diff --git a/.citation_parser_ui.py.swp b/.citation_parser_ui.py.swp
deleted file mode 100644
index 38c0d61d4724d853b03e358ed4916b537560e72f..0000000000000000000000000000000000000000
Binary files a/.citation_parser_ui.py.swp and /dev/null differ
diff --git a/assets/json_text.json b/assets/json_text.json
index b2e4c5f1d417d21f23729da7e833989a82a9eeaf..b8177a35f64f22f16224949cf9e8c88ae7fdbe6b 100644
--- a/assets/json_text.json
+++ b/assets/json_text.json
@@ -1 +1 @@
-{"nodes": [{"doi": "https://doi.org/10.1021/acs.jcim.6b00709", "name": "Matched Molecular Series: Measuring SAR Similarity", "author": ["Emanuel S. R. Ehmki", "Christian Kramer"], "year": "May 1, 2017", "journal": "Journal of Chemical Information and Modeling", "group": "Input", "depth": 0, "citations": 5}, {"doi": "https://doi.org/10.1021/acs.jcim.0c00269", "name": "Matched Molecular Series Analysis for ADME Property Prediction", "author": ["Mahendra Awale", "Sereina Riniker", "Christian Kramer"], "year": "May 5, 2020", "journal": "Journal of Chemical Information and Modeling", "group": "Citedby", "depth": 1, "citations": 6}, {"doi": "https://doi.org/10.1021/acs.jcim.0c00290", "name": "Identification of Bioisosteric Substituents by a Deep Neural Network", "author": ["Peter Ertl"], "year": "June 15, 2020", "journal": "Journal of Chemical Information and Modeling", "group": "Citedby", "depth": 2, "citations": 2}], "links": [{"source": "https://doi.org/10.1021/acs.jcim.0c00269", "target": "https://doi.org/10.1021/acs.jcim.6b00709"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00290", "target": "https://doi.org/10.1021/acs.jcim.0c00269"}]}
\ No newline at end of file
+{"nodes": [], "links": []}
\ No newline at end of file
diff --git a/citation_parser_ui.py b/citation_parser_ui.py
index 2dbd0be7bee696f3a62a68f38ff3a50f6fc5e80c..c2b119dce5075fb6f1e11226dbf866abccd1d4fe 100644
--- a/citation_parser_ui.py
+++ b/citation_parser_ui.py
@@ -42,31 +42,31 @@ app.layout = html.Div([
is_open=False,
),
- # Layer 1: For all mandatory Inputs
+ # Layer 1: For the string input
html.Div([
"Input: ",
# A simple box for inputting a string.
# Value is transmitted upon pressing return or clicking out of the box.
- dcc.Input(id='input-string', value='', type='text',debounce=True,
+ dcc.Input(id='string-input', value='', type='text',debounce=True,
style={ "width": "400px"},
),
]),
- # Layer 1,5: For test
+ # Layer 2: For file input and recursion depths
html.Div([
- "Forward recursion: ",
+ "Cited-by Depth: ",
# Forward recursion. Values between 1 and 10 can be entered.
- dcc.Input(id='forward-depth',value='1',type='number',min='1',max='10',
+ dcc.Input(id='forward-depth',value='1',type='number',min='0',max='5',
style={ "width": "50px"},
),
- "Backward recursion: ",
+ "References Depth: ",
# Backward recursion. Values between 1 and 10 can be entered.
- dcc.Input(id='backward-depth',value='1',type='number',min='1',max='10',
+ dcc.Input(id='backward-depth',value='1',type='number',min='0',max='5',
style={"width": "50px"},
),
# Upload box. Can be used via drag-and-drop or byclicking on it to open a file viewer.
dcc.Upload(
- id="upload-data",
+ id="file-input",
children=html.Div(
#Drag and drop or click to select a file to upload
["Drag and drop"]),
@@ -82,7 +82,7 @@ app.layout = html.Div([
})
]),
- # Layer 2: For the checklist, Remove-/Start-Buttons and input-error-message
+ # Layer 3: For the checklist, Remove-/Start-Buttons and error message
html.Div([
# All input DOIs are collected in this checklist.
# It is initialized to avoid error messages.
@@ -97,7 +97,7 @@ app.layout = html.Div([
# Starts the process that generates a graph.
dbc.Button(id='start-button',children='Generate Graph', color="primary", className="me-1")
]),
- # Layer 3: For additional Options (e.g. Topological Sort)
+ # Layer 4: For additional Options
html.Div([
html.H4('Additional Options'),
# A checklist of all additional options that are listed above.
@@ -105,25 +105,25 @@ app.layout = html.Div([
options=[{'label':k,'value':k} for k in additional_options],
value=[])
]),
- # Layer 4: For the Graph
- html.Div(
- [html.Iframe(
+ # Layer 5: For the Graph and corresponding error messages
+ html.Div([
+ html.Div(id='generate-graph-error',style={'color':'red'}),
+ html.Iframe(
src="assets/index.html",
style={"height": "600px", "width": "100%"},
),
- html.Div(id='test-output')
])
])
@app.callback(
Output('input-checklist','options'),
Output('input-checklist','value'),
- Output('input-string','value'),
+ Output('string-input','value'),
Output('input-err','children'),
- Input('input-string','value'),
+ Input('string-input','value'),
Input('clear-all-button','n_clicks'),
Input('clear-selected-button','n_clicks'),
- Input('upload-data','contents'),
+ Input('file-input','contents'),
State('input-checklist','options'),
State('input-checklist','value'),
State('additional-options','value')
@@ -133,7 +133,7 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
'''
Most important callback function. Updates the checklist that holds all inputs.
State of the checklist as input is needed so that previews entries are readded.
- input-string is required as Output to clear the input box after each input.
+ string-input is required as Output to clear the input box after each input.
Different actions are performed depending on which input triggered the callback.
The value-attribute of input-checklist must be updates so that the values
of deleted elements no longer appear in the list of selected elements.
@@ -168,7 +168,7 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
return all_inputs,list(),'',''
# when a new element is added via dcc.Input
- if 'input-string' in changed_id:
+ if 'string-input' in changed_id:
# Creates a list of previously added inputs to make sure nothing is added twice
currValues = [x['value'] for x in all_inputs]
if input_value not in currValues:
@@ -186,7 +186,10 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
# Creates a more readable string to display in the checklist
rep_str = pub.contributors[0] + ',' + pub.journal + \
',' + pub.publication_date
- all_inputs.append({'label':rep_str, 'value':input_value})
+ # Makes sure not to add the same article with different links
+ currLabels = [x['label'] for x in all_inputs]
+ if rep_str not in currLabels:
+ all_inputs.append({'label':rep_str, 'value':input_value})
# if 'Smart Input' is not selected, the input value is added as is,
# without checking for validity.
@@ -195,7 +198,7 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
return all_inputs,selected_inputs,'',''
# when a txt-file is uploaded
- if 'upload-data.contents' in changed_id:
+ if 'file-input.contents' in changed_id:
if filecontents:
# Skips the info portion that is added when a file is uploaded
found = base64.b64decode(re.search(',(.+?)$', filecontents).group(1))
@@ -215,7 +218,9 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
return all_inputs,selected_inputs,'','{}'.format(err)
rep_str = pub.contributors[0] + ',' + pub.journal + \
',' + pub.publication_date
- all_inputs.append({'label':rep_str, 'value':input_value})
+ currLabels = [x['label'] for x in all_inputs]
+ if rep_str not in currLabels:
+ all_inputs.append({'label':rep_str, 'value':input_value})
else:
all_inputs.append({'label':input_value,'value':input_value})
return all_inputs,selected_inputs,'',''
@@ -244,16 +249,14 @@ def toggle_collapse(n, is_open):
@app.callback(
- Output('test-output','children'),
+ Output('generate-graph-error','children'),
Input('start-button','n_clicks'),
Input('input-checklist','options'),
- Input('input-checklist','value'),
Input('forward-depth','value'),
Input('backward-depth','value'),
State('additional-options','value')
)
-def generate_output(n_clicks,all_inputs,selected_inputs,
- forward_depth,backward_depth,additional_options):
+def generate_output(n_clicks,all_inputs,forward_depth,backward_depth,additional_options):
'''
Basic structure for a callback that generates an output. This is only a
proof of concept and has noting to do with the intended output yet.
@@ -263,8 +266,6 @@ def generate_output(n_clicks,all_inputs,selected_inputs,
:param all_inputs: all labels and values from the checklist,
regardless if they have been checked or not
:type all_inputs: list of dictionaries with 2 entries each
- :param selected_inputs: values of all checked elements
- :type selected_inputs: list of strings
:param forward_depth: forward recursion depth
:type forward_depth: unsigned int
:param backward_depth: backward recursion depth
@@ -278,7 +279,15 @@ def generate_output(n_clicks,all_inputs,selected_inputs,
elif 'Update Automatically' in additional_options \
or 'start-button' in changed_id:
input_links = [x['value'] for x in all_inputs]
- Processing(input_links,int(forward_depth),int(backward_depth),'assets/json_text.json')
+ errors = Processing(input_links,int(forward_depth),int(backward_depth),'assets/json_text.json')
+ if errors:
+ message = ['The following inputs are invalid and were not used:']
+ for error in errors:
+ message.append(html.Br())
+ message.append(error)
+ message = html.P(message)
+ #message = [html.P(error) for error in errors]
+ return message
if __name__ == '__main__':
app.run_server(debug=False)
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