From b18d58bc6cfb41dad18647f517fe38b6da443a52 Mon Sep 17 00:00:00 2001
From: Sebastian David <sebastian.david@uni-hamburg.de>
Date: Thu, 13 Jan 2022 13:52:59 +0100
Subject: [PATCH] full functionality, changed some variable names
---
.citation_parser_ui.py.swp | Bin 20480 -> 0 bytes
assets/json_text.json | 2 +-
citation_parser_ui.py | 67 ++++++++++--------
input/get/__pycache__/__init__.cpython-38.pyc | Bin 157 -> 153 bytes
input/get/__pycache__/acs.cpython-38.pyc | Bin 4197 -> 4193 bytes
.../journal_fetcher.cpython-38.pyc | Bin 3797 -> 3793 bytes
input/get/__pycache__/nature.cpython-38.pyc | Bin 1636 -> 1632 bytes
7 files changed, 39 insertions(+), 30 deletions(-)
delete mode 100644 .citation_parser_ui.py.swp
diff --git a/.citation_parser_ui.py.swp b/.citation_parser_ui.py.swp
deleted file mode 100644
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diff --git a/assets/json_text.json b/assets/json_text.json
index b2e4c5f..b8177a3 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 2dbd0be..c2b119d 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)
diff --git a/input/get/__pycache__/__init__.cpython-38.pyc b/input/get/__pycache__/__init__.cpython-38.pyc
index f12fb9c33e874aa1c55d94725f867ac6503d407e..52f5d64aa3f72e25accf523fb850635617afbf5e 100644
GIT binary patch
delta 75
zcmbQsIFpe(l$V!_fq{YHZpYn;+%_h5`WgATsrtpKNr}ZJnTdJ&1x5K;so5o|`pKEP
Z#kx?QZfT}|W?n&QiGF%&iT=cTIRJuK8JYk9
delta 79
zcmbQqIG2$-l$V!_fq{V`dF8>0+%^_Y$yPC;#i>QbG46@EnRzkknI$pFnYzWg1x5K;
iso5pEWvNApMM<fdC8c@kF`0P<r6n=xsU<NJtK|USp&P6K
diff --git a/input/get/__pycache__/acs.cpython-38.pyc b/input/get/__pycache__/acs.cpython-38.pyc
index 121d1856184f02775d5bb84d081dcd91a648ea67..78c1fb0c8b885e90285224e745b09af56faf9b01 100644
GIT binary patch
delta 81
zcmaE=@KAv-l$V!_fq{YHZpYokb+Q}z44F+V^)vEwQ}v5elM;(dG86Ok3ySiyQnO1^
f^^-Goi*=zq-O^0`%)Elq68-el68+8P%<p&rT2vgS
delta 85
zcmaE;@Kk{>l$V!_fq{V`dF8>xJh_d0hRhbW$yPC;#i>QbG46@EnRzkknI$pFnYzWg
p1x5K;so5pEWvNApMM<fdC8c@kF`0P<r6n=xsU<O+i<#f?006Ok9(e!&
diff --git a/input/get/__pycache__/journal_fetcher.cpython-38.pyc b/input/get/__pycache__/journal_fetcher.cpython-38.pyc
index 72a774c45762b3d4cb37a7089f4d8275dab0e533..af9bd12b47a0bae4c1683adf78d92884b7e51193 100644
GIT binary patch
delta 266
zcmcaAdr_7*l$V!_fq{YHZpYn3?~S}^%#61tmoRI)-C{0EExg5?T2!=>p-7N{f#H{{
zenx(7s(x{5QetsQW@4UxK~a8IYIaGgesZR6u`ZOSTbik#nO9I+qMx2xqQChib0{M>
zNITe!BB9NmtYVC!A`A=+MdBa=S*nC>It!!JW*+XDOg6$GNoEEHhFdI2`T03T5+FV+
zh>!#cawjGw6{VKNr(`CVKukt5X!1ke77;m+GUmjj<RT`JF0fIPEBSN;5DLL8p~+kM
F6aZ@3Lj(W-
delta 270
zcmca8dsUV<l$V!_fq{V`dF8>xRU3KJm>HucmoRI4MKKqp7T#h`Eh<{cP{hx`!0^j6
z*(xTqIJKxa#yv4NGcP7Rvm_=tQ@2>RpeR2pHM>N&EVU@HC@D3wq%<!*CNr;~v?L}y
zwIpWqQ|3@cZjcdRbBY8uyRwQgiV86>FcgV`2xO@Ow&^U45}P@=XENCcf+U$47#MD`
zB<1Jl6p4ZOtRO-hB*>kZlvI>j7N3%tTmmr}$)L%1d0RweK+2dClah;=K)OIiMNKZ{
Q(-A-@1hWJtZ{$+|0Db90u>b%7
diff --git a/input/get/__pycache__/nature.cpython-38.pyc b/input/get/__pycache__/nature.cpython-38.pyc
index 3afb8454a05c8afe9b1f2aba3f534d66cbd8ae3a..ca8c9862b7234c55e49b676136ab64a62f91e58b 100644
GIT binary patch
delta 80
zcmaFD^MHppl$V!_fq{YHZpYn3zm2>mOeQw^8Tq-X`o*b9iNz(EiFx`3Mfq8&*(Is^
e$(g#vx=@~OX{LT=UO{PzetK$&{^m-i*USJZbsP5p
delta 84
zcmaFB^Mr>tl$V!_fq{V`dF8>x&W*e#OcoBwRxzQ)sYS&x?uogXc`@mkB{9jFy2ZK$
oMfq8&*(JJVsYQuJNvWA7rFrQwnRx}JB{Au#B{7>znO-vk0G_ZOL;wH)
--
GitLab