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Commit bcbe550e authored by Malte Schokolowski's avatar Malte Schokolowski
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verarbeitung: changes in initialize_graph

parents 345ee696 100d9e46
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1 merge request!22Added abstracts to json, negative tests and bug fixes
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.DS_Store 0 → 100644
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.citation_parser_ui.py.swp deleted 100644 → 0
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.gitignore
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......@@ -16,6 +16,7 @@ Thumbs.db
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*.pyc
*$py.class
# C extensions
......@@ -38,6 +39,7 @@ wheels/
*.egg-info/
.installed.cfg
*.egg
.start_script.py
MANIFEST
# PyInstaller
......
assets/json_text.json
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{"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": []}
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citation_parser_ui.py → citation_parser_main.py
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......@@ -10,8 +10,13 @@ from dash.exceptions import PreventUpdate
from input.interface import InputInterface
import input.publication
from verarbeitung.process_main import Processing
from dash.dependencies import Input, Output, State #Loading Bar
import plotly.express as px
import dash_bootstrap_components as dbc # pip install dash-bootstrap-components for Loading Bar
app = dash.Dash(__name__)
app = dash.Dash(__name__, external_stylesheets=[dbc.themes.SPACELAB]) #SPACELAB https://bootswatch.com/default/ for more themes)
# List of options when inputting data and generating the graph
additional_options = ['Update Automatically','Smart Input']
......@@ -24,25 +29,47 @@ f.close()
app.layout = html.Div([
# Layer 0: For the Header and Help Function(s)
html.Div([
html.Button(id='show-info',children='Show Info',n_clicks=0),
html.Div(id='info-box')
]),
# Layer 1: For all mandatory Inputs
dbc.Button(
'show Info',
id='collapse-button',
className="me-1",
color="primary",
n_clicks=0,
),
dbc.Collapse(
dbc.Card(dbc.CardBody(html.Div(boxcontent, style={'whiteSpace': 'pre-line'}))),
id='collapse',
is_open=False,
),
# 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 2: For file input and recursion depths
html.Div([
"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"},
),
"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 or click to select a file to upload
["Drag and drop"]),
style={
"width": "30%",
"height": "60px",
......@@ -54,7 +81,8 @@ app.layout = html.Div([
"margin": "10px",
})
]),
# 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.
......@@ -63,13 +91,13 @@ app.layout = html.Div([
# Displays error message if 'Smart Input' is active.
html.Div(id='input-err',style={'color':'red'}),
# Clears the entire list.
html.Button(id='clear-all-button',children='Clear All'),
dbc.Button(id='clear-all-button',children='Clear All', color="primary", className="me-1"),
# Clear all selected elements.
html.Button(id='clear-selected-button',children='Clear Selected'),
dbc.Button(id='clear-selected-button',children='Clear Selected', color="primary", className="me-1"),
# Starts the process that generates a graph.
html.Button(id='start-button',children='Generate 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.
......@@ -77,25 +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')
......@@ -105,7 +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.
......@@ -140,7 +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:
......@@ -158,6 +186,9 @@ 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
# 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,
......@@ -167,7 +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))
......@@ -187,6 +218,8 @@ 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
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})
......@@ -197,33 +230,33 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
if input_value == '':
return list(),list(),'',''
@app.callback(
Output('info-box','children'),
Input('show-info','n_clicks')
Output('collapse', 'is_open'),
[Input('collapse-button', 'n_clicks')],
[State('collapse', 'is_open')],
)
def show_hide_info_box(n_clicks):
def toggle_collapse(n, is_open):
'''
This callback shows and hides the (first) info-box by, checking how often
This callback shows and hides the (first) info-box by, checking how# often
the button has been pressed. The text was loaded at the top.
:param n_clicks: number of times show-info has been clicked.
'type n_clicks: int
'''
if n_clicks % 2 == 0:
return ''
else:
return html.Div(boxcontent, style={'whiteSpace': 'pre-line'})
if n:
return not is_open
return 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.
......@@ -233,8 +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
......@@ -248,7 +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)
verarbeitung/construct_new_graph/add_citations_rec.py
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......@@ -164,12 +164,16 @@ def process_citations_rec(citations_pub_obj_list, search_depth, search_depth_max
'''
# adds next level to nodes/edges
new_citation_pub_obj_save_list = []
for pub in citations_pub_obj_list:
new_citation_pub_obj_list = create_graph_structure_citations(pub, search_depth, search_depth_max, cit_type, test_var)
if len(new_citation_pub_obj_list) > 0:
new_citation_pub_obj_save_list += new_citation_pub_obj_list
# If the maximum depth has not yet been reached, calls function recursivly with increased depth
if (search_depth < search_depth_max):
process_citations_rec(new_citation_pub_obj_list, search_depth+1, search_depth_max, cit_type, test_var)
process_citations_rec(new_citation_pub_obj_save_list, search_depth+1, search_depth_max, cit_type, test_var)
def add_citations(input_nodes, input_edges, citations_pub_obj_list, search_depth, search_depth_max, cit_type, test_var):
......
verarbeitung/new_height.json
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{"nodes": [{"doi": "doi_lg_1_i", "name": "title_lg_1_i", "author": ["contributor_lg_1_i"], "year": "date_lg_1_i", "journal": "journal_lg_1_i", "group": "Input", "depth": 0, "citations": 2}, {"doi": "doi_lg_1_d11", "name": "title_lg_1_d11", "author": ["contributor_lg_1_d11"], "year": "date_lg_1_d11", "journal": "journal_lg_1_d11", "group": "Reference", "depth": -1, "citations": 1}, {"doi": "doi_lg_1_d12", "name": "title_lg_1_d12", "author": ["contributor_lg_1_d12"], "year": "date_lg_1_d12", "journal": "journal_lg_1_d12", "group": "Reference", "depth": -1, "citations": 2}, {"doi": "doi_lg_1_h11", "name": "title_lg_1_h11", "author": ["contributor_lg_1_h11"], "year": "date_lg_1_h11", "journal": "journal_lg_1_h11", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_lg_1_h12", "name": "title_lg_1_h12", "author": ["contributor_lg_1_h12"], "year": "date_lg_1_h12", "journal": "journal_lg_1_h12", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_lg_1_h21", "name": "title_lg_1_h21", "author": ["contributor_lg_1_h21"], "year": "date_lg_1_h21", "journal": "journal_lg_1_h21", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_1_h22", "name": "title_lg_1_h22", "author": ["contributor_lg_1_h22"], "year": "date_lg_1_h22", "journal": "journal_lg_1_h22", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_1_h23", "name": "title_lg_1_h23", "author": ["contributor_lg_1_h23"], "year": "date_lg_1_h23", "journal": "journal_lg_1_h23", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_1_d21", "name": "title_lg_1_d21", "author": ["contributor_lg_1_d21"], "year": "date_lg_1_d21", "journal": "journal_lg_1_d21", "group": "Reference", "depth": -2, "citations": 2}, {"doi": "doi_lg_1_d22", "name": "title_lg_1_d22", "author": ["contributor_lg_1_d22"], "year": "date_lg_1_d22", "journal": "journal_lg_1_d22", "group": "Reference", "depth": -2, "citations": 2}, {"doi": "doi_lg_1_d23", "name": "title_lg_1_d23", "author": ["contributor_lg_1_d23"], "year": "date_lg_1_d23", "journal": "journal_lg_1_d23", "group": "Reference", "depth": -2, "citations": 2}], "links": [{"source": "doi_lg_1_i", "target": "doi_lg_1_d11"}, {"source": "doi_lg_1_i", "target": "doi_lg_1_d12"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h21", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_h23", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d21", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d22", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d12", "target": "doi_lg_1_d23"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}]}
\ No newline at end of file
{"nodes": [{"doi": "doi_lg_1_i", "name": "title_lg_1_i", "author": ["contributor_lg_1_i"], "year": "date_lg_1_i", "journal": "journal_lg_1_i", "group": "Input", "depth": 0, "citations": 2}, {"doi": "doi_lg_1_d11", "name": "title_lg_1_d11", "author": ["contributor_lg_1_d11"], "year": "date_lg_1_d11", "journal": "journal_lg_1_d11", "group": "Reference", "depth": -1, "citations": 1}, {"doi": "doi_lg_1_d12", "name": "title_lg_1_d12", "author": ["contributor_lg_1_d12"], "year": "date_lg_1_d12", "journal": "journal_lg_1_d12", "group": "Reference", "depth": -1, "citations": 2}, {"doi": "doi_lg_1_h11", "name": "title_lg_1_h11", "author": ["contributor_lg_1_h11"], "year": "date_lg_1_h11", "journal": "journal_lg_1_h11", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_lg_1_h12", "name": "title_lg_1_h12", "author": ["contributor_lg_1_h12"], "year": "date_lg_1_h12", "journal": "journal_lg_1_h12", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_lg_1_h21", "name": "title_lg_1_h21", "author": ["contributor_lg_1_h21"], "year": "date_lg_1_h21", "journal": "journal_lg_1_h21", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_1_h22", "name": "title_lg_1_h22", "author": ["contributor_lg_1_h22"], "year": "date_lg_1_h22", "journal": "journal_lg_1_h22", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_1_h23", "name": "title_lg_1_h23", "author": ["contributor_lg_1_h23"], "year": "date_lg_1_h23", "journal": "journal_lg_1_h23", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_1_d21", "name": "title_lg_1_d21", "author": ["contributor_lg_1_d21"], "year": "date_lg_1_d21", "journal": "journal_lg_1_d21", "group": "Reference", "depth": -2, "citations": 2}, {"doi": "doi_lg_1_d22", "name": "title_lg_1_d22", "author": ["contributor_lg_1_d22"], "year": "date_lg_1_d22", "journal": "journal_lg_1_d22", "group": "Reference", "depth": -2, "citations": 2}, {"doi": "doi_lg_1_d23", "name": "title_lg_1_d23", "author": ["contributor_lg_1_d23"], "year": "date_lg_1_d23", "journal": "journal_lg_1_d23", "group": "Reference", "depth": -2, "citations": 2}], "links": [{"source": "doi_lg_1_i", "target": "doi_lg_1_d11"}, {"source": "doi_lg_1_i", "target": "doi_lg_1_d12"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h21", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_h23", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d12", "target": "doi_lg_1_d23"}, {"source": "doi_lg_1_d21", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d22", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}]}
\ No newline at end of file
verarbeitung/test_output.json
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