Addressing SVG and YAML issues from #90

echemdb/data/cv/database.py

@@ -15,7 +15,7 @@
 Search the database for a single publication::
 
     >>> database.filter(lambda entry: entry.source.url == 'https://doi.org/10.1039/C0CP01001D')  # doctest: +REMOTE_DATA
-    [Entry('alves_2011_electrochemistry_6010_p2_2a_solid')]
+    [Entry('alves_2011_electrochemistry_6010_p2_f2a_solid')]
 
 """
 # ********************************************************************
@@ -90,7 +90,7 @@ def create_example(self):
         EXAMPLES::
 
             >>> Database.create_example()
-            [Entry('alves_2011_electrochemistry_6010_p2_2a_solid'), Entry('engstfeld_2018_polycrystalline_17743_4b_1')]
+            [Entry('alves_2011_electrochemistry_6010_p2_f2a_solid'), Entry('engstfeld_2018_polycrystalline_17743_f4b_1')]
 
         """
         from echemdb.data.cv.entry import Entry
@@ -131,7 +131,8 @@ def filter(self, predicate):
 
             >>> database = Database.create_example()
             >>> database.filter(lambda entry: entry.source.url == 'https://doi.org/10.1039/C0CP01001D')
-            [Entry('alves_2011_electrochemistry_6010_p2_2a_solid')]
+            [Entry('alves_2011_electrochemistry_6010_p2_f2a_solid')]
+
 
         The filter predicate can use properties that are not present on all
         entries in the database. If a property is missing the element is
@@ -158,13 +159,13 @@ def __iter__(self):
 
             >>> database = Database.create_example()
             >>> next(iter(database))
-            Entry('alves_2011_electrochemistry_6010_p2_2a_solid')
+            Entry('alves_2011_electrochemistry_6010_p2_f2a_solid')
 
         """
         from echemdb.data.cv.entry import Entry
 
         def get_bibliography(package):
-            bib = Entry(package, bibliography=None).source.bib
+            bib = Entry(package, bibliography=None).source.citation_key
             return self._bibliography.entries.get(bib, None)
 
         return iter([Entry(package, bibliography=get_bibliography(package)) for package in self._packages])

echemdb/data/cv/entry.py

@@ -57,7 +57,7 @@ def identifier(self):
 
             >>> entry = Entry.create_examples()[0]
             >>> entry.identifier
-            'alves_2011_electrochemistry_6010_p2_2a_solid'
+            'alves_2011_electrochemistry_6010_p2_f2a_solid'
 
         """
         return self.package.resources[0].name
@@ -72,7 +72,7 @@ def __dir__(self):
 
             >>> entry = Entry.create_examples()[0]
             >>> dir(entry)
-            ['__class__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattr__', '__getattribute__', '__getitem__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__le__', '__lt__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', '_descriptor', 'bibliography', 'citation', 'create_examples', 'curator', 'data_description', 'df', 'electrochemical_system', 'figure_description', 'identifier', 'package', 'plot', 'profile', 'resources', 'source', 'x', 'x_unit', 'y', 'y_unit', 'yaml']
+            ['__class__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattr__', '__getattribute__', '__getitem__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__le__', '__lt__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', '_descriptor', 'bibliography', 'citation', 'create_examples', 'curation', 'data_description', 'df', 'electrochemical_system', 'figure_description', 'identifier', 'package', 'plot', 'profile', 'resources', 'source', 'version', 'x', 'x_unit', 'y', 'y_unit', 'yaml']
 
         """
         return list(set(dir(self._descriptor) + object.__dir__(self)))
@@ -85,7 +85,7 @@ def __getattr__(self, name):
 
             >>> entry = Entry.create_examples()[0]
             >>> entry.source
-            {'version': 1, 'url': 'https://doi.org/10.1039/C0CP01001D', 'bib': 'alves_2011_electrochemistry_6010', 'figure': '2a', 'curve': 'solid'}
+            {'citation key': 'alves_2011_electrochemistry_6010', 'curve': 'solid', 'url': 'https://doi.org/10.1039/C0CP01001D', 'figure': '2a', 'version': 1}
 
         The returned descriptor can again be accessed in the same way::
 
@@ -103,7 +103,7 @@ def __getitem__(self, name):
 
             >>> entry = Entry.create_examples()[0]
             >>> entry["source"]
-            {'version': 1, 'url': 'https://doi.org/10.1039/C0CP01001D', 'bib': 'alves_2011_electrochemistry_6010', 'figure': '2a', 'curve': 'solid'}
+            {'citation key': 'alves_2011_electrochemistry_6010', 'curve': 'solid', 'url': 'https://doi.org/10.1039/C0CP01001D', 'figure': '2a', 'version': 1}
 
         """
         return self._descriptor[name]
@@ -353,7 +353,7 @@ def __repr__(self):
 
             >>> entry = Entry.create_examples()[0]
             >>> entry
-            Entry('alves_2011_electrochemistry_6010_p2_2a_solid')
+            Entry('alves_2011_electrochemistry_6010_p2_f2a_solid')
 
         """
         return f"Entry({repr(self.identifier)})"
@@ -416,7 +416,7 @@ def create_examples(cls, name="alves_2011_electrochemistry_6010"):
         EXAMPLES::
 
             >>> Entry.create_examples()
-            [Entry('alves_2011_electrochemistry_6010_p2_2a_solid')]
+            [Entry('alves_2011_electrochemistry_6010_p2_f2a_solid')]
 
         """
         import os.path

literature/alves_2011_electrochemistry_6010/alves_2011_electrochemistry_6010.bib

@@ -7,5 +7,5 @@ @article{alves_2011_electrochemistry_6010
   pages={6010--6021},
   year={2011},
   publisher={Royal Society of Chemistry},
-  abstract={We investigated the electrochemical oxidation and reduction processes on ultrahigh vacuum prepared, smooth and structurally well-characterized Ru(0001) electrodes in a CO-saturated and, for comparison, in a CO-free flowing perchloric acid electrolyte by electrochemical methods and by comparison with previous structural data. Structure and reactivity of the adsorbed layers are largely governed by a critical potential of E = 0.57 V, which determines the onset of Oad formation on the COad saturated surface in the positive-going scan and of Oadreduction in the negative-going scan. Oad formation proceeds via nucleation and 2D growth of high-coverage Oad islands in a surrounding COad phase, and it is connected with COadoxidation at the interface between the two phases. In the negative-going scan, mixed (COad + Oad) phases, most likely a (2 $\times$ 2)-(CO + 2O) and a (2$\times$2)-(2CO + O), are proposed to form at E $<$ 0.57 V by reduction of the Oad-rich islands and CO adsorption into the resulting lower-density Oad structures. CO bulk oxidation rates in the potential range E $>$ 0.57 V are low, but significantly higher than those observed during oxidation of pre-adsorbed CO in the CO-free electrolyte. We relate this to high local COad coverages due to CO adsorption in the CO-saturated electrolyte, which lowers the CO adsorption energy and thus the barrier for COadoxidation during CO bulk oxidation.}
+  abstract={We investigated the electrochemical oxidation and reduction processes on ultrahigh vacuum prepared, smooth and structurally well-characterized Ru(0001) electrodes in a CO-saturated and, for comparison, in a CO-free flowing HClO4 electrolyte by electrochemical methods and by comparison with previous structural data. Structure and reactivity of the adsorbed layers are largely governed by a critical potential of E = 0.57 V, which determines the onset of Oad formation on the COad saturated surface in the positive-going scan and of Oadreduction in the negative-going scan. Oad formation proceeds via nucleation and 2D growth of high-coverage Oad islands in a surrounding COad phase, and it is connected with COadoxidation at the interface between the two phases. In the negative-going scan, mixed (COad + Oad) phases, most likely a (2 $\times$ 2)-(CO + 2O) and a (2$\times$2)-(2CO + O), are proposed to form at E $<$ 0.57 V by reduction of the Oad-rich islands and CO adsorption into the resulting lower-density Oad structures. CO bulk oxidation rates in the potential range E $>$ 0.57 V are low, but significantly higher than those observed during oxidation of pre-adsorbed CO in the CO-free electrolyte. We relate this to high local COad coverages due to CO adsorption in the CO-saturated electrolyte, which lowers the CO adsorption energy and thus the barrier for COadoxidation during CO bulk oxidation.}
 }

literature/alves_2011_electrochemistry_6010/alves_2011_electrochemistry_6010_p2_f2a_solid.yaml

@@ -0,0 +1,65 @@
+# This file is part of echemdb (https://github.com/echemdb/website)
+# Details on the meta data structure can be found on https://github.com/echemdb/metadata-schema
+electrochemical system:
+  electrodes:
+    configuration: three
+    reference electrode:
+      source:
+        supplier: homemade
+      type: RHE
+    working electrode:
+      crystallographic orientation: '0001'
+      material: Ru
+      preparation procedure: Sputtering and flash annealing under UHV conditions with
+        repeated cycles of oxygen adsorption and desorption.
+      shape:
+        height:
+          unit: mm
+          value: 2
+        type: hat shaped
+      source:
+        supplier: Mateck
+  electrolyte:
+    components:
+    - name: H2O
+      proportion:
+        unit: volume percent
+        value: 100
+      source:
+        quality: ultrapure water
+        refinement: Millipore MilliQ
+      type: solvent
+    - concentration:
+        unit: mol / l
+        value: 0.1
+      name: HClO4
+      source:
+        supplier: Merck Suprapur
+      type: acid
+    ph:
+      value: 1
+    temperature:
+      unit: K
+      value: 298.15
+    type: aq
+  instrumentation:
+  - type: potentiostat
+  version: 1
+source:
+  citation key: alves_2011_electrochemistry_6010
+  curve: solid
+  url: https://doi.org/10.1039/C0CP01001D
+  figure: 2a
+  version: 1
+version: 1
+curation:
+  version: 1
+  process:
+  - role: curator
+    name: Albert Engstfeld
+    orcid: https://orcid.org/0000-0002-9686-3948
+    date: 2021-07-09
+  - role: reviewer
+    name: Albert Engstfeld
+    orcid: https://orcid.org/0000-0002-9686-3948
+    date: 2022-01-21

literature/briega-martos_2021_cation_XXX/briega-martos_2021_cation_XXX.bib → literature/briega-martos_2021_cation_48/briega-martos_2021_cation_48.bib

@@ -1,4 +1,4 @@
-@article{briega-martos_2021_cation_XXX,
+@article{briega-martos_2021_cation_48,
   title={Cation Effects on Interfacial Water Structure and Hydrogen Peroxide Reduction on Pt (111)},
   author={Briega-Martos, Valent{\'\i}n and Sarabia, Francisco J and Climent, V{\'\i}ctor and Herrero, Enrique and Feliu, Juan M},
   journal={ACS Measurement Science Au},