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Fix empty <title> in AMI-Search dataTables
ami-search creates an empty <title/> in fullDatatables.html element which prevents display.
Trying to use ami to test the dictionary funders, the commands given:
ami -p ami_test_6 search --dictionary funders
After running the Command,
Generic values (AMISearchTool)
================================
-v to see generic values
Specific values (AMISearchTool)
================================
created COMMAND: word(frequencies)xpath:@count>20~w.stopwords:pmcstop.txt_stopwords.txt search(funders)
0 [main] DEBUG org.contentmine.ami.tools.AbstractAMISearchTool - old style search command); to be changed
0 [main] DEBUG org.contentmine.ami.tools.AbstractAMISearchTool - old style search command); to be changed
cProject: ami_test_6
created COMMAND: word(frequencies)xpath:@count>20~w.stopwords:pmcstop.txt_stopwords.txt search(funders)
legacy cmd> word(frequencies)xpath:@count>20~w.stopwords:pmcstop.txt_stopwords.txt
legacy cmd> search(funders)
81 [main] DEBUG org.contentmine.ami.plugins.CommandProcessor - running NORMA -i fulltext.xml -o scholarly.html --transform nlm2html --project ami_test_6
81 [main] DEBUG org.contentmine.ami.plugins.CommandProcessor - running NORMA -i fulltext.xml -o scholarly.html --transform nlm2html --project ami_test_6
!PMC6318360 .!PMC6473713 !PMC6518571 !PMC6553602 !PMC6728053 !PMC6742212 !PMC6853075 !PMC6901221 !PMC6905541 !PMC6924880 !PMC6963280 .!PMC6964091 !PMC6979359 !PMC7032730 !PMC7053713 !PMC7069648 !PMC7077839 !PMC7077840 !PMC7080275 !PMC7081976 !PMC7095334 .!PMC7108131 !PMC7123112 !PMC7146642 !PMC7154513 !PMC7167542 !PMC7169901 !PMC7175453 !PMC7184488 !PMC7185698 !PMC7188427 .!PMC7201909 !PMC7204673 !PMC7215950 !PMC7217455 !PMC7219405 !PMC7219742 !PMC7221944 !PMC7226716 !PMC7235449 !PMC7237041 .!PMC7245636 !PMC7250535 !PMC7253103 !PMC7265527 !PMC7272002 !PMC7276732 !PMC7277812
it created empty file full.datatables.html in the folder ami_test_6 What else can be done?
This is a bug. Can you open the file in a text editor (not word). If there is an element
On Tue, Jun 23, 2020 at 6:05 PM VAISHALI ARORA [email protected] wrote:
Trying to use ami to test the dictionary funders, the commands given: ami -p ami_test_6 search --dictionary funders
After running the Command,
Generic values (AMISearchTool)
-v to see generic values
Specific values (AMISearchTool)
created COMMAND: word(frequencies)xpath:@count>20~w.stopwords:pmcstop.txt_stopwords.txt search(funders) 0 [main] DEBUG org.contentmine.ami.tools.AbstractAMISearchTool - old style search command); to be changed 0 [main] DEBUG org.contentmine.ami.tools.AbstractAMISearchTool - old style search command); to be changed cProject: ami_test_6 created COMMAND: word(frequencies)xpath:@count>20~w.stopwords:pmcstop.txt_stopwords.txt search(funders) legacy cmd> word(frequencies)xpath:@count>20~w.stopwords:pmcstop.txt_stopwords.txt legacy cmd> search(funders) 81 [main] DEBUG org.contentmine.ami.plugins.CommandProcessor - running NORMA -i fulltext.xml -o scholarly.html --transform nlm2html --project ami_test_6 81 [main] DEBUG org.contentmine.ami.plugins.CommandProcessor - running NORMA -i fulltext.xml -o scholarly.html --transform nlm2html --project ami_test_6 !PMC6318360 .!PMC6473713 !PMC6518571 !PMC6553602 !PMC6728053 !PMC6742212 !PMC6853075 !PMC6901221 !PMC6905541 !PMC6924880 !PMC6963280 .!PMC6964091 !PMC6979359 !PMC7032730 !PMC7053713 !PMC7069648 !PMC7077839 !PMC7077840 !PMC7080275 !PMC7081976 !PMC7095334 .!PMC7108131 !PMC7123112 !PMC7146642 !PMC7154513 !PMC7167542 !PMC7169901 !PMC7175453 !PMC7184488 !PMC7185698 !PMC7188427 .!PMC7201909 !PMC7204673 !PMC7215950 !PMC7217455 !PMC7219405 !PMC7219742 !PMC7221944 !PMC7226716 !PMC7235449 !PMC7237041 .!PMC7245636 !PMC7250535 !PMC7253103 !PMC7265527 !PMC7272002 !PMC7276732 !PMC7277812
it created empty file full.datatables.html in the folder ami_test_6 What else can be done?
— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/petermr/openVirus/issues/2#issuecomment-648293289, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFTCS2ECPGGPKQLUNVUUY3RYDOETANCNFSM4LHREOWA .
-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
This is all it displayed, do not contain the element
<?xml version="1.0" encoding="UTF-8"?>
<html xmlns="http://www.w3.org/1999/xhtml">
<head charset="UTF-8">
<title>ami_test_6</title>
<link rel="stylesheet" type="text/css" href="http://ajax.aspnetcdn.com/ajax/jquery.dataTables/1.9.4/css/jquery.dataTables.css"/>
<script src="http://ajax.aspnetcdn.com/ajax/jQuery/jquery-1.8.2.min.js" charset="UTF-8" type="text/javascript"> </script>
<script src="http://ajax.aspnetcdn.com/ajax/jquery.dataTables/1.9.4/jquery.dataTables.min.js" charset="UTF-8" type="text/javascript"> </script>
<script charset="UTF-8" type="text/javascript">$(function() { $("#results").dataTable(); }) </script>
</head>
<body>
<div class="bs-example table-responsive">
<table class="table table-striped table-bordered table-hover" id="results">
<thead>
<tr>
<th>articles</th>
<th>bibliography</th>
</tr>
</thead>
<tbody/>
<tfoot/>
</table>
</div>
</body>
</html>
OK - this is either a bug or you don't have any hits!
Can you install tree (it's a UNIX tool that lists directories to the
console)
Then we can see what's in ami_test_6
I'm looking at miniproject which contains epidemic50noCov
and I issue
tree -h miniproject | more
which shows
miniproject
├── [2.2K] README.md
├── [2.4K] epidemic50noCov
│ ├── [ 576] PMC6808808
│ │ ├── [7.4K] eupmc_result.json
│ │ ├── [7.4K] fulltext.xml
│ │ ├── [ 128] results
│ │ │ ├── [ 224] search
│ │ │ │ ├── [ 96] country
│ │ │ │ │ └── [ 538] results.xml
│ │ │ │ ├── [ 96] disease
│ │ │ │ │ └── [ 584] results.xml
│ │ │ │ ├── [ 96] funders
│ │ │ │ │ └── [ 245] results.xml
│ │ │ │ ├── [ 96] inn
│ │ │ │ │ └── [ 64] empty.xml
│ │ │ │ └── [ 96] tropicalVirus
│ │ │ │ └── [ 74] empty.xml
│ │ │ └── [ 96] word
│ │ │ └── [ 128] frequencies
│ │ │ ├── [1.4K] results.html
│ │ │ └── [1.3K] results.xml
│ │ ├── [ 14K] scholarly.html
│ │ ├── [ 72] search.country.count.xml
│ │ ├── [ 631] search.country.snippets.xml
│ │ ├── [ 72] search.disease.count.xml
│ │ ├── [ 677] search.disease.snippets.xml
│ │ ├── [ 72] search.funders.count.xml
│ │ ├── [ 336] search.funders.snippets.xml
│ │ ├── [ 72] search.inn.count.xml
│ │ ├── [ 57] search.inn.snippets.xml
│ │ ├── [ 72] search.tropicalVirus.count.xml
│ │ ├── [ 57] search.tropicalVirus.snippets.xml
│ │ ├── [ 72] word.frequencies.count.xml
│ │ └── [ 57] word.frequencies.snippets.xml
│ ├── [ 576] PMC6810139
│ │ ├── [7.9K] eupmc_result.json
│ │ ├── [7.7K] fulltext.xml
│ │ ├── [ 128] results
│ │ │ ├── [ 224] search
│ │ │ │ ├── [ 96] country
│ │ │ │ │ └── [ 870] results.xml
│ │ │ │ ├── [ 96] disease
│ │ │ │ │ └── [ 453] results.xml
│ │ │ │ ├── [ 96] funders
│ │ │ │ │ └── [ 68] empty.xml
│ │ │ │ ├── [ 96] inn
│ │ │ │ │ └── [ 64] empty.xml
│ │ │ │ └── [ 96] tropicalVirus
│ │ │ │ └── [ 74] empty.xml
│ │ │ └── [ 96] word
On Wed, Jun 24, 2020 at 5:26 PM VAISHALI ARORA [email protected] wrote:
This is all it displayed, do not contain the element
ami_test_6
articles bibliography — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/petermr/openVirus/issues/2#issuecomment-648925466, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFTCS4OE4YEPZPBSXXMV4TRYISMRANCNFSM4LHREOWA .
-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
QUERY
I gave the command ami -p ami_test_2 search --dictionary viruses
And full data table was created in html looked something like below
How can i put the extracted information into my work?
Well done so far. There is no inbuilt dictionary for "viruses" - it will have to be created. However we have a (small) test dictionary . Try
ami -p ami_test_2 search --dictionary tropicalVirus
On Wed, Jun 24, 2020 at 8:05 PM kareenasingh [email protected] wrote:
QUERY I gave the command ami -p ami_test_2 search --dictionary viruses And full data table was created in html looked something like below [image: Capture new] https://user-images.githubusercontent.com/65625564/85616505-72b63d80-b67b-11ea-9f13-852fe2b38979.PNG
How can i put the extracted information into my work?
— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/petermr/openVirus/issues/2#issuecomment-649009463, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFTCSYZAPLVGX32SQDUK5DRYJE7HANCNFSM4LHREOWA .
-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
Well, I got this in my directory ami_test_6
C:\Users\me>tree ami_test_6
Folder PATH listing for volume OS
Volume serial number is D651-7DC0
C:\USERS\me\AMI_TEST_6
├───PMC6318360
│ └───results
│ └───search
│ └───funders
├───PMC6473713
│ └───results
│ └───search
│ └───funders
├───PMC6518571
│ └───results
│ └───search
│ └───funders
├───PMC6553602
│ └───results
│ └───search
│ └───funders
├───PMC6728053
│ └───results
│ └───search
│ └───funders
├───PMC6742212
│ └───results
│ └───search
│ └───funders
├───PMC6853075
│ └───results
│ └───search
│ └───funders
├───PMC6901221
│ └───results
│ └───search
│ └───funders
├───PMC6905541
│ └───results
│ └───search
│ └───funders
├───PMC6924880
│ └───results
│ └───search
│ └───funders
├───PMC6963280
│ └───results
│ └───search
│ └───funders
├───PMC6964091
│ └───results
│ └───search
│ └───funders
├───PMC6979359
│ └───results
│ └───search
│ └───funders
├───PMC7032730
│ └───results
│ └───search
│ └───funders
├───PMC7053713
│ └───results
│ └───search
│ └───funders
├───PMC7069648
│ └───results
│ └───search
│ └───funders
├───PMC7077839
│ └───results
│ └───search
│ └───funders
├───PMC7077840
│ └───results
│ └───search
│ └───funders
├───PMC7080275
│ └───results
│ └───search
│ └───funders
├───PMC7081976
│ └───results
│ └───search
│ └───funders
├───PMC7095334
│ └───results
│ └───search
│ └───funders
├───PMC7108131
│ └───results
│ └───search
│ └───funders
├───PMC7123112
│ └───results
│ └───search
│ └───funders
├───PMC7146642
│ └───results
│ └───search
│ └───funders
├───PMC7154513
│ └───results
│ └───search
│ └───funders
├───PMC7167542
│ └───results
│ └───search
│ └───funders
├───PMC7169901
│ └───results
│ └───search
│ └───funders
├───PMC7175453
│ └───results
│ └───search
│ └───funders
├───PMC7184488
│ └───results
│ └───search
│ └───funders
├───PMC7185698
│ └───results
│ └───search
│ └───funders
├───PMC7188427
│ └───results
│ └───search
│ └───funders
├───PMC7201909
│ └───results
│ └───search
│ └───funders
├───PMC7204673
│ └───results
│ └───search
│ └───funders
├───PMC7215950
│ └───results
│ └───search
│ └───funders
├───PMC7217455
│ └───results
│ └───search
│ └───funders
├───PMC7219405
│ └───results
│ └───search
│ └───funders
├───PMC7219742
│ └───results
│ └───search
│ └───funders
├───PMC7221944
│ └───results
│ └───search
│ └───funders
├───PMC7226716
│ └───results
│ └───search
│ └───funders
├───PMC7235449
│ └───results
│ └───search
│ └───funders
├───PMC7237041
│ └───results
│ └───search
│ └───funders
├───PMC7245636
│ └───results
│ └───search
│ └───funders
├───PMC7250535
│ └───results
│ └───search
│ └───funders
├───PMC7253103
│ └───results
│ └───search
│ └───funders
├───PMC7265527
│ └───results
│ └───search
│ └───funders
├───PMC7272002
│ └───results
│ └───search
│ └───funders
├───PMC7276732
│ └───results
│ └───search
│ └───funders
├───PMC7277812
│ └───results
│ └───search
│ └───funders
├───PMC7278377
│ └───results
│ └───search
│ └───funders
├───PMC7278987
│ └───results
│ └───search
│ └───funders
└───__cooccurrence
├───funders
└───funders-funders
Thank you, This is an excellent bug report. It looks as if your tree has no data in before you started . Here is mine:
├── PMC6808808 │ ├── eupmc_result.json │ ├── fulltext.xml │ ├── results │ │ ├── search │ │ │ ├── country │ │ │ │ └── results.xml │ │ │ ├── disease │ │ │ │ └── results.xml │ │ │ ├── funders │ │ │ │ └── results.xml │ │ │ ├── inn │ │ │ │ └── empty.xml │ │ │ └── tropicalVirus │ │ │ └── empty.xml │ │ └── word │ │ └── frequencies │ │ ├── results.html │ │ └── results.xml │ ├── scholarly.html │ ├── search.country.count.xml │ ├── search.country.snippets.xml ...
(The ... means I have clipped the rest).
You can see that this CTree has
-
fulltext.xml(the fulltext downloaded from EPMC) -
scholarly.html(the fulltext converted into HTML)
You do not have fulltext.xml . Do you remember how you created the
CProject - because it's called ami_test_6 I am guessing it was edited
from somewhere. And I think some other interns have files with the same
type of name. If files are edited it's hard to keep records which is why we
should do operations with ami3 or the other tools. I'm going to post a
link to this in case other have the problem.
Hi @vaishaliarora277, what do you see when you specify the /F option? I recently learned that the tree utility on Windows works different from the unix tree utility: on Windows by default only the directory names are shown, on unix it also shows file names. To get the same behaviour, we need to specify tree /F on Windows. What do you see when you run the below:
C:\Users\me>tree /F ami_test_6
Hi @remkop , thank you very much! Well, I got this (on using the UNIX Tree tool) and yes it is shown differently from the one in Windows.
C:\Users\me>tree /F ami_test_6
Folder PATH listing for volume OS
Volume serial number is D651-7DC0
C:\USERS\ME\AMI_TEST_6
│ commonest.dataTables.html
│ count.dataTables.html
│ entries.dataTables.html
│ eupmc_fulltext_html_urls.txt
│ eupmc_results.json
│ full.dataTables.html
│ New Text Document.txt
│ search.funders.count.xml
│ search.funders.documents.xml
│ search.funders.snippets.xml
│ word.frequencies.count.xml
│ word.frequencies.documents.xml
│ word.frequencies.snippets.xml
│
├───PMC6318360
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6473713
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6518571
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6553602
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6728053
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6742212
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6853075
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6901221
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6905541
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6924880
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6963280
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6964091
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6979359
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7032730
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7053713
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7069648
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7077839
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7077840
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7080275
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7081976
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7095334
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7108131
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7123112
│ │ eupmc_result.json
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7146642
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7154513
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7167542
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7169901
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7175453
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7184488
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7185698
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7188427
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7201909
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7204673
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7215950
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7217455
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7219405
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7219742
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7221944
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7226716
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7235449
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7237041
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7245636
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7250535
│ │ eupmc_result.json
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7253103
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7265527
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7272002
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7276732
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7277812
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7278377
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC7278987
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
└───__cooccurrence
│ allPlots.svg
│
├───funders
│ histogram.csv
│ histogram.svg
│
└───funders-funders
cooccur.csv
Thanks Vaishali, this makes sense:
(HINT - no need to post the whole output, just enough to show the general problems):
Well, I got this (on using the UNIX Tree tool) and yes it is shown
differently from the one in Windows.
C:\Users\me>tree /F ami_test_6
Folder PATH listing for volume OS
Volume serial number is D651-7DC0
C:\USERS\ME\AMI_TEST_6
│ commonest.dataTables.html
│ count.dataTables.html
│ entries.dataTables.html
│ eupmc_fulltext_html_urls.txt
│ eupmc_results.json
│ full.dataTables.html
│ New Text Document.txt
│ search.funders.count.xml
│ search.funders.documents.xml
│ search.funders.snippets.xml
│ word.frequencies.count.xml
│ word.frequencies.documents.xml
│ word.frequencies.snippets.xml
│
├───PMC6318360
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
├───PMC6473713
│ │ eupmc_result.json
│ │ fulltext.pdf
│ │ search.funders.count.xml
│ │ search.funders.snippets.xml
│ │ word.frequencies.count.xml
│ │ word.frequencies.snippets.xml
│ │
│ └───results
│ └───search
│ └───funders
│ empty.xml
│
... (this means I have truncated/snipped the output
I can now see the probable cause:
You have a fulltext.pdf but no fulltext.xml . You need a -x flag
in getpapers.
I need to add a checker to ami that warns of this. It's not wrong
not to have XML files but it means we can't build a data table. The
problem is that some articles only have PDF. What I probably need to
do is refactor the ami search to have better checks. I have started
doing this (and adding Lucene) but at present I have other
priorities.
However I will try to create a validator.
On Sun, Jun 28, 2020 at 9:25 AM VAISHALI ARORA [email protected] wrote:
Hi @remkop https://github.com/remkop , thank you very much! Well, I got this (on using the UNIX Tree tool) and yes it is shown differently from the one in Windows.
C:\Users\me>tree /F ami_test_6 Folder PATH listing for volume OS Volume serial number is D651-7DC0 C:\USERS\ME\AMI_TEST_6 │ commonest.dataTables.html │ count.dataTables.html │ entries.dataTables.html │ eupmc_fulltext_html_urls.txt │ eupmc_results.json │ full.dataTables.html │ New Text Document.txt │ search.funders.count.xml │ search.funders.documents.xml │ search.funders.snippets.xml │ word.frequencies.count.xml │ word.frequencies.documents.xml │ word.frequencies.snippets.xml │ ├───PMC6318360 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC6473713 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC6518571 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC6553602 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC6728053 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC6742212 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC6853075 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC6901221 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC6905541 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC6924880 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC6963280 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC6964091 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC6979359 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7032730 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7053713 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7069648 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7077839 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7077840 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7080275 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7081976 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7095334 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7108131 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7123112 │ │ eupmc_result.json │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7146642 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7154513 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7167542 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7169901 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7175453 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7184488 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7185698 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7188427 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7201909 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7204673 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7215950 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7217455 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7219405 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7219742 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7221944 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7226716 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7235449 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7237041 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7245636 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7250535 │ │ eupmc_result.json │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7253103 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7265527 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7272002 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7276732 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7277812 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7278377 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ ├───PMC7278987 │ │ eupmc_result.json │ │ fulltext.pdf │ │ search.funders.count.xml │ │ search.funders.snippets.xml │ │ word.frequencies.count.xml │ │ word.frequencies.snippets.xml │ │ │ └───results │ └───search │ └───funders │ empty.xml │ └───__cooccurrence │ allPlots.svg │ ├───funders │ histogram.csv │ histogram.svg │ └───funders-funders cooccur.csv
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