I have been using a Unix shell to download raw reads using sratoolkit/2.8.2-1. The SRA files are from the NCBI database e.g. for "https://www.ncbi.nlm.nih.gov/sra?term=SRX1157907". When I use the prefetch command (e.g. prefetch SRR2172947) consistently get the error of "path not found while resolving tree within virtual file system module - 'SRR2172948' cannot be found." I can download other SRA files like SRR12626663 without a problem, but the mentioned link has some problem.
Would it be possible to please guide me on how to solve this problem?
Human genomics data in NCBI's SRA is often under controlled access through the dbGaP system. One must request access to these files and follow special protocols to download such data. For example, researchers must demonstrate valid research needs to gain access approval and agree to follow protocols to ensure the data is securely stored.
Related
I utilize the Apache VFS library to access files on a remote server. Some files are symbolic links and when we get the file size of these files, it comes back as 80 bytes. I need to get the actual file size. Any ideas on how to accomplish this?
Using commons-vfs2 version 2.1.
OS is Linux/Unix.
You did not say which protocol/provider you are using. However it most likely also does not matter: none of them implement symlink chasing as far as I know (besides local). You only get the size reported by the server for the actual directory entry.
VFS is a rather high level abstraction, if you want to commandeer a protocol client more specially, using commons-net or httpclient or whatever protocol you want to use gives you much more options.
I've created a SAP program and I want to deploy it in another SAP system.
I know I can import the Transport Request files with the created program to the new system but I'm looking for other options.
Is it possible to "install"/import my program to another SAP system?
Regards
I can only think you don't want to use the transport system because the systems are not part of the same landscape? If so, you can still use the transport system, you just need to manually move the required files around.
But, there is another approach you can follow - using SAPlink. It's an open source program that allows you download ABAP source, dictionary objects, etc. from one system into files and then upload them into another system. Of course, both systems will need to have SAPlink installed for this to work.
This is somewhat by design, SAP is the largest OTS system available and there has to be some controls to ensure that people can not install software if they are not specifically given the authorization to do so.
Even to use SAPlink ( that mjturner suggests ) requires you to have the ability to install that software first and I doubt you will find it in very many productive landscapes so likely that wont be an option.
Assuming you have a developer authorization you can always download the source code from your development SAP system and then upload from within the ABAP editor (SE38) using utilities -> More utilities->Upload/Download. Note that this doesn't work in the class editor so cut and paste is another option.
Later.......
There are three ways to move transports from one system to another.
1. Moving the transport files form the directories “data” and “cofiles” manually.
When the transport is released in the source system SAP automatically puts the transport files into the transport directory on file system. This files easily can be copied to the second system an be imported via transaction “STMS”.
2. Using CAR files
CAR files are packed files like a zip file. The contain the data and cofiles.
car.exe -cvf packedFile.car data\R900000.XXX cofiles\K900000.XXX
(car.exe is a SAP standard tool, XXX is the system ID)
This CAR files can be imported via transaction SAINT. This allows import files from frontend into the data and cofiles directory without direct access to the file system. After importing the file via SAINT the transport can be imported using STMS. This is be the common way to transport software to other systems outside the current landscape.
3. Using SAR and PAT files
These files are more special. They allow to install software as Add-On in SAP. This is required if the program should be certified by SAP. They have to be created using the AAK (SAP Add-On Assembly Kit). Unfortunately, I have not created this files myself yet. But it seems to be very complex to get this running, because there are some checks which have to be passed. The files can be imported via transaction SPAM (upload) and SAINT (import).
I have installed Aerospike in Ubuntu. When I run aql command "show namespaces", it shows namespaces "test" and "bar". I tried to find out that where are they in hard drive or what is their exact location in ubuntu but no vain. Can anyone help me?
You wouldn't see any of the namespaces directly exposed on your file system when running Aerospike.
Having said that, the "bar" and "test" namespaces are default in the configuration file and both should be configured as 'storage engine memory' which means that the data will be stored in memory and not on your hard drive. Even if you were to switch those to be 'storage engine device', and either configure the underlying device as a raw SSD one or using a file, you would still not see any direct mention of the namespace...
When using raw SSD, Aerospike bypasses the file system and directly manages blocks on the device.
When using a file, Aerospike also manages blocks on the file system which makes the file not 'readable'.
There is a possibility to see existing namespace and to create other namespaces,
If you have installed Aerospike in ubuntu then see the file /etc/aerospike/aerospike.conf . This configuration file has namespaces
I have Created my one Package with Config file and working very good in BIDS, DTEXEC.EXE and DTEXECUI.exe on remote server But we are using some third Party tool for scheduling the jobs( I cant say). and It wont run in it, it creates an error "the config file is invalid and errors for file location path." what should I do?
Appreciate your help.
Given that your package works fine from BIDS and when you manually execute it, this strongly smells of a permission issue.
You will need to look at the Active Directory user that runs the mysterious third party scheduling tool. You will need to ensure that account (domain\ThirdPartySchedulerService) has read access to DriveLetter:\path\to\config.dtsconfig
Also note that if there is an assumption about a drive letter being mapped, it may not apply to service accounts. Similar statement about access to network shares.
I cannot use the Resource File API from within a file system plugin due to a PlatSec issue:
*PlatSec* ERROR - Capability check failed - Can't load filesystemplugin.PXT because it links to bafl.dll which has the following capabilities missing: TCB
My understanding of the issue is that:
File system plugins are dlls which are executed within the context of the file system process. Therefore all file system plugins must have the TCB PlatSec privilege which in turn means they cannot link against a dll that is not in the TCB.
Is there a way around this (without resorting to a text file or an intermediate server)? I suspect not - but it would be good to get a definitive answer.
The Symbian file server has the following capabilities:
TCB ProtServ DiskAdmin AllFiles PowerMgmt CommDD
So any DLL being loaded into the file server process must have at least these capabilities. There is no way around this, short of writing a new proxy process as you allude to.
However, there is a more fundamental reason why you shouldn't be using bafl.dll from within a fileserver plugin: this DLL provides utility functions which interface to the file servers client API. Attempting to use it from within the filer server will not work; at best, it will lead to the file server deadlocking as it attempts to connect to itself.
I'd suggest rethinking that you're trying to do, and investigating an internal file-server API to achieve it instead.
Using RFs/RFile/RDir APIs from within a file server plugin is not safe and can potentially lead to deadlock if you're not very careful.
Symbian 9.5 will introduce new APIs (RFilePlugin, RFsPlugin and RDirPlugin) which should be used instead.
Theres a proper mechanism for communicating with plugins, RPlugin.
Do not use RFile. I'm not even sure that it would work as the path is checked in Initialise of RFile functions which is called before the plugin stack.
Tell us what kind of data you are storing in the resource file.
Things that usually go into resource files have no place in a file server plugin, even that means hardcoding a few values.
Technically, you can send data to a file server plugin using RFile.Write() but that's not a great solution (intercept RFile.Open("invalid file name that only your plugin understands") in the plugin).
EDIT: Someone indicated that using an invalid file name will not let you send data to the plugin. hey, I didn't like that solution either. for the sake of completness, I should clarify. make up a filename that looks OK enough to go through to your plugin. like using a drive letter that doesn't have a real drive attached to it (but will still be considered correct by filename-parsing code).
Writing code to parse the resource file binary in the plugin, while theoratically possible, isn't a great solution either.