalab_widgets_base/__init__.py

@@ -79,4 +79,4 @@
     "viewer",
 ]
 
-__version__ = "1.0.0"
+__version__ = "1.1.0"

aiidalab_widgets_base/codes.py

@@ -3,7 +3,7 @@
 from subprocess import check_output
 
 import ipywidgets as ipw
-from aiida.orm import Code, Computer, QueryBuilder, User
+from aiida.orm import Code, QueryBuilder, User
 from aiida.plugins.entry_point import get_entry_point_names
 from IPython.display import clear_output
 from traitlets import Bool, Dict, Instance, Unicode, Union, dlink, link, validate
@@ -157,9 +157,8 @@ class AiiDACodeSetup(ipw.VBox):
     """Class that allows to setup AiiDA code"""
 
     label = Unicode()
-    computer = Union([Unicode(), Instance(Computer)], allow_none=True)
-
-    input_plugin = Unicode()
+    computer = Unicode(allow_none=True)
+    input_plugin = Unicode(allow_none=True)
     description = Unicode()
     remote_abs_path = Unicode()
     prepend_text = Unicode()
@@ -178,20 +177,19 @@ def __init__(self, path_to_root="../", **kwargs):
         link((inp_label, "value"), (self, "label"))
 
         # Computer on which the code is installed. Two dlinks are needed to make sure we get a Computer instance.
-        inp_computer = ComputerDropdown(
+        self.inp_computer = ComputerDropdown(
             path_to_root=path_to_root, layout={"margin": "0px 0px 0px 125px"}
         )
-        dlink((inp_computer, "selected_computer"), (self, "computer"))
-        dlink((self, "computer"), (inp_computer, "selected_computer"))
+        dlink((self, "computer"), (self.inp_computer, "selected_computer"))
 
         # Code plugin.
-        inp_code_plugin = ipw.Dropdown(
+        self.inp_code_plugin = ipw.Dropdown(
             options=sorted(get_entry_point_names("aiida.calculations")),
             description="Code plugin:",
             layout=ipw.Layout(width="500px"),
             style=style,
         )
-        link((inp_code_plugin, "value"), (self, "input_plugin"))
+        link((self.inp_code_plugin, "value"), (self, "input_plugin"))
 
         # Code description.
         inp_description = ipw.Text(
@@ -233,8 +231,8 @@ def __init__(self, path_to_root="../", **kwargs):
                     ipw.VBox(
                         [
                             inp_label,
-                            inp_computer,
-                            inp_code_plugin,
+                            self.inp_computer,
+                            self.inp_code_plugin,
                             inp_description,
                             inp_abs_path,
                         ]
@@ -247,6 +245,11 @@ def __init__(self, path_to_root="../", **kwargs):
         ]
         super(AiiDACodeSetup, self).__init__(children, **kwargs)
 
+    @validate("input_plugin")
+    def _validate_input_plugin(self, proposal):
+        plugin = proposal["value"]
+        return plugin if plugin in self.inp_code_plugin.options else None
+
     def _setup_code(self, _=None):
         """Setup an AiiDA code."""
         with self._setup_code_out:
@@ -257,26 +260,47 @@ def _setup_code(self, _=None):
             if not self.remote_abs_path:
                 print("You did not specify absolute path to the executable.")
                 return
+            if not self.inp_computer.selected_computer:
+                print(
+                    "Please specify a computer that is configured in your AiiDA profile."
+                )
+                return False
+            if not self.input_plugin:
+                print(
+                    "Please specify an input plugin that is installed in your AiiDA environment."
+                )
+                return False
             if self.exists():
-                print(f"Code {self.label}@{self.computer.label} already exists.")
+                print(
+                    f"Code {self.label}@{self.inp_computer.selected_computer.label} already exists."
+                )
                 return
-            code = Code(remote_computer_exec=(self.computer, self.remote_abs_path))
+            code = Code(
+                remote_computer_exec=(
+                    self.inp_computer.selected_computer,
+                    self.remote_abs_path,
+                )
+            )
             code.label = self.label
             code.description = self.description
             code.set_input_plugin_name(self.input_plugin)
             code.set_prepend_text(self.prepend_text)
             code.set_append_text(self.append_text)
             code.store()
             code.reveal()
-            full_string = f"{self.label}@{self.computer.label}"
+            full_string = f"{self.label}@{self.inp_computer.selected_computer.label}"
             print(check_output(["verdi", "code", "show", full_string]).decode("utf-8"))
 
     def exists(self):
         """Returns True if the code exists, returns False otherwise."""
         from aiida.common import MultipleObjectsError, NotExistent
 
+        if not self.label:
+            return False
         try:
-            Code.get_from_string(f"{self.label}@{self.computer.label}")
+            Code.get_from_string(
+                f"{self.label}@{self.inp_computer.selected_computer.label}"
+            )
             return True
         except MultipleObjectsError:
             return True

aiidalab_widgets_base/computers.py

@@ -908,12 +908,13 @@ def _validate_selected_computer(self, change):
         if isinstance(computer, str):
             if computer in self.computers:
                 return self.computers[computer]
-            self.output.value = f"""No computer named '<span style="color:red">{computer}</span>'
-            was found in your AiiDA database."""
+            self.output.value = f"""Computer instance '<span style="color:red">{computer}</span>'
+            is not configured in your AiiDA profile."""
+            return None
 
         if isinstance(computer, Computer):
             if computer.label in self.computers:
                 return computer
-            self.output.value = f"""The computer instance '<span style="color:red">{computer}</span>'
-            supplied was not found in your AiiDA database."""
+            self.output.value = f"""Computer instance '<span style="color:red">{computer.label}</span>'
+            is not configured in your AiiDA profile."""
         return None

aiidalab_widgets_base/databases.py

@@ -181,6 +181,7 @@ def __init__(
         title: str = None,
         **kwargs,
     ) -> None:
+        providers_header = ipw.HTML("<h4>Select a provider</h4>")
         providers = OptimadeQueryProviderWidget(
             embedded=embedded,
             width_ratio=kwargs.pop("width_ratio", None),
@@ -207,7 +208,7 @@ def __init__(
         layout = kwargs.pop("layout", {"width": "auto", "height": "auto"})
 
         super().__init__(
-            children=(providers, filters),
+            children=(providers_header, providers, filters),
             layout=layout,
             **kwargs,
         )

aiidalab_widgets_base/elns.py

@@ -15,30 +15,48 @@
 
 
 def connect_to_eln(eln_instance=None, **kwargs):
+
+    # assuming that the connection can only be established to the ELNs
+    # with the stored configuration.
     try:
         with open(ELN_CONFIG, "r") as file:
             config = json.load(file)
     except (FileNotFoundError, json.JSONDecodeError, KeyError):
-        return None
+        return (
+            None,
+            f"Can't open '{ELN_CONFIG}' (ELN configuration file). Instance: {eln_instance}",
+        )
 
+    # If no ELN instance was specified, trying the default one.
     if not eln_instance:
         eln_instance = config.pop("default", None)
 
-    if eln_instance:
+    if eln_instance:  # The ELN instance could be identified.
         if eln_instance in config:
             eln_config = config[eln_instance]
             eln_type = eln_config.pop("eln_type", None)
-        else:
-            eln_type = None
+        else:  # The selected instance is not present in the config.
+            return None, f"Didn't find configuration for the '{eln_instance}' instance."
+
+        # If the ELN type cannot be identified - aborting.
         if not eln_type:
-            return None
-        eln = get_eln_connector(eln_type)(
-            eln_instance=eln_instance, **eln_config, **kwargs
-        )
+            return None, f"Can't identify the type of {eln_instance} ELN."
+
+        # Everything is alright, can populate the ELN connector
+        # with the required info.
+        try:
+            eln = get_eln_connector(eln_type)(
+                eln_instance=eln_instance, **eln_config, **kwargs
+            )
+        except NotImplementedError as err:
+            return None, str(err)
         eln.connect()
-        return eln
+        return eln, None
 
-    return None
+    return (
+        None,
+        "No ELN instance was provided, the default ELN instance is not configured either. Set a default ELN or select an ELN instance.",
+    )
 
 
 class ElnImportWidget(ipw.VBox):
@@ -52,11 +70,11 @@ def __init__(self, path_to_root="../", **kwargs):
         error_message = ipw.HTML()
         super().__init__(children=[error_message], **kwargs)
 
-        eln = connect_to_eln(**kwargs)
+        eln, msg = connect_to_eln(**kwargs)
 
         if eln is None:
             url = f"{path_to_root}aiidalab-widgets-base/notebooks/eln_configure.ipynb"
-            error_message.value = f"""Warning! The access to ELN {kwargs['eln_instance']} is not configured. Please follow <a href="{url}" target="_blank">the link</a> to configure it."""
+            error_message.value = f"""Warning! The access to ELN is not configured. Please follow <a href="{url}" target="_blank">the link</a> to configure it.</br> More details: {msg}"""
             return
 
         traitlets.dlink((eln, "node"), (self, "node"))
@@ -93,13 +111,13 @@ def __init__(self, path_to_root="../", **kwargs):
             self._output,
             self.message,
         ]
-        self.eln = connect_to_eln()
+        self.eln, msg = connect_to_eln()
         if self.eln:
             traitlets.dlink((self, "node"), (self.eln, "node"))
         else:
             self.modify_settings.disabled = True
             send_button.disabled = True
-            self.message.value = f"""Warning! The access to an ELN is not configured. Please follow <a href="{self.path_to_root}/aiidalab-widgets-base/notebooks/eln_configure.ipynb" target="_blank">the link</a> to configure it."""
+            self.message.value = f"""Warning! The access to ELN is not configured. Please follow <a href="{self.path_to_root}/aiidalab-widgets-base/notebooks/eln_configure.ipynb" target="_blank">the link</a> to configure it.</br> </br> More details: {msg}"""
 
         super().__init__(children=children, **kwargs)
 
@@ -261,7 +279,14 @@ def check_connection(self, _=None):
 
     def display_eln_config(self, value=None):
         """Display ELN configuration specific to the selected type of ELN."""
-        eln_class = get_eln_connector(self.eln_types.value)
+        try:
+            eln_class = get_eln_connector(self.eln_types.value)
+        except NotImplementedError as err:
+            with self._output:
+                clear_output()
+                display(ipw.HTML("&#10060;" + str(err)))
+                return
+
         self.eln = eln_class(
             eln_instance=self.eln_instance.label if self.eln_instance.value else "",
             **self.eln_instance.value,

aiidalab_widgets_base/structures.py

@@ -3,6 +3,7 @@
 
 import datetime
 import io
+import tempfile
 from collections import OrderedDict
 
 # ASE imports
@@ -61,7 +62,7 @@ def __init__(
         editors=None,
         storable=True,
         node_class=None,
-        **kwargs
+        **kwargs,
     ):
         """
         Arguments:
@@ -389,11 +390,12 @@ def _on_file_upload(self, change=None):
             if frmt == "cif":
                 self.structure = CifData(file=io.BytesIO(item["content"]))
             else:
-                self.structure = self._validate_and_fix_ase_cell(
-                    get_ase_from_file(
-                        io.StringIO(item["content"].decode()), format=frmt
+                with tempfile.NamedTemporaryFile(suffix=f".{frmt}") as temp_file:
+                    temp_file.write(item["content"])
+                    temp_file.flush()
+                    self.structure = self._validate_and_fix_ase_cell(
+                        get_ase_from_file(temp_file.name)
                     )
-                )
             self.file_upload.value.clear()
             break