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186 lines
27 KiB
186 lines
27 KiB
// |
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// ReaderTests.swift |
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// ReaderTests |
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// |
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// Created by Shadowfacts on 10/29/21. |
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// |
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|
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import XCTest |
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import Reader |
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//import SwiftSoup |
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|
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class ReaderTests: XCTestCase { |
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|
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override func setUpWithError() throws { |
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// Put setup code here. This method is called before the invocation of each test method in the class. |
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} |
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|
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override func tearDownWithError() throws { |
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// Put teardown code here. This method is called after the invocation of each test method in the class. |
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} |
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func testExample() throws { |
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// This is an example of a functional test case. |
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// Use XCTAssert and related functions to verify your tests produce the correct results. |
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} |
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// HTML parsing comparison conducted on iPhone 12 Pro |
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// SwiftSoup: approx 0.53 sec |
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// lol-html: approx 0.003 sec |
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|
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// note: when testing this, make sure to set the Reader scheme to build in release mode for fair comparison |
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// func testSwiftSoupPerformance() { |
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// self.measure { |
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// for i in 0..<100 { |
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// if i % 10 == 0 { |
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// print(i) |
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// } |
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// let doc = try! SwiftSoup.parseBodyFragment(html) |
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// let excerpt = try! doc.text() |
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// } |
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// } |
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// } |
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func testLolHtmlPerformance() { |
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self.measure { |
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for i in 0..<100 { |
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if i % 10 == 0 { |
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print(i) |
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} |
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let excerpt = ExcerptGenerator.excerpt(from: html) |
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} |
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} |
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} |
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let html = """ |
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<div class="page" id="readability-page-1"><div data-reactid="221"><div data-reactid="222"><p><u>On Tuesday, Republicans</u> on the House Committee on Oversight and Reform <a href="https://republicans-oversight.house.gov/wp-content/uploads/2022/01/Letter-Re.-Feb-1-Emails-011122.pdf">released a letter </a>that |
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paints a damning picture of U.S. government officials wrestling with |
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whether the novel coronavirus may have leaked out of a lab they were |
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funding, acknowledging that it may have, and then keeping the discussion |
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from spilling out into public view.</p><p>The letter, signed by James Comer, R-Ky., and Jim Jordan, R-Ohio, was followed by pages of notes on <a href="https://s3.documentcloud.org/documents/20793561/leopold-nih-foia-anthony-fauci-emails.pdf">emails</a> that were first obtained through the Freedom of Information Act by <a href="https://www.buzzfeednews.com/article/nataliebettendorf/fauci-emails-covid-response">BuzzFeed News</a> and the <a href="https://www.washingtonpost.com/politics/interactive/2021/tony-fauci-emails/">Washington Post</a>, |
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but were heavily redacted when published in June 2021. The redacted |
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emails included the agenda for a February 1, 2020, telephone conference |
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between National Institute of Allergy and Infectious Diseases director |
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Anthony Fauci; his then-boss, former National Institutes of Health |
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director Francis Collins; and several of the world’s leading |
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virologists. The communications contained extensive notes summarizing |
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what was said during the call, but their substance was hidden at the |
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time.</p><p>Oversight Committee staff were able to view the full emails |
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“in camera,” which means they could physically look at them and take |
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notes but couldn’t take copies with them. The information released |
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Tuesday for the first time reveals the content of notes taken on the |
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February 1 call.</p></div><a data-reactid="223" href="https://beta.documentcloud.org/documents/21177759-house-oversight-letter-and-email-transcriptions"><img data-reactid="224" 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"></a><div data-reactid="272"><p>On |
|
that call, virologists Michael Farzan and Robert Garry told Fauci and |
|
Collins the virus might have leaked from the Wuhan lab. It might have |
|
been genetically engineered, the transcription of Garry’s notes |
|
suggests, but this now seems unlikely. Another possibility, put forward |
|
by Farzan, was that it could have been evolved in the lab through a |
|
process known as serial passage.</p><p>“The email is out-of-context,” |
|
Garry wrote Wednesday in an email to The Intercept. “This was one email |
|
among many I was sharing with my colleagues.”</p></div><div data-reactid="283"><p>The |
|
two methods represent two different ideas behind the so-called lab-leak |
|
hypothesis. The one that gained notoriety early in the pandemic is |
|
genetic engineering, where scientists insert and delete nucleotides in |
|
the virus’s genetic code, in this case viral RNA, to turn it into |
|
something new. This version forms the basis of accusations that the |
|
virus was intentionally created as a bioweapon — which practically every |
|
credible scientist has dismissed as an illogical conspiracy, but was |
|
quickly embraced by former President Donald Trump and much of the |
|
American right wing, souring scientists, liberals, and the mainstream on |
|
the possibility of lab origin. The less lurid but seemingly more |
|
plausible version is the idea of evolution through serial passage, in |
|
which scientists allow a virus to jump between host species or cell |
|
cultures, spurring new mutations.</p><p>The day before the call, Scripps |
|
Research infectious disease expert Kristian Andersen had warned Fauci |
|
that the virus may have been engineered in a lab, noting that he and |
|
several other high-profile scientists “all find the genome inconsistent |
|
with expectations from evolutionary theory.” The scientists agreed to |
|
have a conference call the next day. “It was a very productive |
|
back-and-forth conversation where some on the call felt it could |
|
possibly be an engineered virus,” Fauci told Alison Young, <a href="https://www.usatoday.com/story/opinion/2021/06/17/covid-19-fauci-lab-leaks-wuhan-china-origins/7737494002/">writing for USA Today</a>, in June 2021.</p><p>Not long after the call, Andersen was the lead author on a <a href="https://www.nature.com/articles/s41591-020-0820-9">paper in Nature Medicine</a> |
|
titled “The Proximal Origin of SARS-CoV-2.” The paper proposed “two |
|
scenarios that can plausibly explain the origin of SARS-CoV-2: (i) |
|
natural selection in an animal host before zoonotic transfer; and (ii) |
|
natural selection in humans following zoonotic transfer.” For the |
|
scientists and pundits who sought to discount the emerging lab-leak |
|
hypothesis, it offered the authoritative proof they needed. The paper |
|
has since been accessed more than 5.6 million times, with over 2,000 |
|
citations.</p><p>The authors acknowledged a third scenario, “selection |
|
during passage,” but they discussed it briefly and presented it as by |
|
far the least plausible. The newly released notes from the call, |
|
however, suggest that the scientists Fauci consulted initially |
|
considered that possibility to be much more serious than the paper let |
|
on.</p></div><div data-reactid="285"><p>On February 2, Jeremy Farrar, an |
|
infectious disease expert and the director of Wellcome, sent around |
|
notes, including to Fauci and Collins, summarizing what some of the |
|
scientists had said on the call. Farzan, a Scripps professor who studied |
|
the spike protein on the 2003 SARS virus, “is bothered by the furin |
|
site and has a hard time explain that as an event outside the lab |
|
(though, there are possible ways in nature, but highly unlikely),” |
|
Farrar’s note reads, referring to a spike protein feature that aids |
|
interaction with furin, a common enzyme in human lung cells. Farzan |
|
didn’t think the site was the product of “directed engineering,” but |
|
found that the changes would be “highly compatible with the idea of |
|
continued passage of the virus in tissue culture.”</p><p>According to |
|
the transcribed notes, Garry, a professor at the Tulane University |
|
School of Medicine, said on the call that he had aligned the SARS-CoV-2 |
|
genome with that of RaTG13, a 96-percent similar virus isolated from |
|
bats at the Wuhan Institute of Virology that was long regarded as the |
|
new virus’s closest known relative — though a closer one <a href="https://www.nature.com/articles/d41586-021-02596-2">has since been identified</a>. |
|
Garry found that the spike proteins of RaTG13 and SARS-CoV-2, which |
|
makes the latter so infectious, were nearly identical. The key |
|
distinction was in the ability of the new virus’s spike protein to |
|
interact with furin, which Garry found too perfect to make natural |
|
sense. “I just can’t figure out how this gets accomplished in nature,” |
|
he said.</p><p>“My initial impression and that of others about the |
|
[furin cleavage site] was wrong. I changed my mind with new |
|
information/new data,” Garry wrote to The Intercept. “That’s how science |
|
works. No one was trying to mislead the public. What was in the |
|
Proximal Origins paper was our best analysis — it’s held up extremely |
|
well.”</p></div><div data-reactid="287"><p>As they discussed what to |
|
present to the public, the scientists determined that questions of |
|
potential lab origin might prove more trouble than they’re worth. “Given |
|
the evidence presented and the discussions around it, I would conclude |
|
that a follow-up discussion on the possible origin of 2019-nCoV would be |
|
of much interest,” wrote Ron Fouchier, a virologist at the Erasmus MC |
|
Center for Viroscience in the Netherlands, on February 2. Years earlier, |
|
Fouchier’s gain-of-function research had brought the discipline under |
|
fire for <a href="https://www.science.org/content/article/exclusive-controversial-experiments-make-bird-flu-more-risky-poised-resume">a 2011 experiment</a> |
|
in which he infected ferrets in adjacent cages with the avian influenza |
|
virus, allowing it to become airborne and infect mammals. “However, |
|
further debate about such accusations would unnecessarily distract top |
|
researchers from their active duties and do unnecessary harm to science |
|
in general and science in China in particular,” Fouchier wrote.</p><p>Farzan, Fauci, and Fouchier did not immediately respond to The Intercept’s requests for comment.</p><p>Several |
|
of the scientists on the email chain ended up co-authoring the Nature |
|
Medicine paper with Andersen and Garry. In a February 4 email, which |
|
House Republicans presented as a response to a first copy of the draft, |
|
Fauci wrote: “?? Serial passage in ACE2-transgenic mice.”</p><p>The |
|
early draft has not been made public, so we don’t know what, exactly, |
|
sparked Fauci’s reaction. But his words, which refer to the process of |
|
passaging a virus in “humanized” laboratory mice — or mice that have |
|
been genetically modified to express receptors for human ACE2, an enzyme |
|
that occurs in the lungs — do not appear in the published paper.</p><p>“Neither |
|
Drs. Fauci or Collins edited our Proximal Origins paper in any way. The |
|
major feedback we got from the Feb 1 teleconference was: 1. Don’t try |
|
to write a paper at all — it’s unnecessary or 2. If you do write it |
|
don’t mention a lab origin as that will just add fuel to the |
|
conspiracists,” Garry wrote on Wednesday.</p><p>When the paper appeared |
|
in Nature Medicine on March 17, 2020, it noted near the end that in |
|
order for the novel coronavirus to have emerged in a lab via serial |
|
passage, scientists would have to conduct those experiments using a |
|
relative with very high genetic similarity, but there was no evidence |
|
that such experiments had been done. The authors added, “Subsequent |
|
generation of a polybasic cleavage site,” which lets the virus process |
|
furin, “would have then required repeated passage in cell culture or |
|
animals with ACE2 receptors similar to those of humans, but such work |
|
has also not previously been described.”</p><p>Though the paper was |
|
publicly embraced by the scientific community and the mainstream media, |
|
Collins worried that its impact wasn’t sufficient. “Wondering if there |
|
is something NIH can do to help put down this very destructive |
|
conspiracy,” Collins wrote on April 16, 2020, in reference to a Fox News |
|
segment on the lab-leak theory. “I hoped the Nature Medicine article on |
|
the genomic sequence of SARS-CoV-2 would settle this. But probably |
|
didn’t get much visibility. Anything more we can do?”</p><p>“I would not do anything about this right now,” Fauci replied. “It is a shiny object that will go away in times.”</p></div></div></div> |
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""" |
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}
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