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WGSExtract / WGSExtract.github.io

WGS Extract WWW home
https://WGSExtract.github.io/
GNU General Public License v3.0
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unable to extract the zip file #4

Closed jadenfox9 closed 3 years ago

jadenfox9 commented 3 years ago

The zip file (WGSExtractBetav2b_full.zip) downloads fine from google drive, https://drive.google.com/u/0/uc?id=1F_vclX1FPibnBdSyQ25OXPHzJUl6dwcJ&export=download has 4.82gb

but it encounters errors on extraction using a variety of different apps (Mac 10.15.7)

RandyHarr commented 3 years ago

Jaden, thank you for finding us here to open an inquiry. There is no question the MacOS platform has been a struggle for tools like ours over the last 6 months as Apple tightens security around non-App store released products on their platform. Killing the researcher environment that Unix and the Mac in Bioinformatics has long enjoyed. Zip files with binary blobs, compiled Applescripts, use of BASH scripting language and such are all being constantly blocked in new and different ways.

Could you provide any more details as to your issue? In most cases (on Catalina especially), MacOS will automatically unzip the files and scan them. Deciding whether to jail the directory depending on what it finds. So hopefully, that is not the issue. Next, even though it puts the folder in Downloads, it cannot be executed from there. As described in the manual, it cannot be in Downloads or Documents. Often best to simply move it to your home directory itself. They have now separated the file system (hidden to you for the most part) between the system area and user space. And disallow system space modifications -- only allowing their OS there to ease updates and improve security (in their view). Make sure to do the Mac overlay onto your main Zip content. You may have to allow Security & Privacy (Privacy) tab access to the Start_MacOSX, Install_MacOSX and Uninstall_MacOSX scripts after moving all the files to your home folder; say like ~/WGSEv2. (Use Apple-Key Shift H in the GUI to get to your home; something they hide in Finder in general.) You set the permission by navigating to the files under the Privacy Tabs Full Access option. Holding the CTRL key while clicking the app to open will given you the option to bypass the security setting.

Often, even after allowing it though, Apple still has the files in Jail (known by seeing an error with a super long, cryptic path with the name "Translocation" in the middle.) Your best bet is to open a Terminal shell, as described in the manual, cd'ing to the install directory, and starting the app's BASH shell scripts directly. Like ./Install_MacOSX.sh.

I Just went through the process from download to install on a clean MacOSX Catalina installation in this way.

I never noticed before, If you open a compiled Applescript "Package Contents" (right click) and navigate down Contents/MacOS then you can click on the applet there with no issue and it runs. If you go down Contents/Resources/Scripts there is a main.scpt file. If you copy that to the top level, rename to the Applet name (say Install_MacOSX.scpt) and then compile it with the Applescript compiler (see manual), you then have a working single-click icon. Our system is Python code and binary blobs of Bioinformatic reference files. All executables come via the Install script calling MacPorts and similar.

jadenfox9 commented 3 years ago

Hi Randy,

Not much else to say, it acted as if the file is corrupted. Clicking on the zip file (still in my downloads folder) to uncompress gives me this error:

Screen Shot 2021-02-24 at 9 07 21 AM

So I tried to uncompress the same file with another unzipper and got a slightly different error:

Screen Shot 2021-02-24 at 9 12 22 AM

This is NOT acting like a Security & Privacy issue, those I would recognize and are fairly easy to resolve. This is just acting like a corrupted file. Yet, it looks like it has a lot of content (4.82gb)

Screen Shot 2021-02-24 at 9 15 32 AM
RandyHarr commented 3 years ago

Odd. My test earlier was by clicking on the link. Although more so on the Win10 systems, the Google SPAM system can be an issue for some that have download managers. They get the HTML code to the link instead of the download file itself. We just recently moved the release to Google Drive but it appears this may be a mistake. Have found no way around their SPAM system for >100MB files even though we pay for the service. How did you do the download? Via Safari?

jadenfox9 commented 3 years ago

I downloaded it in Chrome (up-to-date) but let me try Safari...

RandyHarr commented 3 years ago

That would be odd that Google Chrome on a Mac cannot download from Google Drive ...

jadenfox9 commented 3 years ago

I just tried with Firefox, that also failed...

But surprise, surprise... SAFARI WORKED! :)

I have the files now!

Screen Shot 2021-02-24 at 10 18 52 PM
RandyHarr commented 3 years ago

Glad to hear. I added a note to the home page that should appear shortly.

Let me know how it goes so we can close the thread out if successful. Also, if you have ideas for improvement in document, release notes and such, let us know that as well. A major rewrite is due out soon -- in Alpha testing now.

RandyHarr commented 3 years ago

Since you opened a new issue in this same but continuing topic, I am closing this one.