text:
Config directories don't mount inside VM

Hello,
I'm trying to configure wifibox as AP. I added passthru device and started wifibox:
service wireguard start
wifibox console:
localhost:~# ifconfig
localhost:~#

localhost:~# mount
/dev/root on / type squashfs (ro,relatime,errors=continue)
devtmpfs on /dev type devtmpfs (rw,nosuid,noexec,relatime,size=10240k,nr_inodes=13653,mode=755)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
tmpfs on /run type tmpfs (rw,nosuid,nodev,size=22496k,nr_inodes=819200,mode=755)
mqueue on /dev/mqueue type mqueue (rw,nosuid,nodev,noexec,relatime)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)
shm on /dev/shm type tmpfs (rw,nosuid,nodev,noexec,relatime)
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)
debugfs on /sys/kernel/debug type debugfs (rw,nosuid,nodev,noexec,relatime)
tmpfs on /tmp type tmpfs (rw,relatime,size=128k)

localhost:~# cat /etc/fstab
tmpfs      /tmp       tmpfs    size=128K                                     0 0
config     /media/etc 9p       trans=virtio,ro,noatime,nodiratime,norelatime 0 0
var        /var       9p       trans=virtio,rw                               0 0
app_config /etc/hostapd 9p trans=virtio,rw 0 0

localhost:~# mount app_config
mount: permission denied (are you root?)
localhost:~# id
uid=0(root) gid=0(root) groups=0(root),1(bin),2(daemon),3(sys),4(adm),6(disk),10(wheel),11(floppy),20(dialout),26(tape),27(video)

As you see, VM doesn't mount config directories. And as a result, doesn't bringing up network interfaces.
Debug logs:
2023-02-22T11:38:23+0200 DEBUG Program started as /usr/local/sbin/wifibox, with arguments: start
2023-02-22T11:38:23+0200 INFO  Begin: wifibox start
2023-02-22T11:38:23+0200 DEBUG start=GN
2023-02-22T11:38:23+0200 INFO  Creating bridge interface: wifibox0
2023-02-22T11:38:23+0200 DEBUG [ifconfig] wifibox0
2023-02-22T11:38:23+0200 INFO  Linking tap interface to wifibox0: tap0
2023-02-22T11:38:23+0200 INFO  vmm.ko is expected at path: /boot/kernel/vmm.ko
2023-02-22T11:38:23+0200 INFO  vmm.ko is found at path: /boot/kernel/vmm.ko
2023-02-22T11:38:23+0200 DEBUG assert loaded: kmod=vmm, kmod_file=/boot/kernel/vmm.ko
2023-02-22T11:38:24+0200 DEBUG assert hardware support present: iommu=1, amdvi=0
2023-02-22T11:38:24+0200 DEBUG Backends reported by bhyve:
2023-02-22T11:38:24+0200 DEBUG [bhyve] ahci
2023-02-22T11:38:24+0200 DEBUG [bhyve] ahci-hd
2023-02-22T11:38:24+0200 DEBUG [bhyve] ahci-cd
2023-02-22T11:38:24+0200 DEBUG [bhyve] e1000
2023-02-22T11:38:24+0200 DEBUG [bhyve] dummy
2023-02-22T11:38:24+0200 DEBUG [bhyve] hda
2023-02-22T11:38:24+0200 DEBUG [bhyve] fbuf
2023-02-22T11:38:24+0200 DEBUG [bhyve] amd_hostbridge
2023-02-22T11:38:24+0200 DEBUG [bhyve] hostbridge
2023-02-22T11:38:24+0200 DEBUG [bhyve] lpc
2023-02-22T11:38:24+0200 DEBUG [bhyve] nvme
2023-02-22T11:38:24+0200 DEBUG [bhyve] passthru
2023-02-22T11:38:24+0200 DEBUG [bhyve] virtio-9p
2023-02-22T11:38:24+0200 DEBUG [bhyve] virtio-blk
2023-02-22T11:38:24+0200 DEBUG [bhyve] virtio-console
2023-02-22T11:38:24+0200 DEBUG [bhyve] virtio-input
2023-02-22T11:38:24+0200 DEBUG [bhyve] virtio-net
2023-02-22T11:38:24+0200 DEBUG [bhyve] virtio-rnd
2023-02-22T11:38:24+0200 DEBUG [bhyve] virtio-scsi
2023-02-22T11:38:24+0200 DEBUG [bhyve] uart
2023-02-22T11:38:24+0200 DEBUG [bhyve] xhci
2023-02-22T11:38:24+0200 INFO  Bringing up null-modem devices for console connection
2023-02-22T11:38:24+0200 DEBUG assert loaded: kmod=nmdm, kmod_file=nmdm
2023-02-22T11:38:24+0200 INFO  Null-modem devices are available
2023-02-22T11:38:24+0200 INFO  Waiting for bhyve to start up
2023-02-22T11:38:24+0200 DEBUG Program started as /usr/local/sbin/wifibox, with arguments: _manage_vm
2023-02-22T11:38:24+0200 DEBUG assert daemonized: parent=daemon
2023-02-22T11:38:24+0200 INFO  VM manager launched
2023-02-22T11:38:24+0200 INFO  Gathering necessary configuration files for launching the guest
2023-02-22T11:38:24+0200 INFO  Pulling bhyve options from configuration file
2023-02-22T11:38:24+0200 DEBUG cpus=1, memory=128M, passthru=0/20/3, console=yes
2023-02-22T11:38:24+0200 INFO  Guest console is configured to use
2023-02-22T11:38:24+0200 INFO  Passthru device is configured: 0/20/3
2023-02-22T11:38:24+0200 INFO  PPT driver is configured for pci0:20:3 device
2023-02-22T11:38:24+0200 INFO  tap interface is configured: tap0
2023-02-22T11:38:24+0200 INFO  Launching guest wifibox from /usr/local/share/wifibox with grub-bhyve
2023-02-22T11:38:24+0200 INFO  Application config is found at /usr/local/etc/wifibox/hostapd
2023-02-22T11:38:24+0200 INFO  Application config will be mounted writeable
2023-02-22T11:38:24+0200 DEBUG Devices: virtio-blk,/usr/local/share/wifibox/disk.img virtio-9p,config=/usr/local/etc/wifibox/appliance,ro virtio-9p,var=/var/run/wifibox/appliance virtio-9p,app_config=/usr/local/etc/wifibox/hostapd
2023-02-22T11:38:24+0200 DEBUG Arguments:  -S -M 128M -r host -c /dev/nmdm-wifibox.1A -d /usr/local/share/wifibox wifibox
2023-02-22T11:38:24+0200 INFO  Launching guest wifibox from /usr/local/share/wifibox with bhyve
2023-02-22T11:38:24+0200 DEBUG Arguments:  -c 1 -m 128M -AHP -u -S -l com1,/dev/nmdm-wifibox.1A -s 0,hostbridge -s 31,lpc -s 4:0,virtio-blk,/usr/local/share/wifibox/disk.img -s 4:1,virtio-9p,config=/usr/local/etc/wifibox/appliance,ro -s 4:2,virtio-9p,var=/var/run/wifibox/appliance -s 4:3,virtio-9p,app_config=/usr/local/etc/wifibox/hostapd -s 5:0,e1000,tap0 -s 6:0,passthru,0/20/3 wifibox
2023-02-22T11:38:24+0200 DEBUG [bhyve] wrmsr to register 0x140(0) on vcpu 0
2023-02-22T11:38:24+0200 DEBUG [bhyve] rdmsr to register 0x64d on vcpu 0
2023-02-22T11:38:24+0200 DEBUG [bhyve] rdmsr to register 0x64e on vcpu 0
2023-02-22T11:38:24+0200 DEBUG [bhyve] rdmsr to register 0x34 on vcpu 0
2023-02-22T11:38:25+0200 INFO  Guest wifibox has started up
2023-02-22T11:38:25+0200 INFO  Guest is managed by PID 7301
2023-02-22T11:38:25+0200 INFO  Bringing up Unix Domain Socket pass-through
2023-02-22T11:38:25+0200 INFO  Found guest IP address: 10.0.0.2
2023-02-22T11:38:25+0200 INFO  Configured sockets: [path=/var/run/hostapd/wlan0,user=root,group=0,mode=770,port=1200]
2023-02-22T11:38:25+0200 INFO  Hooking up 10.0.0.2:1200 as /var/run/hostapd/wlan0 (root:0@770)
2023-02-22T11:38:25+0200 INFO  End: wifibox start
2023-02-22T11:38:28+0200 DEBUG Program started as /usr/local/sbin/wifibox, with arguments: console
2023-02-22T11:38:28+0200 INFO  Begin: wifibox console

Don't have any idea where should I dig to solve this problem. Could you please advise me?
Also please add sample configuration about creating AP. man 8 wifibox has nice samples but nothing regarding hostapd config or setup AP in general. It would be great to have hostapd/hostapd.conf with commented sample configuration. Users could just uncomment sample config and edit it according to their needs instead of reading man hostapd.
Thank you!

Additional info:
OS: FreeBSD 13.1-STABLE
wifibox-core-0.11.0:
Options        :
	BHYVE_PLUS     : off
	RECOVER_NONE   : off
	RECOVER_RESTART_VMM: on
	RECOVER_SUSPEND_GUEST: off

wifibox-alpine-20230213:
Options        :
	APP_HOSTAPD    : on
	APP_WPA_SUPPLICANT: off
	COMP_GZIP      : off
	COMP_LZ4       : off
	COMP_LZO       : off
	COMP_XZ        : off
	COMP_ZSTD      : on
	FW_ATH10K      : off
	FW_ATH11K      : off
	FW_ATMEL       : off
	FW_B43         : off
	FW_B43LEGACY   : off
	FW_BRCM        : off
	FW_IPW2100     : off
	FW_IPW2200     : off
	FW_IWL3945     : off
	FW_IWL4965     : off
	FW_IWLWIFI     : on
	FW_MARVELL     : off
	FW_MEDIATEK    : off
	FW_RT61        : off
	FW_RTLWIFI     : off
	FW_RTW88       : off
	FW_RTW89       : off
	FW_TI          : off
	UDS_PASSTHRU   : on
	XX_DRIVER_WL   : off
	XX_FORWARDING  : off
	XX_MDNS        : off
	XX_TCPDUMP     : off

Intel(R) Wireless-AC 9560 160MHz, REV=0x318

Hi @iron-udjin, thanks for the report!
I could not yet reproduce this on 12.4-RELEASE but I have not yet given it up...  Based on the log, everything goes as expected.  Could you please include the VM's logs as well?  You can find this at /var/run/wifibox/appliance/log/, these are the dmesg and messages files.
Regarding the AP sample configuration, I am not sure this is the responsibility of Wifibox.  Similarly to wpa_supplicant.conf(5), the hostapd.conf(5) might be different by each use case, there is no generic recipe for either of them.  What Wifibox currently does is that it points to the authoritative sources: in the "Configuration" section of wifibox(8) it said that "check the sample configuration files provided in the  %%ETCDIR%%/wifibox directory and follow the instructions to create a working configuration".  There you shall find a hostapd/hostapd.conf.sample file, which will then point to /usr/share/examples/hostapd/hostapd.conf on your local system, the file you were asking for.  I admit the level of indirection may be too deep here, but it is flexible.
Of course, I can include here the hostapd.conf(5) that I used for testing if you wish, but that is not so generic.

Could you please include the VM's logs as well? You can find this at /var/run/wifibox/appliance/log/

This directory is empty:
IRON ~ # wifibox status
wifibox is run by PID 54913.
IRON ~ # ls -la /var/run/wifibox/appliance/log
IRON ~ #

Of course, I can include here the hostapd.conf(5) that I used for testing if you wish, but that is not so generic.

Generic config could be something like https://wiki.gentoo.org/wiki/Hostapd:
# the interface used by the AP
interface=wlan0
# "g" simply means 2.4GHz band
hw_mode=g
# the channel to use
channel=10
# limit the frequencies used to those allowed in the country
ieee80211d=1
# the country code
country_code=FR
# 802.11n support
ieee80211n=1
# QoS support, also required for full speed on 802.11n/ac/ax
wmm_enabled=1
# the name of the AP
ssid=somename
# 1=wpa, 2=wep, 3=both
auth_algs=1
# WPA2 only
wpa=2
wpa_key_mgmt=WPA-PSK
rsn_pairwise=CCMP
wpa_passphrase=somepassword

Looks like the VirtFS/9P mounts do not work at all, although the messages in the log do not indicate any related problems.

Is not there anything unusual present the dmesg(8) output of the host itself?  Could you please try to grab the VM dmesg output from the console for me?  I am mostly interested in the potential error messages, i.e. missed mounts and such.

dmesg from host system: https://pastebin.com/QRkCkG5A
dmesg from VM: https://pastebin.com/87AmxRrE

Thanks!  No indication of any mount errors in either of the logs, though -- that is even stranger.  I should really try to reproduce this locally.  By the way, does wpa_supplicant work for you on the same configuration?

By the way, does wpa_supplicant work for you on the same configuration?

No, it doesn't work. The same problem with config direstories mount.

Where is VirtFS functionality is located? Possibly there is some module missing or something like that... Here is my kernel config: https://pastebin.com/A4B401Wy

Here is my /etc/src.conf: https://pastebin.com/E7senNkT

If I recall correctly, the implementation of VirtFS/9p does not require any special support from the side of the kernel and the base system.  It is a shipped as a library (lib9p.so) which is then linked to the bhyve binary.  If you can see virtio-9p in the output of bhyve -s help you shall be set.  That is confirmed in your case, because Wifibox checks this on startup so it would refuse to work anyway, but I could see that in the output of the debug log too.
However, something else might be broken that affects the lib9p.so library and causes this kind of trouble.

I'm afraid it could be bug in bhyve which is in -STABLE. How can I debug it? I guess I need to send bug report before -STABLE become 13.2-RELEASE.

Unfortunately I do not have any direct experience with tracking down issues like that one.  It might be a good idea to report this problem in the FreeBSD Project right away (given the timing) where developers will tell you what to do or even quickly realize what to revert.

Ok, thank you. Let's close this issue as the problem is not within wifibox itself.

What about posting the link to the upstream bug report and leave it open until resolved?  This may help others to learn about the problem.  We have done something similar in the past.

Ok, let's leave it as is.

To track issue with bhyve: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=269827

Hello. Here I'm running FreeBSD-13.2-BETA and virtio-9p works correctly adding : *-s 11,virtio-9p,sharename=/ *  between the bhyve parameters.

I tried to reproduce the problem with 13.2-STABLE, version n254667-bc68c55166ad (snapshot from 2023-02-23), I could not.  This version might not be recent enough or this issue has something to do with your custom configuration.

I tried to rebuild kernel with GENERIC config or even deploy kernel image from here - still have no luck. It seems the problem somewhere inside bhyve. Trying to figure out where exactly.

Here is how you can investigate the behavior of the virtio-9p backend in bhyve.  First create and install a version of the bhyve binary that includes debug symbols and not optimized.
# cd /usr/src/usr.sbin/bhyve
# make DEBUG_FLAGS="-O0 -g"
# make install

In result, debug symbols for bhyve will be installed as /usr/lib/debug/sbin/bhyve.debug, along with an updated version of /usr/sbin/bhyve (this is for 12.4-RELEASE but it should be the same on other major versions):
# file /usr/lib/debug/usr/sbin/bhyve.debug
/usr/lib/debug/usr/sbin/bhyve.debug: ELF 64-bit LSB executable, x86-64, version 1 (FreeBSD), no program header, for FreeBSD 12.4, FreeBSD-style, with debug_info, not stripped

Then create a dummy bhyve VM, which will be called test here, that mimics the execution of wifibox.  Start with preparing the launch by grub-bhyve:
# /usr/local/sbin/grub-bhyve -S -M 64M -r host -d /usr/local/share/wifibox test

And then it becomes possible to start bhyve through lldb, the system debugger:
# lldb -- /usr/sbin/bhyve -c 1 -m 64M -AHP -u -S -s 0,hostbridge -s 31,lpc -s 4:0,virtio-blk,/usr/local/share/wifibox/disk.img -s 4:1,virtio-9p,config=/usr/local/etc/wifibox/appliance,ro -s 4:2,virtio-9p,var=/var/run/wifibox/appliance -s 4:3,virtio-9p,app_config=/usr/local/etc/wifibox/wpa_supplicant test
(lldb) target create "/usr/sbin/bhyve"
Current executable set to '/usr/sbin/bhyve' (x86_64).
(lldb) settings set -- target.run-args  "-c" "1" "-m" "64M" "-AHP" "-u" "-S" "-s" "0,hostbridge" "-s" "31,lpc" "-s" "4:0,virtio-blk,/usr/local/share/wifibox/disk.img" "-s" "4:1,virtio-9p,config=/usr/local/etc/wifibox/appliance,ro" "-s" "4:2,virtio-9p,var=/var/run/wifibox/appliance" "-s" "4:3,virtio-9p,app_config=/usr/local/etc/wifibox/wpa_supplicant" "test"

Use lldb commands to check how the arguments of the pci_vt9p_init function are flowing through.  This C function is responsible for making the 9P protocol work.
(lldb) b pci_vt9p_init
Breakpoint 1: where = bhyve`pci_vt9p_init + 35 at pci_virtio_9p.c:242:11, address = 0x000000000023e663

Once the breakpoint is set, start the application, which should immediately be stopped in response to that:
(lldb) r
Process 19852 launched: '/usr/sbin/bhyve' (x86_64)
Process 19852 stopped
* thread #1, name = 'bhyve', stop reason = breakpoint 1.1
    frame #0: 0x000000000023e663 bhyve`pci_vt9p_init(ctx=0x000000080029c180, pi=0x0000000800b2c500, opts="config=/usr/local/etc/wifibox/appliance,ro") at pci_virtio_9p.c:242:11
   239           bool ro = false;
   240           cap_rights_t rootcap;
   241
-> 242           if (opts == NULL) {
   243                   printf("virtio-9p: share name and path required\n");
   244                   return (1);
   245           }

The execution of the function can be stepped by the s (step) command and the state of the variables in scope can be investigated by the var command:
(lldb) var
(vmctx *) ctx = 0x000000080029c180
(pci_devinst *) pi = 0x0000000800b2c500
(char *) opts = 0x000000080029c10e "config=/usr/local/etc/wifibox/appliance,ro"
(cap_rights_t) rootcap = {
  cr_rights = ([0] = 140737488347616, [1] = 0)
}
(bool) ro = false
(char *) rootpath = 0x0000000000000000
(char *) sharename = 0x0000000000000000
(char *) opt = <variable not available>

(int) rootfd = <variable not available>

(pci_vt9p_softc *) sc = <variable not available>

That way, for example, it can be tracked how the sharename variable gets its value:
[..]
(lldb) s
Process 19852 stopped
* thread #1, name = 'bhyve', stop reason = step in
    frame #0: 0x000000000023e6db bhyve`pci_vt9p_init(ctx=<unavailable>, pi=0x0000000800b2c500, opts="ro") at pci_virtio_9p.c:255:15
   252                           }
   253
   254                           sharename = strsep(&opt, "=");
-> 255                           rootpath = opt;
   256                           continue;
   257                   }
   258
(lldb) p sharename
(char *) $0 = 0x000000080029c10e "config"

Ideally, this should give us some ideas about why the things are not going right.

Can you try it with freebsd 13.1-RELEASE ? it always worked great 4 me. Now
Im using 13.2-BETA and it still works.
Il dom 26 feb 2023, 23:34 PÁLI Gábor János @.***> ha
scritto:

Here is how you can investigate the behavior of the virtio-9p backend in
bhyve. First create and install a version of the bhyve binary that
includes debug symbols and not optimized.
cd /usr/src/usr.sbin/bhyve
make DEBUG_FLAGS="-O0 -g"
make install
In result, debug symbols for bhyve will be installed as
/usr/lib/debug/sbin/bhyve.debug, along with an updated version of
/usr/sbin/bhyve (this is for 12.4-RELEASE but it should be the same on
other major versions):
file /usr/lib/debug/usr/sbin/bhyve.debug/usr/lib/debug/usr/sbin/bhyve.debug: ELF 64-bit LSB executable, x86-64, version 1 (FreeBSD), no program header, for FreeBSD 12.4, FreeBSD-style, with debug_info, not stripped
Then create a dummy bhyve VM, which will be called test here, that mimics
the execution of wifibox. Start with preparing the launch by grub-bhyve:
/usr/local/sbin/grub-bhyve -S -M 64M -r host -d /usr/local/share/wifibox test
And then it becomes possible to start bhyve through lldb, the system
debugger:
lldb -- /usr/sbin/bhyve -c 1 -m 64M -AHP -u -S -s 0,hostbridge -s 31,lpc -s 4:0,virtio-blk,/usr/local/share/wifibox/disk.img -s 4:1,virtio-9p,config=/usr/local/etc/wifibox/appliance,ro -s 4:2,virtio-9p,var=/var/run/wifibox/appliance -s 4:3,virtio-9p,app_config=/usr/local/etc/wifibox/wpa_supplicant test(lldb) target create "/usr/sbin/bhyve"Current executable set to '/usr/sbin/bhyve' (x86_64).(lldb) settings set -- target.run-args  "-c" "1" "-m" "64M" "-AHP" "-u" "-S" "-s" "0,hostbridge" "-s" "31,lpc" "-s" "4:0,virtio-blk,/usr/local/share/wifibox/disk.img" "-s" "4:1,virtio-9p,config=/usr/local/etc/wifibox/appliance,ro" "-s" "4:2,virtio-9p,var=/var/run/wifibox/appliance" "-s" "4:3,virtio-9p,app_config=/usr/local/etc/wifibox/wpa_supplicant" "test"
Use lldb commands to check how the arguments of the pci_vt9p_init
https://cgit.freebsd.org/src/tree/usr.sbin/bhyve/pci_virtio_9p.c?h=stable/13#n251
function are flowing through. This C function is responsible for making the
9P protocol work.
(lldb) b pci_vt9p_init
Breakpoint 1: where = bhyve`pci_vt9p_init + 35 at pci_virtio_9p.c:242:11, address = 0x000000000023e663
Once the breakpoint is set, start the application, which should
immediately be stopped in response to that:
(lldb) r
Process 19852 launched: '/usr/sbin/bhyve' (x86_64)
Process 19852 stopped

thread #1, name = 'bhyve', stop reason = breakpoint 1.1
frame #0: 0x000000000023e663 bhyve`pci_vt9p_init(ctx=0x000000080029c180, pi=0x0000000800b2c500, opts="config=/usr/local/etc/wifibox/appliance,ro") at pci_virtio_9p.c:242:11
239           bool ro = false;
240           cap_rights_t rootcap;
241
-> 242           if (opts == NULL) {
243                   printf("virtio-9p: share name and path required\n");
244                   return (1);
245           }

The execution of the function can be stepped by the s (step) command and
the state of the variables in scope can be investigated by the var
command:
(lldb) var
(vmctx *) ctx = 0x000000080029c180
(pci_devinst *) pi = 0x0000000800b2c500
(char *) opts = 0x000000080029c10e "config=/usr/local/etc/wifibox/appliance,ro"
(cap_rights_t) rootcap = {
cr_rights = ([0] = 140737488347616, [1] = 0)
}
(bool) ro = false
(char *) rootpath = 0x0000000000000000
(char *) sharename = 0x0000000000000000
(char *) opt =
(int) rootfd =
(pci_vt9p_softc *) sc =
That way, for example, it can be tracked how the sharename variable gets
its value:
[..]
(lldb) s
Process 19852 stopped

thread #1, name = 'bhyve', stop reason = step in
frame #0: 0x000000000023e6db bhyve`pci_vt9p_init(ctx=, pi=0x0000000800b2c500, opts="ro") at pci_virtio_9p.c:255:15
252                           }
253
254                           sharename = strsep(&opt, "=");
-> 255                           rootpath = opt;
256                           continue;
257                   }
258
(lldb) p sharename
(char *) $0 = 0x000000080029c10e "config"

Ideally, this should give us some ideas about why the things are not going
right.
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Here is how you can investigate

Oh... thanks for such detailed instructions! Using debugger I found that the problem is in lack of CAPSUIM support. I've rebuilded world + kernel and everything works as expected:
wifibox:~# mount | grep config
config on /media/etc type 9p (ro,sync,dirsync,noatime,nodiratime,access=client,trans=virtio)
app_config on /etc/wpa_supplicant type 9p (rw,sync,dirsync,relatime,access=client,trans=virtio)

That's really weird that bhyve doesn't allow to mount VirtFS/9p share without any error or warning in logs.
Thanks a lot for your help!

I am glad that finally we could find the root cause.  I have posted the conclusion to the FreeBSD ticket in case folks do not want to read through the comments there.  I may even submit a patch for bhyve to address the issue, if time permits.  Until it is resolved, I would leave this ticket open.

authors: Marietto2008 iron-udjin pgj

repo: pgj/freebsd-wifibox


text:
Use stdint.h and stdbool.h for communication protocol

Currently, we are using the standard C data types in our structs.
This issue is about using the data types defined in stdint.h and stdbool.h instead such as int8_t, uint8_t and so on instead.
Then we can reimplement management.c and expand json.c to support all of these

@jesperpedersen I can work on this!(while working on the direct io issue)

@shikharish This is a complex issue - as we basically require a full implementation of JSON data types

@jesperpedersen Can you tell more about the issue? Do I have to replace all the structs with defined data types? And then reimplement management.c to support the data types similar to the current implementation of int64 and so?

@shikharish I would begin with supporting all intXX_t, uintXX_t and bool in json.h - a lot of can probably be copy'n'paste once you get started.
Then look at management.c and see what it uses and work your way backwards through the structs

Remember the _array version as well...

source: gharchive/issue

authors: jesperpedersen shikharish

repo: pgmoneta/pgmoneta

license_type: permissive

license_source: github-api


text:
mob_init fails

Hej,
I got an issue when trying to init the database by mob_init in the step where it tries to mirror https://share.corefacility.ca/index.php/s/oeufkw5HyKz0X5I/download. The returned error is
ERROR: Download failed with error (6, 'Could not resolve host: share.corefacility.ca').
I check the required software which is as it should be.
Is this a local issue or an issue on the mirrored site?
Hope someone can help.

Invm i had an old version installed. everything works with 3.1.8.

repo: phac-nml/mob-suite


text:
Command " FILE "

We use command syntaxs "_FILE" , inside and Zephir Program which contains Eval ()
and generate and error
Warning: require(cryptcode_runner/cryptcode_runner/wp-blog-header.php): failed to open stream: No such file or directory in cryptcode_runner/cryptcode_runner/app.zep:41 on line 2
Fatal error: require(): Failed opening required 'cryptcode_runner/cryptcode_runner/wp-blog-header.php' (include_path='.:/usr/share/php') in cryptcode_runner/cryptcode_runner/app.zep:41 on line 2

Why zephir eval () evaluate inside in *.zep file not the php code who call Zephir Extension ?

Could you please provide script to reproduce, Zephir version (commit) and PHP version.

Thisis the code
namespace Cryptcode_runner;
class App
{
private static _validCiphers = ["aes-128-cbc": 16, "aes-192-cbc": 24, "aes-256-cbc": 32];
private static function _testRequirements()
{
    if(!extension_loaded("openssl")) { throw new \Exception("OpenSSL extension must be loaded!"); }
    if(!function_exists("openssl_encrypt")) { throw new \Exception("Could not find function openssl_encrypt!"); }
    if(!function_exists("openssl_decrypt")) { throw new \Exception("Could not find function openssl_decrypt!"); }
}

private static function getKey(string cipher)
{
  var key = "Secr3t123!";
  var cipherLength;
  let cipherLength = App::_validCiphers[cipher];
  return substr(sha1(key), 0, cipherLength);
}

private static function decrypt(string cipher, string code)
{
    // Make sure all requirements are met
    App::_testRequirements();

    let cipher = cipher->lower();
    if(!array_key_exists(cipher, App::_validCiphers))
    {
      throw new \Exception(cipher . " is not among the list of valid ciphers: " . join(", ",App::_validCiphers));
    }

    var tmp = base64_decode(code);
    var iv = substr(tmp,0,openssl_cipher_iv_length(cipher));
    var enc = substr(tmp,openssl_cipher_iv_length(cipher));
    return openssl_decrypt(enc, cipher, App::getKey(cipher), OPENSSL_RAW_DATA, iv);
}

public static function run(string cipher, string code)
{
    return eval(App::decrypt(cipher, code));
}

}
The above code is to encrypt
<?php
/**
 * Front to the WordPress application. This file doesn't do anything, but loads
 * wp-blog-header.php which does and tells WordPress to load the theme.
 *
 * @package WordPress
 */

/**
 * Tells WordPress to load the WordPress theme and output it.
 *
 * @var bool
 */
define('WP_USE_THEMES', true);

/** Loads the WordPress Environment and Template */
require( dirname( __FILE__ ) . '/wp-blog-header.php' );

If we run eval() inside Zephir which have "require( dirname( __FILE__ ) ".
There would be an error because Zepir acessed the *.Zep file location , not the php location which running inside zephir functions .

PHP Version 7.0
When we eval() this code require( dirname( FILE ) . '/wp-blog-header.php' )
There is always an error where Zephir locate magic constaant "FILE "

So var tmp = base64_decode(code); has the __FILE__, right?

Yup inside eval () has the code FILE,

Well, it is impossible for now to pass PHP code inside Zephir and then eval it with __FILE__.  I want to close this issue because I don't want a bunch of these lying around. If anyone wants to get started, I'd love that.

I find a workaround, it's not nice but yet useful, tested under zephir 0.12.0, PHP 7.2.17.
Pass your __DIR__, and __FILE__ as PHP super global variable, and then access them in zephir extensions.
For example:
<?php
// set super global variables before using the extension
$_ENV['filename'] = __FILE__;
$_ENV['filepath'] = dirname(__FILE__);
$_ENV['dirname'] = __DIR__;
$_ENV['stuff'] = 'blah blah blah';
// now $_ENV contains all information we need
Utils\UsefulClass::showMeSomething();

Then use them in your extension:
namespace Utils;

class UsefulClass {
    public static function showMeSomething() {
        echo _ENV['filename'];
        echo _ENV['filepath'];
        echo _ENV['dirname'];
        echo _ENV['stuff'];
    }
}

If you need to eval some code containing __DIR__ or other magic constants, you could always do a string replace and replace them with things like "\"" . _ENV["dirname"] . "\"" to get the correct value, note the quote concatenated outside.

@romizone, can you provide both encryption and decryption code here

authors: Zhwt atishamte romizone sergeyklay

repo: phalcon/zephir

license: mit

license_source: bigquery


text:
Dumplicate Extension Globals key prefix

Here is the config.json
{
    "namespace": "utils",
    "name": "utils",
    "description": "An utils helper extension",
    "author": "aiddroid",
    "version": "0.0.1",
    "verbose": false,
    "requires": {
        "extensions": []
    },
    "globals": {
        "utils.enable_cache": {
            "type": "bool",
            "default": true
        }
    }
}

but got "utils.utils.enable_cache" in phpinfo().

Fixed in the development branch. Thank you for contributing

authors: aiddroid sergeyklay


text:
[NFR] ClassDefinition implement docblock

Need to implement getting for docblocks for ClassDefinition
and stubs generator for it

---
Want to back this issue? **[Post a bounty on it!](https://www.bountysource.com/issues/7666119-nfr-classdefinition-implement-docblock?utm_campaign=plugin&utm_content=tracker%2F280146&utm_medium=issues&utm_source=github)** We accept bounties via [Bountysource](https://www.bountysource.com/?utm_campaign=plugin&utm_content=tracker%2F280146&utm_medium=issues&utm_source=github).

+1

I think this is done via https://github.com/phalcon/zephir/commit/cefdc33b28c674b8caf09fe1a15e488dd53cae8e.

@mruz Yeap, I will close this

authors: mruz ovr


text:
logs error to output when Slack API call fails

uses URI object so we can get request uri from any error later
refactors tasks

This doesn't resolve #36 but it at least logs HTTP errors so and end-user can easily see something is wrong.

@seankibler Thank you!

source: gharchive/pull-request

authors: phallstrom seankibler

repo: phallstrom/slackistrano


text:
🛑 blog.progettodighe is down

In 7a8eeac, blog.progettodighe (https://blog.progettodighe.it) was down:

HTTP code: 0
Response time: 0 ms

Resolved: blog.progettodighe is back up in f93d4f2.

repo: phante/prdi-status

license: MIT


text:
Move utility functions from admiralonco over

See https://github.com/pharmaverse/admiralonco/issues/100

@thomas-neitmann @bundfussr @bms63 i'm looking further into this and count_vals, max_cond, min_cond i guess will all be taken care of as they already had moved from admiralonco -> admiral.
i'm assuming filter_confirmation would stay in admiral, and filter_pd would stay in admiralonco.
then the only one left in admiralonco would be aval_resp - which is very onco specific so personally i would leave it, but happy to move that here if you feel like we should stick to the rule of all utility functions always living in admiraldev.
let me know thoughts!

i'm looking further into this and count_vals, max_cond, min_cond i guess will all be taken care of as they already had moved from admiralonco -> admiral.

I wasn't aware of that. Is there a PR for including these function in {admiral}?

i'm assuming filter_confirmation would stay in admiral, and filter_pd would stay in admiralonco.

Agree.

then the only one left in admiralonco would be aval_resp - which is very onco specific so personally i would leave it, but happy to move that here if you feel like we should stick to the rule of all utility functions always living in admiraldev.

I'd suggest to keep it in {admiralonco}.

Thanks Thomas! On the last point, if the others agree then i could close this issue and delete the branch i had started.
For the admiral PR for your first question see https://github.com/pharmaverse/admiral/pull/1294

authors: rossfarrugia thomas-neitmann

repo: pharmaverse/admiraldev


text:
Enhancements to graphical_component_analysis

Enhancements proposed related to phasorpy.components.graphical_component_analysis:

[ ] Optimize number of steps (fractions) based on radius of cursor.
[ ] Validate with real data and SimFCS output from similar functions
[ ] Compare performance of SimFCS graphical analysis with phasorpy.components.graphical_component_analysis and add results to benchmarks tutorial.

I have been working on finding the optimal number of fractions based on radius of cursor, but found it's a little bit tricky with the current implementation of graphical_component_analysis since the lines between components can have different lengths.
The step size can be easily optimized though, since we can think that it has to be at least 2*radius to cover all points along the line, but this can create a too coarse resolution. One good compromise would for the step size to be radius/2, which ensures a good resolution without adding too much steps.
The problem as I said before is that the lengths of the line between components can be different, and since the radius is the same, finding an optimal number steps would mean that the histogram along each line between components will have different number of fractions and can be difficult to compare within the same histogram. One alternative would be to find the optimal number of steps for the longest line segment between components, and use that same number for the other combinations of components. Although it should not be computationally too costly, this can make the function more complex.

Also, with the current implementation of graphical_component_analysis, when no fraction is given (default is None), it raises the following error:
ValueError: fractions is not a one-dimensional array

Considering this, it can be a good idea to have a default value for the number of fractions, wether it's the proposed solution raised above, or another value (for example what SimFCS does).

repo: phasorpy/phasorpy


text:
Index out of bound when reading TSV w/o header

Problem seems to lie in the fact that Columns list is initialized to an empty list, but in object FieldValue(int i) it is checked to be not null and not checked to be an empty list causing an attempt to use Columns list for data conversion and failure to find column since list is empty.
Sample code:
            using (var streamReader = new StreamReader(_sourceBcpFilePath))
            {
                using (var bcpReader = new CsvReader(streamReader, false, _delimiter, _quote, _escape, _comment, ValueTrimmingOptions.All))
                {

. . .
bcpReader.GetValue(0);
. . .
}
}

You should submit a unit test that shows this error.

Fixed by https://github.com/phatcher/CsvReader/commit/6e255008f730a67448801c47dae6145dd02f8bc9#diff-0d66ae192d7d3c3db093c6b8df11677b

Suggested unit-test:
using (var reader = new StringReader("1,1,2,Hello\r\n3,3,4,World"))
{
using (var csvReader = new CsvReader(reader, false, '\t', '\0', '\0', '#', ValueTrimmingOptions.All))
{
while (csvReader.ReadNextRecord())
{
for (int i = 0; i < csvReader.FieldCount; i++)
{
var record = (csvReader as IDataRecord);
record.GetValue(I);
}
}
}
}

authors: INRIX-Mark-Gershaft joshgo

repo: phatcher/CsvReader


text:
Flex "upload" function so users can define local system instead of S3

In order to allow users to have a customised version of PGB working locally we need to address the way patient files are uploaded.
Currently, all goes to our S3:
aws s3 ls --profile phenopolis s3://phenopolis-website-uploads
PRE PH00000001/
PRE PH00008258/
PRE PH00008268/
PRE PH00008628/
PRE PH00008629/
PRE vcf/

And it's essentially done in React (frontend) via Uppy with some support endpoints in views/upload.py (but only for managing files, not for really uploading them).
Uppy seems to be very powerful and entails several options for upload including "local device".
We need, somehow, to have this option, for "local device". However, how is it going to be configured, either via frontend or in, e.g., public.env file, is still an opened question.

I would argue that the easiest option is to have a local S3-compatible storage system (e.g. Minio) - and then everything would be compatible with minimal changes?
With docker-compose - it should be super simple to get minio running - and mount a local hard drive path to Minio

I'll work on it.

See #386

@IsmailM
I tried to work on upload.py so to get rid of the two s3_client1 and s3_client2 and use endpoint_url="http://minio-server:9000" but I didn't get it to work.
What happens is that the actions using uppy (the JS module) for presign (upload) and for download, do request localhost (for delete and listing minio-server works fine).
If I try, e.g., to download a file, it redirects the browser to e.g.
http://minio-server:9000/phenopolis-website-uploads/PH00008258/PH00008258_mytest2.vcf?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=minio%2F20220212%2Feu-west-2%2Fs3%2Faws4_request&X-Amz-Date=20220212T103411Z&X-Amz-Expires=300&X-Amz-SignedHeaders=host&X-Amz-Signature=91e96208259aa285dcb63a03d5882b9f2a09efdb16db2573ef61d5cb9e0c0f4d
and that won't work for the host.
Uploading fails, as I said, and though I thought it was a CORS issue, I don't think it is, and your suggestion to add in nginx.conf didn't work anyway.
So, I'm still using two s3_clients approach with some simplification. It works with Wasabi as well.
Please see my last commit in #386.

authors: IsmailM alanwilter


text:
Add support for new mobile bar/left ribbon replacement

Describe the feature
Hey Phillip,
I hope you're doing well! With the new public release, I thought I might ask about a feature I'd like to see in the mobile app.
I would love if the settings for the left ribbon would now be applied to its new replacement in the mobile app, the long press menu on the right of the "tool bar" (next to the tab switcher).
Do you think this is possible?
Does this fix a problem? If so, specify.
I think that this would be a nice addition to the plugin as it would bring the functionality on par with the desktop experience. Many people on Discord have asked about it as well.
Did you consider other alternatives?
There aren't really any alternatives. The left ribbon settings are currently useless on mobile and I don't know of any other plugin which modifies that list of commands.
Screenshots and recordings
I'll clarify the position in the tool bar with two screenshots in a few minutes. Okay, for anyone else reading this, this is the button I'm talking about:

Yes, that is definitely something I will be working on! Stay tuned for the next update 👀

also just confirming that this doesn't work on android but mostly so I get the notification when it's solved! :)

I miss the left ribbon 😞

Has been following this issue for a while, and updated to 0.3.0 as soon as I heard (the number of plugins I have installed has made my mobile toolbar basically unusable). However, even testing on a fresh vault, I wasn't able to get commands hidden:

iOS 15, Obsidian Mobile v1.4.1, tested on a fresh vault.

seconded, we may need a new issue created

Alternatively if I can at least order the custom commands up top that will already be super useful #10 (related)

Can be a good workaround until this is fixed.

and perhaps a useful feature of itself

Is v3.0 supposed to address adding/hiding on the new mobile(phone) ribbon on the bottom right? Adding commands to the ribbon works for me, but can't hide the defaults (and therefore can't order properly). (?_?)

y'all, we should make new issues. lots of creators don't have notifications on old issues. highly recommend new issues.

y'all, we should make new issues. lots of creators don't have notifications on old issues. highly recommend new issues.

I do read all the issues! I just don't have enough time to work on Commander at the moment. If someone knows a fix for this, I would greatly appreciate a PR, otherwise it might take a few more weeks

authors: MystreAqui brimwats leoccyao lguenth phibr0 tonyxiao trainbuffer


text:
After log out the current user is not null

Im doing user.logOut(), and then Im checking if the currentUser!=null but it is retuning not null.
Here is the current user after log out:

I usually check for objectId if currentUser != null

Hey, is this still an issue?
I can look into this tonight before creating a new release.

Yes we can check for the objectId, but in the other sdks we just need to check for currentUser!=null

Hey,
I'll look into this tonight. I'd prefer not to have a current user if there is no objectId. I potentially might make a method as well called something like, isUserAvailable that returns a bool or something.

Fixed in the latest release

authors: Atteprojects pcegarra phillwiggins


text:
Any reason why at_evaluator using .to_s instead of a plain comparison?

This is more of a question, but it's something that has come to huge confusion for me.
In here: https://github.com/philostler/rspec-sidekiq/blob/develop/lib/rspec/sidekiq/matchers/have_enqueued_job.rb#L29
def at_evaluator(value)
  return false if job['at'].blank?
  value.to_time.to_s == Time.at(job['at']).to_s
end

Is there any reason why this isn't using a simple comparison? value.to_time == Time.at(job['at']).
I tend to have a lot of issues/confusion when value is in a different time zone.

☝ I'm happy to PR this if there is a consensus.

I agree, the timezone issue #124 make this really difficult to debug.
I would prefer a comparison using .to_f instead (which is probably the same as direct comparison?)

I think it should work with .utc https://github.com/philostler/rspec-sidekiq/pull/146

Believe this was fixed with https://github.com/wspurgin/rspec-sidekiq/commit/dcc6d037a2333a5af73ead81809b484fd0e9ac13 though it's not a direct comparison as a to_int is used to avoid fractional second mismatches.

authors: a0s dpoetzsch mvalipour wspurgin

repo: philostler/rspec-sidekiq


text:
Missing orientations for Iphone

After build the project, only one orientation for Iphone is defined, however for Ipad are all defined.
<preference name="orientation" value="default" />

<key>UISupportedInterfaceOrientations~ipad</key>
<array>
  <string>UIInterfaceOrientationPortrait</string>
  <string>UIInterfaceOrientationLandscapeLeft</string>
  <string>UIInterfaceOrientationPortraitUpsideDown</string>
  <string>UIInterfaceOrientationLandscapeRight</string>
</array>
<key>UISupportedInterfaceOrientations</key>
<array>
  <string>UIInterfaceOrientationPortrait</string>
</array>

I believe the underlying Cordova issue, CB-6026, is resolved, and so should this.
Closing this issue. If it still does not work with the latest phonegap-cli, please re-open.

authors: filmaj lopezdonaque

repo: phonegap/phonegap-cli


text:
Fix: Replace proposed with accepted

This pull request

[x] replaces proposed with accepted

💁♂ Since clock.md resides in proposed/, I would assume that it has been proposed.

Thank you, @drupol!

repo: php-fig/clock


text:
Change the name to socket client

This is not really an adapter, but a client.
WDYT @joelwurtz ?

:+1: This make sense

Done

authors: joelwurtz sagikazarmark

repo: php-http/socket-adapter


text:
🛑 phpMyFAQ Homepage is down

In b80bdbc, phpMyFAQ Homepage (https://www.phpmyfaq.de) was down:

HTTP code: 0
Response time: 0 ms

Resolved: phpMyFAQ Homepage is back up in f1053a5.


text:
🛑 phpMyFAQ API is down

In a77868c, phpMyFAQ API (https://api.phpmyfaq.de/versions) was down:

HTTP code: 0
Response time: 0 ms

Resolved: phpMyFAQ API is back up in 32244a2.


text:
🛑 phpMyFAQ Demo is down

In 7c30146, phpMyFAQ Demo (https://demo.phpmyfaq.de) was down:

HTTP code: 0
Response time: 0 ms

Resolved: phpMyFAQ Demo is back up in c3454e6.


text:
🛑 phpMyFAQ API is down

In 0d417bb, phpMyFAQ API (https://api.phpmyfaq.de/versions) was down:

HTTP code: 0
Response time: 0 ms

Resolved: phpMyFAQ API is back up in ea8933b after 6 minutes.


text:
Update composer.json to make it work with Symfony 2.6

I want to use pmd in a Symfony project 2.6 but the composer requirement doesnt pass.

Should be fixed now

authors: Adel-E manuelpichler

repo: phpmd/phpmd


text:
Permissions to this repo

I've set this repo so that only @ascii-soup and @martindilling have admin access. The idea being that they are the gatekeepers and only they merge stuff in. I'm pretty sure we agreed they would be in charge of merges at the last meetup.
@garethellis36 has asked for access as well, I'm totally cool with that, but can we have an agreement on whether I should just give everyone access to it, or do we actually like having only the gatekeepers with access.
@garethellis36 did you want to merge permissions or another thing that needed admin privileges?

To be honest I don't see a problem with us that are more active having admin access, at least until it becomes a problem?
I think it's most likely to become a problem when the project is further on, and there are more PRs with potential breaking changes :)

authors: martindilling olorton

repo: phpoxford/spires


text:
fix(CLI): Match repo_sync events to the correct response

We use phrase-cli in our CI/CD pipeline to automate merges to our repositories. However, the recent changes introduced in #735 have broken our process.
While upgrading our pipeline to use repo_sync, I encountered the following issues with phrase-cli:
Issues Description

Missing event_type and pull_request_url

The phrase-cli does not provide the event_type of the sync event or the pull_request_url. These details are critical for avoiding multiple merge requests in our CI/CD.
The API returns type instead of event_type, which caused discrepancies in the schemas. I’ve updated the schemas in this PR to match the API response.

Reproduction
Example with phrase-cli:
$ phrase repo_syncs show --id $SYNC_EVENT_ID --repo_sync_id $GITLAB_SYNC_ID --account_id $ACCOUNT_ID
{
  "id": "<REDACTED>",
  "created_at": "2024-12-19T17:35:52Z",
  "status": "success",
  "auto_import": false
}

Example with curl (fetching type but missing pull_request_url):
 curl -X GET "https://api.phrase.com/v2/accounts/ $ACCOUNT_ID/repo_syncs/$GITLAB_SYNC_ID/events/$SYNC_EVENT_ID?access_token=$PHRASE_ACCESS_TOKEN"  -H "Accept: application/json"
{
     "id": "<REDACTED>",
     "type":"export",
     "created_at":"2024-12-19T17:35:52Z",
     "status":"success",
     "auto_import":false
}

I’ve updated the schemas in this PR to match the API response.

Command Parsing conflicts::

When parsing the commands in api_repo_syncs.go#L169 and api_repo_syncs.go#L499, a conflict arises as shown in (this snippet)[https://go.dev/play/p/DoeBHQOf-oI]

For instance, the output of the help command demonstrates duplicate show commands:

> $ phrase repo_syncs --help                                                                                ⬡ 20.12.1
RepoSyncs API

Usage:
  phrase repo_syncs [command]

Available Commands:
  activate    Activate a Repo Sync
  deactivate  Deactivate a Repo Sync
  events      Repository Syncs History
  export      Export to code repository
  import      Import from code repository
  list        Get Repo Syncs
  show        Get a single Repo Sync Event <----- TWO SHOW COMMAND
  show        Get a single Repo Sync <----- TWO SHOW COMMAND

I changed the operationId to be repo_sync/events_show so it will create a new command events_show avoiding the conflict

Extra fixes:
Documentation Discrepancy:
Some API references use repo_sync where they should use repo_syncs.
The API documentation for Get a Single Repo Sync Event incorrectly references the command as repo_sync_event. So I  took the opportunity to correct this in the documentation.
Request for Additional Fix
API does not return the pull_request_url. This seems to be in a private repository. It would be great if this could be addressed as it’s essential for our CI/CD workflow.

Just taggin @theSoenke to visibility :)

hey @horstmannmat thanks a lot for the quick reaction and your PR. I will review it and test it immediately, and also open an internal ticket for pull request URL.

@horstmannmat the PR url is also exposed now:
$ ~/Downloads/phrase_linux_amd64 repo_sync_events show --account_id [REDACTED] --repo_sync_id e50b5024d11e675903ce37cca933dcf0 --id e51a1ccb6392bdf57f654aa64184b321
{
 "id": "e51a1ccb6392bdf57f654aa64184b321",
 "type": "export",
 "created_at": "2024-03-08T08:27:24Z",
 "status": "success",
 "pull_request_url": "https://github.com/jablan/phrase_test/pull/4"
}

@jablan Thank you so much, for your quick response :)
just a additional comment, by any chances you guys plan to add a automerge option to the export command or the webhook?
Right now  we cannot you webhook due the lack of this option.
What we are doing it is: our CICD we export via cli and wait - once the MR is ready, we set it to auto merge

hey @horstmannmat I'm not familiar with auto merge feature, but it seems that setting it on a PR is (still?) not supported through Github API

authors: horstmannmat jablan

repo: phrase/openapi


text:
BASIL-error

Dear BASIL-developer,
we are using oxford_asl for analyzing a pASL experiment. However,  we are currently facing an error that I am not able to figure out.
You can find the terminal output attached.
Thank you very much and best wishes,
Christian
Terminal output:
(base) christian@xlsserver:/data/Christian/sub-021/ses-03$ oxford_asl -i perf/sub-021_ses-03_run-01_asl -c perf/sub-021_ses-03_run-01_m0scan_flirt --fslanat=anat/sub-021_ses-03_run-01_T1w.anat --mc --wp --spatial --tis 1.99 --iaf=tc -o perf/cbf_run-01 --bolus 0.7 --tr=4.6 --cmethod=voxel --fmap=fmap/sub-021_ses-03_run-01_phasediff --fmapmagbrain=fmap/sub-021_ses-03_run-01_magnitude1_fsl-bet --fmapmag=fmap/sub-021_ses-03_run-01_magnitude1 --pedir=-y --echospacing=0.00061 --region-analysis
OXFORD_ASL - running
Version: v4.0.29-dirty Mon Feb 20 16:19:06 2023
Input file: perf/sub-021_ses-03_run-01_asl
Analysis in white paper mode
Pre-processing
Using structural images (bias corrected) from fsl_anat: anat/sub-021_ses-03_run-01_T1w.anat
Standard brain is: /usr/local/fsl/data/standard/MNI152_T1_2mm
Structural to standard transformation warp: anat/sub-021_ses-03_run-01_T1w.anat/T1_to_MNI_nonlin_coeff.nii.gz
Motion Correction
Motion correction to calibration image
Bolus duration: 0.7
Number of TIs in list: 1
TIs list: --ti1=1.99
Input ASL format is: tc
Input block format is: rpt
Number of voxels is:655360
Number of repeats in data is:4
Outputting ASL data mean at each TI
Done.
Number of inversion times: 1
Number of timepoints in data: 4
Number of repeats in data: 4
Operating in Single TI mode
1.99 1.99 1.99 1.99
1.99
Using FSL_ANAT outputs at: anat/sub-021_ses-03_run-01_T1w.anat
Bias field extracted from anat/sub-021_ses-03_run-01_T1w.anat sucessfully
Defaulting brain extracted mean ASL image as initial registration reference
Using brain extracted mean ASL image as initial registration reference
Creating WMseg for BBR registration
Performing registration
Using /tmp/fsl_vjf_kxhf_ox_asl/meanasl_brain as base for inital registration
Initial registration is FLIRT only
Performing registration
ASL_REG
Input file is: /tmp/fsl_vjf_kxhf_ox_asl/meanasl_brain
Registration MAIN stage (FLIRT)
Tidying up
ASL_REG - Done.
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/tmp_asl_reg/lowtohigh"
Generating calibration image in structural space
Creating mask
Generating dilated mask for initial BASIL runs
Distortion Correction using asl_reg
Performing registration
ASL_REG
Input file is: /tmp/fsl_vjf_kxhf_ox_asl/pwi
Creating output directory
Registration FINAL stage (BBR)
Registering fieldmap to structural
Running BBR with fieldmap
1.000113 0.997557 -0.069762 0.003601 0.000000 0.069843 0.995126 -0.069617 0.000000 0.001274 0.069699 0.997567 0.000000 -14.691910 2.985404 18.631045 1.000000
Making warp fields and applying registration to EPI series
BBR end
Saving FINAL output
Tidying up
ASL_REG - Done.
Applying combined warps to original data:

Warp: /tmp/fsl_vjf_kxhf_ox_asl/asldist_warp
Jacobian: /tmp/fsl_vjf_kxhf_ox_asl/distcorr/jacobian
Applying warps to ASL data
Moco: /tmp/fsl_vjf_kxhf_ox_asl/asldata.cat
Applying warps to calibration data
Calib->ASL: /tmp/fsl_vjf_kxhf_ox_asl/calib2asl.mat
Number of voxels is:655360
Number of repeats in data is:4
Outputting ASL data mean at each TI
Done.
T1: 1.65
T1b: 1.65
Setting up BASIL
pASL model
Fixed bolus duration
Variable arterial arrival time
Setting prior/initial (tissue/gray matter) bolus arrival time to 0
Single volume: informative noise prior will be used
Using SNR of 10 to set noise std dev
Runtime error (func=(main), adr=29): Square root of a negative number
Using a prior noise sd of:
Instructing BASIL to use automated spatial smoothing
BASIL options (/tmp/fsl_vjf_kxhf_ox_asl/basil_options.txt):

#FABBER options created by Oxford_asl --t1=1.65 --t1b=1.65 --tau=0.7 --bat=0 --prior-noise-stddev= --save-model-fit
Calling BASIL on data - conventional perusion image
Initial run of BASIL on data where we have avareged all repeats at each TI
Run time basil options:
--spatial
Creating output directory: /tmp/fsl_vjf_kxhf_ox_asl/init/basil
STEP 1: VB - Tissue
Welcome to FABBER 4.0.11-12-g99c29e6-dirty
Last commit: Wed May 11 07:38:41 2022
Logfile started: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step1/logfile
NEWMAT exception caught in fabber:
Invalid value given for option: = (Failed to convert to required type)
Final logfile: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step1/logfile
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/init/basil/step1/finalMVN"
STEP 2: Spatial VB Tissue - init with STEP 1
Welcome to FABBER 4.0.11-12-g99c29e6-dirty
Last commit: Wed May 11 07:38:41 2022
Logfile started: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/logfile
NEWMAT exception caught in fabber:
Invalid value given for option: = (Failed to convert to required type)
Final logfile: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/logfile
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/finalMVN"
End.
Using BASIL step /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/mean_ftiss
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/mean_ftiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718723 Aborted                 (core dumped) fslmaths ${finalstep}/mean_ftiss -thr 0 $2/ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/mean_delttiss
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/mean_delttiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718726 Aborted                 (core dumped) fslmaths ${finalstep}/mean_delttiss -thr 0 $2/delttiss
Fabber variance calculator
Working in /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2
Calculating variance for: ftiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_vjf_kxhf_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=128, y=128, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=1.5mm, y=1.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
Voxel data not found: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/finalMVN (File is invalid or does not exist)
Calculating variance for: delttiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_vjf_kxhf_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=128, y=128, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=1.5mm, y=1.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
Voxel data not found: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/finalMVN (File is invalid or does not exist)
Done.
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/var_ftiss
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/var_ftiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718739 Aborted                 (core dumped) fslmaths ${finalstep}/var_ftiss -bin -add 1 -uthr 1 -mul 1e12 -add ${finalstep}/var_ftiss $2/var_ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/var_delttiss
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/var_delttiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718741 Aborted                 (core dumped) fslmaths ${finalstep}/var_delttiss -bin -add 1 -uthr 1 -mul 1e12 -add ${finalstep}/var_delttiss $2/var_delttiss
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/finalMVN"
Main run of BASIL on ASL data
Run time basil options:
--spatial
Initial MVN for BASIL is: /tmp/fsl_vjf_kxhf_ox_asl/init/finalMVN
Creating output directory: /tmp/fsl_vjf_kxhf_ox_asl/basil
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/init/finalMVN"
STEP 1: VB - Tissue - init with STEP 0
Welcome to FABBER 4.0.11-12-g99c29e6-dirty
Last commit: Wed May 11 07:38:41 2022
Logfile started: /tmp/fsl_vjf_kxhf_ox_asl/basil/step1/logfile
NEWMAT exception caught in fabber:
Invalid value given for option: = (Failed to convert to required type)
Final logfile: /tmp/fsl_vjf_kxhf_ox_asl/basil/step1/logfile
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/basil/step1/finalMVN"
STEP 2: Spatial VB Tissue - init with STEP 1
Welcome to FABBER 4.0.11-12-g99c29e6-dirty
Last commit: Wed May 11 07:38:41 2022
Logfile started: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/logfile
NEWMAT exception caught in fabber:
Invalid value given for option: = (Failed to convert to required type)
Final logfile: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/logfile
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/basil/step2/finalMVN"
End.
Using BASIL step /tmp/fsl_vjf_kxhf_ox_asl/basil/step2
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/mean_ftiss
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/mean_ftiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718791 Aborted                 (core dumped) fslmaths ${finalstep}/mean_ftiss -thr 0 $2/ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/mean_delttiss
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/mean_delttiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718793 Aborted                 (core dumped) fslmaths ${finalstep}/mean_delttiss -thr 0 $2/delttiss
Fabber variance calculator
Working in /tmp/fsl_vjf_kxhf_ox_asl/basil/step2
Calculating variance for: ftiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_vjf_kxhf_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=128, y=128, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=1.5mm, y=1.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
Voxel data not found: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/finalMVN (File is invalid or does not exist)
Calculating variance for: delttiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_vjf_kxhf_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=128, y=128, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=1.5mm, y=1.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
Voxel data not found: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/finalMVN (File is invalid or does not exist)
Done.
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/var_ftiss
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/var_ftiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718805 Aborted                 (core dumped) fslmaths ${finalstep}/var_ftiss -bin -add 1 -uthr 1 -mul 1e12 -add ${finalstep}/var_ftiss $2/var_ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/var_delttiss
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/var_delttiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718807 Aborted                 (core dumped) fslmaths ${finalstep}/var_delttiss -bin -add 1 -uthr 1 -mul 1e12 -add ${finalstep}/var_delttiss $2/var_delttiss
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/basil/step2/finalMVN"
Performing final registration
Performing registration
ASL_REG
Input file is: /tmp/fsl_vjf_kxhf_ox_asl/ftiss
Registration FINAL stage (BBR)
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/ftiss
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: /tmp/fsl_vjf_kxhf_ox_asl/ftiss
Aborted (core dumped)
'/tmp/fsl_vjf_kxhf_ox_asl/mask.nii.gz' and '/tmp/fsl_vjf_kxhf_ox_asl/mask.nii.gz' are the same file
Running BBR
Image Exception : #63 :: No image files match: /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Image Exception : #22 :: Failed to read volume /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Error : No image files match: /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Failed to read volume /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Error : No image files match: /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Could not open matrix file /tmp/fsl_llo_qz1e_asl_reg/low2high_final.mat
Image Exception : #63 :: No image files match: /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Image Exception : #22 :: Failed to read volume /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Error : No image files match: /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
terminate called after throwing an instance of 'std::runtime_error'
what():  Failed to read volume /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Error : No image files match: /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
/usr/local/fsl/bin/epi_reg: line 390: 1718967 Aborted                 (core dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} --premat=${vout}.mat --interp=spline
BBR end
Saving FINAL output
cp: cannot stat '/tmp/fsl_llo_qz1e_asl_reg/low2high_final.mat': No such file or directory
Could not find a supported file with prefix "/tmp/fsl_llo_qz1e_asl_reg/low2high_final"
'/tmp/fsl_vjf_kxhf_ox_asl/tissseg.nii.gz' and '/tmp/fsl_vjf_kxhf_ox_asl/tissseg.nii.gz' are the same file
Tidying up
ASL_REG - Done.
Generating calibration image in structural space
Generating analysis mask from final structural registration
Using user-supplied structural->standard space warp to generate cortical GM/WM masks
T1t (for calibration): 1.3
Doing calibration using voxelwise M0 map
mkdir: cannot create directory 'perf/cbf_run-01/calib': File exists
Correcting the calibration (M0) image for short TR (using T1 of tissue 1.3)
Number of voxels is:216468
Number of repeats in data is:1
Start extrapolation!
Done.
Output: ftiss perfusion / /
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl///ftiss"
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
terminate called after throwing an instance of 'std::runtime_error'
what():  Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
/usr/local/fsl/bin/oxford_asl: line 268: 1722736 Aborted                 (core dumped) applywarp --in=$tempdir/$subdir_in/$param --out=$outdir/std_space/$subdir_out/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Mean perfusion in gm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Mean perfusion in cortical gm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/std_space///perfusion
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: perf/cbf_run-01/std_space///perfusion
/usr/local/fsl/bin/oxford_asl: line 354: 1722741 Aborted                 (core dumped) fslmaths $outdir/std_space/$subdir_out/$parname -div $normval $outdir/std_space/$subdir_out/${parname}_norm
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: perf/cbf_run-01/native_space///perfusion
/usr/local/fsl/bin/oxford_asl: line 354: 1722744 Aborted                 (core dumped) fslmaths $outdir/native_space/$subdir_out/$parname -div $normval $outdir/native_space/$subdir_out/${parname}_norm
Image Exception : #63 :: No image files match: perf/cbf_run-01/struct_space///perfusion
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: perf/cbf_run-01/struct_space///perfusion
/usr/local/fsl/bin/oxford_asl: line 354: 1722746 Aborted                 (core dumped) fslmaths $outdir/struct_space/$subdir_out/$parname -div $normval $outdir/struct_space/$subdir_out/${parname}_norm
Output: delttiss arrival / /
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl///delttiss"
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///delttiss
terminate called after throwing an instance of 'std::runtime_error'
what():  Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///delttiss
/usr/local/fsl/bin/oxford_asl: line 268: 1722752 Aborted                 (core dumped) applywarp --in=$tempdir/$subdir_in/$param --out=$outdir/std_space/$subdir_out/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///arrival
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Mean arrival in gm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///arrival
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Mean arrival in cortical gm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Mean perfusion in wm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Mean perfusion in cerebral wm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///arrival
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Mean arrival in wm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///arrival
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Mean arrival in cerebral wm is
Output: var_ftiss perfusion_var / /
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl///var_ftiss"
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
terminate called after throwing an instance of 'std::runtime_error'
what():  Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
/usr/local/fsl/bin/oxford_asl: line 268: 1722769 Aborted                 (core dumped) applywarp --in=$tempdir/$subdir_in/$param --out=$outdir/std_space/$subdir_out/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
(standard_in) 1: syntax error
Image Exception : #63 :: No image files match: perf/cbf_run-01/std_space///perfusion_var
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: perf/cbf_run-01/std_space///perfusion_var
/usr/local/fsl/bin/oxford_asl: line 378: 1722775 Aborted                 (core dumped) fslmaths $outdir/std_space/$subdir_out/${parname}_var -div $normval $outdir/std_space/$subdir_out/${parname}_var_norm
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion_var
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: perf/cbf_run-01/native_space///perfusion_var
/usr/local/fsl/bin/oxford_asl: line 378: 1722777 Aborted                 (core dumped) fslmaths $outdir/native_space/$subdir_out/${parname}_var -div $normval $outdir/native_space/$subdir_out/${parname}_var_norm
Image Exception : #63 :: No image files match: perf/cbf_run-01/struct_space///perfusion_var
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: perf/cbf_run-01/struct_space///perfusion_var
/usr/local/fsl/bin/oxford_asl: line 378: 1722779 Aborted                 (core dumped) fslmaths $outdir/struct_space/$subdir_out/${parname}_var -div $normval $outdir/struct_space/$subdir_out/${parname}_var_norm
Output: var_delttiss arrival_var / /
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl///var_delttiss"
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
terminate called after throwing an instance of 'std::runtime_error'
what():  Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
/usr/local/fsl/bin/oxford_asl: line 268: 1722790 Aborted                 (core dumped) applywarp --in=$tempdir/$subdir_in/$param --out=$outdir/std_space/$subdir_out/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
/usr/local/fsl/bin/oxford_asl: line 313: 1722794 Aborted                 (core dumped) fslmaths $tempdir/$subdir_in/$param -div $Moval -mul $multiplier $tempdir/$subdir_in/${param}_calib
Output: ftiss_calib perfusion_calib / /
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib"
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
terminate called after throwing an instance of 'std::runtime_error'
what():  Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
/usr/local/fsl/bin/oxford_asl: line 268: 1722801 Aborted                 (core dumped) applywarp --in=$tempdir/$subdir_in/$param --out=$outdir/std_space/$subdir_out/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion_calib
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Mean perfusion_calib in gm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion_calib
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Mean perfusion_calib in cortical gm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion_calib
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Mean perfusion_calib in wm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion_calib
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Mean perfusion_calib in cerebral wm is
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
terminate called after throwing an instance of 'std::runtime_error'
what():  No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
/usr/local/fsl/bin/oxford_asl: line 313: 1722808 Aborted                 (core dumped) fslmaths $tempdir/$subdir_in/$param -div $Moval -mul $multiplier $tempdir/$subdir_in/${param}_calib
Output: var_ftiss_calib perfusion_var_calib / /
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib"
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
terminate called after throwing an instance of 'std::runtime_error'
what():  Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
/usr/local/fsl/bin/oxford_asl: line 268: 1722814 Aborted                 (core dumped) applywarp --in=$tempdir/$subdir_in/$param --out=$outdir/std_space/$subdir_out/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Regionwise analysis

Using oxford_asl output in perf/cbf_run-01/native_space
Traceback (most recent call last):
File "/usr/local/fsl/bin/oxford_asl_roi_stats", line 10, in
sys.exit(main())
File "/usr/local/fsl/lib/python3.10/site-packages/oxford_asl/roi_stats.py", line 594, in main
asl_ref = Image(os.path.join(outdir, "perfusion"))
File "/usr/local/fsl/lib/python3.10/site-packages/fsl/data/image.py", line 1246, in init
image      = op.abspath(addExt(image))
File "/usr/local/fsl/lib/python3.10/site-packages/fsl/data/image.py", line 1951, in addExt
raise e
File "/usr/local/fsl/lib/python3.10/site-packages/fsl/data/image.py", line 1938, in addExt
return fslpath.addExt(prefix,
File "/usr/local/fsl/lib/python3.10/site-packages/fsl/utils/path.py", line 196, in addExt
raise PathError('Could not find a supported file '
fsl.utils.path.PathError: Could not find a supported file with prefix "perf/cbf_run-01/native_space/perfusion"
Output is perf/cbf_run-01/
OXFORD_ASL - done.

I'm in the process of updating oxford_asl to v4.0.29-5-g09a5cba-dirty (fsl-oxford_asl=v4.0.29 via conda) in ASLPrep (see https://github.com/PennLINC/aslprep/pull/399) and am getting the same error. Does anyone know what causes it?

authors: ChristianNSchmitz tsalo


text:
🛑 JellyFin is down

In 92a608c, JellyFin (https://netflix.pivrous.wtf) was down:

HTTP code: 502
Response time: 649 ms

Resolved: JellyFin is back up in b887a51.

repo: piaverous/status


text:
🛑 FreeDMR IT Bridge is down

In 3ada0c4, FreeDMR IT Bridge (https://dashboard.freedmr.it) was down:

HTTP code: 0
Response time: 0 ms

Resolved: FreeDMR IT Bridge is back up in b9c7d0b.

repo: picchiosat/HBLink-Uptime


text:
🛑 APRS is down

In f739bc1, APRS (https://aprs.hblink.it) was down:

HTTP code: 0
Response time: 0 ms

Resolved: APRS is back up in 535e834.

Resolved: APRS is back up in 535e834.


text:
Render process (11786)'s crash wasn't handled by all associated webviews, triggering application crash.

Environment

Technology
Version

Flutter version
3.3.0

Plugin version
5.4.3+7

Android version
Android 10,level 29

iOS version

Xcode version

Stacktrace/Logcat
09-19 14:04:50.994 12140 12140 F chromium: [FATAL:crashpad_client_linux.cc(561)] Render process (17621)'s crash wasn't handled by all associated webviews, triggering application crash.

Possible Cause
https://www.jianshu.com/p/29a8dce65634

I'm having the exact same problem! Been stuck with for a week, is there any solution ?

onRenderProcessGone method should be implemented by all webviews in the app, otherwise once webview process crashes, it will crash the app
https://developer.android.com/reference/android/webkit/WebViewClient#onRenderProcessGone(android.webkit.WebView, android.webkit.RenderProcessGoneDetail)

@huangsir0 Are you have any solution?

@androideveloper Thanks for the hint on the onRenderProcessGone override.
I have implemented this method via androidOnRenderProcessGone in this plugin (on v5, I think it has changed in v6). Where I try to recreate the InAppWebView via a new Key.
However, I still see crashes with the error: [FATAL:crashpad_client_linux.cc(732)] Render process (2370)'s crash wasn't handled by all associated  webviews, triggering application crash. in the Play Console.
Example implementation:
    String inAppWebViewKeyString = Uuid().v4().toString();
    Uri? currentUri; // tracked via the controller

    final webview = InAppWebView(
      key: Key(inAppWebViewKeyString),
      initialUrlRequest: URLRequest(
        url: currentUri,
      ),
      initialOptions: InAppWebViewGroupOptions(
        android: AndroidInAppWebViewOptions(
          useOnRenderProcessGone: true,
        ),
      ),
      androidOnRenderProcessGone: (controller, details) {
        // reload the creashed webview
        setState(() {
          inAppWebViewKeyString = Uuid().v4().toString();
        });
      },
    );

Any ideas? I'd really appreciate any points anyone might have :)

Yor crashing webview might come from another internal dependency/sdk that you don't control.


text:
[iOS] InAppWebView flickering when overScrolled

[x] I have read the Getting Started section
[x] I have already searched for the same problem

Device information:
Description

v6.0.0
Install on iOS
Enable pullToRefreshController
Pull down enough distance, still hold touching, pull up to a specific position, flickering occurs:

*** Debug
onOverScrolled: (InAppWebViewController controller, int x, int y, bool clampedX, bool clampedY) {
// Pull down, y can be:
-12
-56
-250
// Pull up, y can be:
-250
-156
-92
// Still pull up, Flickering <=== Bug here
- 126
- 111
- 96
// Continue pull up, y can be:
- 91
-84
-56
...
0
},

It seems it’s how native pull to refresh works on iOS, that is different from Android.
I didn’t find any better solution than the current one.
On Android, if you still hold touching, the refresh callback is not called. Instead on iOS, after a little while, it gets called automatically on native side, so this happens.
If you find anything to make it work better on Swift native side, share it or make a pull request about it, thanks.

It seems this behaviour is the same also on other iOS Apps, such as LinkedIn.

authors: pichillilorenzo synd-guide


text:
[Snyk] Security upgrade mongoose from 4.2.4 to 8.8.3

Snyk has created this PR to fix 1 vulnerabilities in the npm dependencies of this project.
Snyk changed the following file(s):

package.json
package-lock.json

Vulnerabilities that will be fixed with an upgrade:

Issue
Score

Improper Neutralization of Special Elements in Data Query Logic SNYK-JS-MONGOOSE-8446504
  167

[!IMPORTANT]

Check the changes in this PR to ensure they won't cause issues with your project.
Max score is 1000. Note that the real score may have changed since the PR was raised.
This PR was automatically created by Snyk using the credentials of a real user.

Note: You are seeing this because you or someone else with access to this repository has authorized Snyk to open fix PRs.
For more information:
🧐 View latest project report
📜 Customise PR templates
🛠 Adjust project settings
📚 Read about Snyk's upgrade logic

Learn how to fix vulnerabilities with free interactive lessons:
🦉 Improper Neutralization of Special Elements in Data Query Logic

:tada: Snyk checks have passed. No issues have been found so far.
:white_check_mark: code/snyk check is complete. No issues have been found. (View Details)

:tada: Snyk checks have passed. No issues have been found so far.
:white_check_mark: security/snyk check is complete. No issues have been found. (View Details)
:white_check_mark: license/snyk check is complete. No issues have been found. (View Details)

repo: pickford-snyk/nodejs-goof


text:
🛑 Blog is down

In cd07a94, Blog (https://www.pickyzz.dev) was down:

HTTP code: 521
Response time: 68 ms

Resolved: Blog is back up in 87ed3a9.

repo: pickyzz/uptime-monitor


text:
pico-web role not portable

The scripts used in ansible/roles/pico-web/tasks/auto_configure.yml are based in the root level of the ansible directory [PLAYBOOK_DIR]. When these roles are used in a playbook outside this directory the local lookup fails.
This prevents the role from being used in a playbook outside this directory, like one might want to do for a custom deployment.
Below is an example of the lookup failure.
Could not find or access 'scripts/add_shell_server.py'
Searched in:
        [PICO BASE]/ansible/roles/pico-web/files/scripts/add_shell_server.py
        [PICO BASE]/ansible/roles/pico-web/scripts/add_shell_server.py
        [PICO BASE]/ansible/roles/pico-web/tasks/files/scripts/add_shell_server.py
        [PICO BASE]/ansible/roles/pico-web/tasks/scripts/add_shell_server.py
        [PLAYBOOK_DIR]/files/scripts/add_shell_server.py
        [PLAYBOOK_DIR]/scripts/add_shell_server.py on the Ansible Controller.

PR #230 fixes this.

Thanks! PR has been merged.

authors: maverickwoo royragsdale

repo: picoCTF/picoCTF


text:
Nextcloud & Pico = Erreur interne du serveur

Hi there,
I installed Pico on Nextcloud 18.0.3 and as soon as I try to modify index.md (with sample_pico templates) I get the folowing error in web page

Erreur interne du serveur
La page demandée du site Web n'a pas été créée, le serveur n'a pas pu traiter votre demande.

wich is an error from the server.
So impossible to access web pages index.md.

Please refer to https://help.nextcloud.com/c/apps/cms-pico/128 for getting help about Pico CMS for Nextcloud. This is the repository of Pico. You can find the app's repository here: https://github.com/nextcloud/cms_pico. Since I can't transfer issues from this repo to the cms_pico repo, please open a new issue there. When doing so please also attach your Nextcloud log.

Hi,
OK, thanks

repo: picocms/Pico


text:
Disabled Button Skin

At the moment, there seems to be no support for a disabled button.
All the button skins currently have a hover/click effect even if disabled, so it's impossible to get a pseudo-disabled skin with what's available.

@Sylencia You are right
Solution (using existing disabled class)
<button class="btn disabled">primary button</button>
.btn.disabled{      cursor: not-allowed;   background-color:white;   opacity:.5; }

@Sylencia Add the class disabled or the attribute disabled for a disabled button. I am adding the example to the doc.

authors: Randore Sylencia picturepan2


text:
Avoid merge conflicts

Merged locally to fix conflicts and bring dimensions branch up to speed with MapProxy's main branch.
cc @tomkralidis

+1 from me.  cc @ingenieroariel

Thanks @InesBosch for updating this branch, hope it can make it upstream!

authors: InesBosch ingenieroariel tomkralidis

repo: piensa/mapproxy


text:
Freeze when returning back to the app on iOS

Unfortunately, I don't have any logs.
The app just freezes completely when returning back from iOS maps.

I have a similar issue. Returning back to the app from IOS maps crashes the app for me on IOS version (14.4). Launcher does not work (does not initiate IOS maps) on IOS version (14.3)

+1 @pikaju

You can workaround by setting forceSafariVC: false
The real cause is that something is blocking the thread, for me it was another buggy widget on the screen.
When you return back after launching a map url, app can't resume because something is using the thread already and locked it.
Try debugging your and url_launcher to see if this is the cause

authors: AAverin alymoursy shantaly

repo: pikaju/flutter-maps-launcher


text:
Add "Installing Non-JS Packages" section back to the docs

Tried to find latest version (I think it is this). This will fix issue #1124. Needs review since this information may be outdated but this will fix the broken link.
Changes

Adds "Installing Non-JS Packages" section back to the docs

Testing
Docs only
Docs
Docs only

Thanks for the support.
a) I realized, its only snowpack.config.js  usage on docu page, maybe you want ot change it to .json format as well.
b) seems like you are using old version of snowpack, as it tells me:
[snowpack] [Snowpack v1 -> v2] top-level rollup config is now installOptions.rollup.
when applying
/* snowpack.config.js */
module.exports = {
rollup: {
plugins: [require('rollup-plugin-sass')()],
},
};

authors: melissamcewen raDiesle

repo: pikapkg/snowpack


text:
🛑 www.pik.farm is down

In b9e1f45, www.pik.farm (https://pik.farm) was down:

HTTP code: 0
Response time: 0 ms

Resolved: www.pik.farm is back up in cdd83dd after 29 minutes.

repo: pikfarm/PikfarmStatus


text:
🛑 Stripe Test Endpoint URL is down

In 50aaed5, Stripe Test Endpoint URL ($STRIPETESTAPI) was down:

HTTP code: 0
Response time: 0 ms

Resolved: Stripe Test Endpoint URL is back up in 5e77434 after 25 minutes.


text:
🛑 www.pikfarm.com is down

In 90c5c05, www.pikfarm.com (https://www.pikfarm.com) was down:

HTTP code: 0
Response time: 0 ms

Resolved: www.pikfarm.com is back up in 4aa82ba after 1 hour, 25 minutes.


text:
How to observe battery voltage

I want to send me an event in advance before shutdown.
The main question is: where to observe voltage of LiPo ?

I guess I found it by myself https://github.com/pimoroni/clean-shutdown/blob/master/daemon/usr/bin/cleanshutd#L86-L88

repo: pimoroni/clean-shutdown


text:
Prune bot dependencies to runtime deps only

Aws-sdk notably never needs to be included - we should forcibly strip that out.

repo: pimterry/dev-bot


text:
Additional functions for Index.list and Pinecone.Builder

Is this your first time submitting a feature request?

[X] I have searched the existing issues, and I could not find an existing issue for this feature
[X] I am requesting a straightforward extension of existing functionality

Describe the feature
Hi guys,
For Pinecone.Builder, I want to specify my own custom PineconeConfig with a custom managed channel:
i.e.
val builder = Pinecone.Builder(pineconeConfig.apiKey)
builder.setPineconeConfig(pineconeConfig)
The reason is we use customManagedChannel for the PineconeConfig with some additional configuration.

For Index.list api, we want to call list with a paginationToken, but not a prefix.
That's currently not possible from what I'm seeing in your Index.java.
    public ListResponse list(String namespace) {
        this.validateListEndpointParameters(namespace, (String)null, (String)null, (Integer)null, true, false, false, false);
        ListRequest listRequest = ListRequest.newBuilder().setNamespace(namespace).build();
        return this.blockingStub.list(listRequest);
    }

    public ListResponse list(String namespace, int limit) {
        this.validateListEndpointParameters(namespace, (String)null, (String)null, limit, true, false, false, true);
        ListRequest listRequest = ListRequest.newBuilder().setNamespace(namespace).setLimit(limit).build();
        return this.blockingStub.list(listRequest);
    }

However, it is possible if I just use your RESTful apis.
Describe alternatives you've considered

Who will this benefit?
Those who want more control.
Are you interested in contributing this feature?
Sure
Anything else?

I can submit these changes if you'd like?

PR to address my first point;
https://github.com/pinecone-io/pinecone-java-client/pull/129

Sorry I was out for a few days and I misled you before but for custom Managed gRPC channel, we instantiate the PineconeConfig class followed by PineconeConnection class and finally the Index or AsyncIndex class depending on the stub you'll like to use. So the code will look something like this:
import io.grpc.ManagedChannel;
import io.pinecone.clients.Index;
import io.pinecone.configs.PineconeConfig;
import io.pinecone.configs.PineconeConnection;
import io.grpc.netty.GrpcSslContexts;
import io.grpc.netty.NegotiationType;
import io.grpc.netty.NettyChannelBuilder;
import io.pinecone.exceptions.PineconeException;

import javax.net.ssl.SSLException;
import java.util.Arrays;
import java.util.concurrent.TimeUnit;

public class Example {
    public static void main(String[] args) {
        // Instantiate PineconeConfig object to set customManagedChannel
        PineconeConfig config = new PineconeConfig("PINECONE_API_KEY");

        // Endpoint: format the endpoint by removing https://
        // https://github.com/pinecone-io/pinecone-java-client/blob/main/src/main/java/io/pinecone/configs/PineconeConnection.java#L170
        String endpoint = "indexName-abcd123.svc.abcd-1234-a12b.pinecone.io";
        NettyChannelBuilder builder = NettyChannelBuilder.forTarget(endpoint);
        // Create custom channel
        try {
            builder = builder.overrideAuthority(endpoint)
                    .negotiationType(NegotiationType.TLS)
                    .keepAliveTimeout(5, TimeUnit.SECONDS)
                    .sslContext(GrpcSslContexts.forClient().build());
        } catch (SSLException e) {
            throw new PineconeException("SSL error opening gRPC channel", e);
        }

        // Build the managed channel with the configured options
        ManagedChannel channel = builder.build();
        config.setCustomManagedChannel(channel);

        // Instantiate the PienconeConnection object
        PineconeConnection connection = new PineconeConnection(config);
        Index index = new Index(connection, "serve1");
        // Data plane operations
        // 1. Upsert data
        System.out.println(index.upsert("v1", Arrays.asList(1F, 2F, 3F)));
        // 2. Describe index stats
        System.out.println(index.describeIndexStats());
    }
}

Seems to work.
Thanks!!

We appreciate you guys being open to contributions. :)

repo: pinecone-io/pinecone-java-client


text:
[Explorer] Incorrect usage of UNION and LIMIT

Hi, I have some problems with the question
Question ID:
13f17c8f-23cd-498c-b5d8-7761ace957c8
Question Link:
how many github events are stored
Error type:
error-validate-sql
Error message:
Incorrect usage of UNION and LIMIT

dup of https://github.com/pingcap/ossinsight/issues/1315

repo: pingcap/ossinsight


text:
parser: support ALTER PARTITION clause

What problem does this PR solve?
As title, it follows the first task of https://github.com/pingcap/tidb/issues/18405.
Check List
Tests

Unit test
Integration test

Code changes

Has exported function/method change

Related changes

Need to update the documentation
Need to be included in the release note

/merge

Please give another LGTM @kennytm

/merge

/merge

authors: djshow832 kennytm xhebox

repo: pingcap/parser


text:
*: add a API to reset the TS

Signed-off-by: nolouch nolouch@gmail.com

What problem does this PR solve?
For backup tool. Supports this API.
What is changed and how it works?
add an API.
Check List
Tests

Unit test

Codecov Report

Merging #1819 into master will increase coverage by 0.04%.
The diff coverage is 82.35%.

@@            Coverage Diff             @@
##           master    #1819      +/-   ##
==========================================
+ Coverage      78%   78.04%   +0.04%
==========================================
  Files         167      169       +2
  Lines       16473    16513      +40
==========================================
+ Hits        12849    12888      +39
+ Misses       2580     2579       -1
- Partials     1044     1046       +2

Impacted Files
Coverage Δ

pkg/tsoutil/tso.go
100% <100%> (ø)

server/api/router.go
100% <100%> (ø)
:arrow_up:

tools/pd-ctl/pdctl/command/tso_command.go
64.7% <100%> (-3.72%)
:arrow_down:

server/handler.go
51.74% <60%> (+0.1%)
:arrow_up:

server/api/recovery.go
76.92% <76.92%> (ø)

server/tso/tso.go
78.74% <84%> (-0.16%)
:arrow_down:

client/client.go
68.6% <0%> (-1.3%)
:arrow_down:

server/grpc_service.go
57.04% <0%> (-0.44%)
:arrow_down:

... and 2 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update f1f4553...7ff46d9. Read the comment docs.

/ok-to-test

PTAL @lhy1024 @rleungx @overvenus

/rebuild

/merge

/cherry-pick

authors: codecov-io nolouch

repo: pingcap/pd


text:
namespace: refactor namespace api.

At the global router level, all requests towards /pd/api/v1/classifier/* will be redirected to current namespace classifier (if it implements http.Handler).

I think we should rename Namespace in pd-ctl to TableNamespace too.

You are right. I plan to do it after merge this PR.

Got it.
LGTM
PTAL @nolouch

authors: disksing siddontang


text:
Continue to refine show error message

Feature Request
Is your feature request related to a problem? Please describe:

Describe the feature you'd like:

Describe alternatives you've considered:

Teachability, Documentation, Adoption, Migration Strategy:

Show more detail error information

show one error is enough

too long error message overflow

repo: pingcap/tidb-dashboard


text:
fix: make debug api compatible with old tidb-dashboard backend api

TODO
fix i18n

Codecov Report

Merging #1417 (f4842a7) into master (10c5a29) will increase coverage by 0.01%.
The diff coverage is n/a.

Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1417      +/-   ##
==========================================
+ Coverage   27.58%   27.59%   +0.01%
==========================================
  Files          93       93
  Lines        9972     9972
==========================================
+ Hits         2751     2752       +1
+ Misses       7041     7040       -1
  Partials      180      180

Flag
Coverage Δ

be_unit_test
27.59% <ø> (+0.01%)
:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.

Continue to review full report at Codecov.

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remain todo: (will fix in another PR)

fix i18n

authors: baurine codecov-commenter