Merge branch 'develop'

Author: yakutovicha

aiidalab_widgets_base/__init__.py

@@ -4,11 +4,12 @@
 if not is_dbenv_loaded():
     load_dbenv(profile=settings.AIIDADB_PROFILE)
 
-from .structures import StructureUploadWidget  # noqa
-from .structures_multi import MultiStructureUploadWidget  # noqa
 from .codes import CodeDropdown, AiiDACodeSetup, extract_aiidacodesetup_arguments # noqa
 from .computers import SshComputerSetup, extract_sshcomputersetup_arguments # noqa
 from .computers import AiidaComputerSetup, extract_aiidacomputer_arguments # noqa
+from .databases import CodQueryWidget # noqa
 from .display import aiidalab_display # noqa
+from .structures import StructureUploadWidget  # noqa
+from .structures_multi import MultiStructureUploadWidget  # noqa
 
-__version__ = "0.3.0b1"
+__version__ = "0.4.0b1"

aiidalab_widgets_base/codes.py

@@ -41,7 +41,8 @@ def __init__(self, input_plugin, text='Select code:', **kwargs):
         self.dropdown = ipw.Dropdown(description=text, disabled=True)
         self._btn_refresh = ipw.Button(description="Refresh", layout=ipw.Layout(width="70px"))
         self._btn_refresh.on_click(self.refresh)
-        self._setup_another = ipw.HTML(value="""<a href=./setup_code.ipynb target="_blank">Setup new code</a>""")
+        # TODO: use base_url here
+        self._setup_another = ipw.HTML(value="""<a href=../aiidalab-widgets-base/setup_code.ipynb target="_blank">Setup new code</a>""")
         self.output = ipw.Output()
 
         children = [ipw.HBox([self.dropdown, self._btn_refresh, self._setup_another]),

aiidalab_widgets_base/databases.py

@@ -0,0 +1,101 @@
+from __future__ import print_function
+import ipywidgets as ipw
+
+from aiida.tools.dbimporters.plugins.cod import CodDbImporter
+
+class CodQueryWidget(ipw.VBox):
+    '''Query structures in Crystallography Open Database (COD)
+    Useful class members:
+    :ivar has_structure: link to a method to be overloaded. It is called evey time when `self.drop_structure`
+    widget has changed its name
+    :vartype has_structure: function
+    '''
+
+    def __init__(self, **kwargs):
+        description = ipw.HTML("""<h3>Get crystal structures from
+    <a href="http://www.crystallography.net">Crystallography Open Database</a></h3>
+    <b>Queries by formula</b>
+    <br>
+    For the queries by formula please adhere to the Hill notation.
+    The chemical symbol of an element should be followed by its number in the structure,
+    except when there is only one atom.
+    When the structure does NOT contain carbon atoms, all the elements are listed alphabetically.
+    Example: <i>O2 Si</i>.
+    <br>
+    In case the structure DOES contain carbon atoms its number following the 'C' symbol is indicated first.
+    If hydrogen is also present in the structure then 'H' symbol and its number is indicated second.
+    The remaining elements are listed in the alphabetical order. Example: <i>C H4 N2 O</i>.
+    <br>
+    <b>Queries by the structure id number</b>
+    <br>
+    For the queries by structure id, plese provide the database id number. Example: <i>1008786</i>
+    """)
+        layout = ipw.Layout(width="400px")
+        style = {"description_width":"initial"}
+        self.inp_elements = ipw.Text(description="", value="", placeholder='e.g.: Ni Ti or id number', layout=layout, style=style)
+        self.btn_query = ipw.Button(description='Query')
+        self.query_message = ipw.HTML("Waiting for input...")
+        self.drop_structure = ipw.Dropdown(description="", options=[("select structure",{"status":False})],
+                                           style=style, layout=layout )
+        self.link = ipw.HTML("Link to the web-page will appear here")
+        self.structure_ase = None
+
+        self.btn_query.on_click(self._on_click_query)
+        self.drop_structure.observe(self._on_select_structure, names=['value'])
+
+        children = [description,
+                    ipw.HBox([self.btn_query, self.inp_elements]),
+                    self.query_message,
+                    ipw.HBox([self.drop_structure, self.link])]
+        super(CodQueryWidget, self).__init__(children=children, **kwargs)
+
+    def _query(self, idn=None,formula=None):
+        importer = CodDbImporter()
+        if idn is not None:
+            return importer.query(id=idn)
+        elif formula is not None:
+            return importer.query(formula=formula)
+
+    def _on_click_query(self, change):
+        structures = [("select structure", {"status":False})]
+        idn = None
+        formula = None
+        self.query_message.value = "Quering the database ... "
+        try: 
+            idn = int(self.inp_elements.value)
+        except:
+            formula = str(self.inp_elements.value)
+
+        for entry in self._query(idn=idn, formula=formula):
+            try:
+                entry_cif = entry.get_cif_node()
+                formula = entry_cif.get_ase().get_chemical_formula()
+            except:
+                continue
+            entry_add = ("{} (id: {})".format(formula, entry.source['id']),
+                            {
+                                "status": True,
+                                "cif": entry_cif,
+                                "url": entry.source['uri'],
+                                "id": entry.source['id'],
+                            }
+                        )
+            structures.append(entry_add)
+
+        self.query_message.value += "{} structures found".format(len(structures)-1)
+        self.drop_structure.options = structures
+
+    def _on_select_structure(self, change):
+        selected = change['new']
+        if selected['status'] is False:
+            self.structure_ase = None
+            return
+        self.structure_ase = selected['cif'].get_ase()
+        formula = self.structure_ase.get_chemical_formula()
+        struct_url = selected['url'].split('.cif')[0]+'.html'
+        self.link.value='<a href="{}" target="_blank">COD entry {}</a>'.format(struct_url, selected['id'])
+        if not self.on_structure_selection is None:
+            self.on_structure_selection(structure_ase=self.structure_ase, name=formula)
+
+    def on_structure_selection(self, structure_ase=None, name=None):
+        pass