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petermr / openVirus

aggregation of scholarly publications and extracted knowledge on viruses and epidemics.
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Fix empty <title> in AMI-Search dataTables #2

Open petermr opened 4 years ago

petermr commented 4 years ago

ami-search creates an empty <title/> in fullDatatables.html element which prevents display.

vaishaliarora277 commented 4 years ago

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?

petermr commented 4 years ago

This is a bug. Can you open the file in a text editor (not word). If there is an element delete it and redisplay. I will try to fix in the next day.</p> <p>On Tue, Jun 23, 2020 at 6:05 PM VAISHALI ARORA <a href="mailto:notifications@github.com">notifications@github.com</a> wrote:</p> <blockquote> <p>Trying to use ami to test the dictionary funders, the commands given: ami -p ami_test_6 search --dictionary funders</p> <p>After running the Command,</p> <h1>Generic values (AMISearchTool)</h1> <p>-v to see generic values</p> <h1>Specific values (AMISearchTool)</h1> <p>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</p> <p>it created empty file <em>full.datatables.html</em> in the folder <em>ami_test_6</em> What else can be done?</p> <p>— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <a href="https://github.com/petermr/openVirus/issues/2#issuecomment-648293289">https://github.com/petermr/openVirus/issues/2#issuecomment-648293289</a>, or unsubscribe <a href="https://github.com/notifications/unsubscribe-auth/AAFTCS2ECPGGPKQLUNVUUY3RYDOETANCNFSM4LHREOWA">https://github.com/notifications/unsubscribe-auth/AAFTCS2ECPGGPKQLUNVUUY3RYDOETANCNFSM4LHREOWA</a> .</p> </blockquote> <p>-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/vaishaliarora277"><img src="https://avatars.githubusercontent.com/u/66777688?v=4" />vaishaliarora277</a> commented <strong> 4 years ago</strong> </div> <div class="markdown-body"> <p>This is all it displayed, do not contain the element <title/></p> <pre><code><?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> </code></pre> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/petermr"><img src="https://avatars.githubusercontent.com/u/733515?v=4" />petermr</a> commented <strong> 4 years ago</strong> </div> <div class="markdown-body"> <p>OK - this is either a bug or you don't have any hits!</p> <p>Can you install <code>tree</code> (it's a UNIX tool that lists directories to the console)</p> <p>Then we can see what's in ami_test_6</p> <p>I'm looking at <code>miniproject</code> which contains <code>epidemic50noCov</code></p> <p>and I issue</p> <pre><code> tree -h miniproject | more </code></pre> <p>which shows</p> <pre><code> 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</code></pre> <p>On Wed, Jun 24, 2020 at 5:26 PM VAISHALI ARORA <a href="mailto:notifications@github.com">notifications@github.com</a> wrote:</p> <blockquote> <p>This is all it displayed, do not contain the element <title/></p> <p><?xml version="1.0" encoding="UTF-8"?></p> <html xmlns="http://www.w3.org/1999/xhtml"> <head charset="UTF-8"> <title>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

kareenasingh commented 4 years ago

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 Capture new

How can i put the extracted information into my work?

petermr commented 4 years ago

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 notifications@github.com 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

vaishaliarora277 commented 4 years ago

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
petermr commented 4 years ago

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

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.

remkop commented 4 years ago

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
vaishaliarora277 commented 4 years ago

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
petermr commented 4 years ago

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 notifications@github.com 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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