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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
This commit is part of merge request !22. Comments created here will be created in the context of that merge request.
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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"}]}
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verarbeitung/test_output.json
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