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Serialize multiple protobuf messages in java and desesrialize them in Python

I want to store a bunch of protobuf messages in a file, and read them later.
In java, I can just use 'writeDelimitedTo' and 'parseDelimitedFrom' to read and write to a file. However, I want to read it in Python, which only seems to have a 'ParseFromString' method.
Some SO questions are very similar, such as, Parsing Protocol Buffers, written in Java and read in Python, but that is only for a single message: not for multiple.

From the proto guide it is written that you need to deal yourself with the size of your message:
Streaming Multiple Messages
If you want to write multiple messages to a single file or stream, it
is up to you to keep track of where one message ends and the next
begins. The Protocol Buffer wire format is not self-delimiting, so
protocol buffer parsers cannot determine where a message ends on their
own. The easiest way to solve this problem is to write the size of
each message before you write the message itself. When you read the
messages back in, you read the size, then read the bytes into a
separate buffer, then parse from that buffer. (If you want to avoid
copying bytes to a separate buffer, check out the CodedInputStream
class (in both C++ and Java) which can be told to limit reads to a
certain number of bytes.)
https://developers.google.com/protocol-buffers/docs/techniques
A simple solution could be for you to serialize each proto in base64, on a new line in your file.
Doing so, it would be pretty easy on python to parse and use them.

Entering data into an InputStream

I know that InputStreams are for reading, and OutputStreams are for writing... but if I have an application that passes all data from an InputStream to the remote side and pushes all received data from that remote side to the OutputStream and I need to send dynamic data to that remote side... how would I enter it into the InputStream? I can do this easily in the Java console since anything entered in is put into System.in and sent to that remote side, and anything coming back is processed through System.out, but obviously I cannot use a Java console in production. How would I emulate this functionality e.g. create a button that sends "command X\r" as if it were typed into the java console?
Note: For background, I'm using JSch to SSH into a Cisco ASA. Where I have set Channel.setInputStream(System.in) and Channel.setOutputStream(System.out) to communicate through console successfully.

I am not familiar with JSch, and I suspect you have this backwards. First, according to their example, you should actually be executing commands with Channel.setCommand(). Then you can use Channel.getInputStream() to obtain a stream that you can read the remote response from.
That aside, a cursory glance at the documentation seems to suggest that you should use the channel's existing streams and read to / write from them, e.g.:
OutputStream out = Channel.getOutputStream();
String str = "command X\r";
out.write(str.getBytes("us-ascii"));
This would make more sense and is much easier to deal with on your end.
However, as to the general question regarding InputStreams: You can use any InputStream as a source for data. It just so happens that System.in is one that comes from standard input (which is essentially a file).
If you want to use data constructed on the fly, you could use a ByteArrayInputStream, e.g.:
String str = "command X\r";
InputStream in = new ByteArrayInputStream(str.getBytes("us-ascii"));
// do stuff with in
You can use any character encoding you want if us-ascii is not appropriate.
But, again, I suspect you are doing this slightly backwards.

Can proc_open (php => java) have multiple input streams?

I'm using proc_open in php to call java application, send a large text to it for processing and capture a returned result. Is it possible to pass several text strings (input streams) instead of just one?
This is what I've got at the moment:
fwrite($pipes[0], $input);
fclose($pipes[0]);
$output = stream_get_contents($pipes[1]);
fclose($pipes[1]);
If I do something like this, java still recognizes it as one input stream:
fwrite($pipes[0], $input);
fwrite($pipes[0], $input1);
fwrite($pipes[0], $input2);
fclose($pipes[0]);
$output = stream_get_contents($pipes[1]);
fclose($pipes[1]);
So is something like this possible at all? If not, any alternatives? I can't use command line params because it's a large text with multiple lines.

It depends what you are trying to do, and what the java application expects.
If you want the Java application to see the concatenation of $input, $input2 and $input3, then sure ... your code will do that.
If you want the Java to be able to automatically see those inputs as distinct streams, then no. As far as the Java IO system is concerned, the bytes are just bytes. There are no natural boundaries ... apart from the ultimate end of the (combined) stream.
If you want the Java to see one stream that it can then split into three streams, then it is possible, but it will require some programming effort.
On the PHP side, you have to add some kind of "framing" information to the stream that tells the Java side where one "stream" ends and the next one starts.
On the Java side, you have to look for / interpret that framing information.
The framing could be done by sending a byte count for each stream followed by the bytes, or it could be done with marker characters or sequences that designate the end of a stream.

Nope, a process has only a single standard input stream, as well as a single standard output stream and a single standard error (output) stream (this is true for every process not just java or php).
You can set up some socket communication, e.g. a client-server architecture, that would allow for multiple streams, but would only help if both client (php) and server (java) can do multi threading.
You can send through the pipe some delimiter sequence, so java can distinguish the three input strings
You can simply use more than one proc_open
EDIT:
You can use files instead of the stdin and stdout (php and java could share those)
You can use unix pipes (similar to the socket solution), but this is pretty hard to implement.

How do i start reading byte through input stream from a specific Location in the stream?

I am using URL class in java and I want to read bytes through Input Stream from a specific byte location in the stream instead of using skip() function which takes a lot of time to get to that specific location.

I suppose it is not possible and here is why: when you send GET request, remote server does not know that you are interested in bytes from 100 till 200 - he sends you full document/file. So you need to read them, but don't need to handle them - that is why skip is slow.
But: I am sure that you can tell server (some of them support it, some - don't) that you want 100+ bytes of file.
Also: see this to get in-depth knowledge about skip mechanics: How does the skip() method in InputStream work?

The nature of streams mean you will need to read through all the data to get to the specific place you want to start from. You will not get faster than skip() unfortunately.

The simple answer is that you can't.
If you perform a GET that requests the entire file, you will have to use skip() to get to the part that you want. (And in fact, the slowness is most likely because the server has to send all of the data that is being skipped to the client. That is how TCP/IP works ...)
However, there is a possible alternative. The HTTP 1.1 specification supports partial fetching documents using the Range header. If your server supports this, then you can request the server to send you just the range of the document that you are interested in. However, you may need to deal with the case where the server ignores the Range header and sends the entire document anyway.

Passing strings[]'s as byte[]

I'm working on a network in which my python script will communicate with my java application. The python script is passing a DataPacket (just a packet that holds some strings and a little other data) to the java server for processing. I know how to pack the information into a byte array, but how do I unpack it to be used as strings? What I've got so far is I have to parse the arrays of data in the packet and send it in bits and pieces. Is this the only way to do this? Can I use ByteInputStream and if so how?
thanks
~Aedon

I'm not sure that what you're doing is quite right, in that you're fragmenting your strings into separate packets. This could cause problems with multibyte strings.
However, you may wish to check out ByteArrayOutputStream. You can write into this, then convert to a String using toString(enc), where enc is the encoding you've used in your Python to convert your strings into bytes in the first place.
Looking at your comment below, it appears you need some means to serialise in Python and deserialise in Java. Leaving aside solutions like XML serialisation, have you looked at possible solutions like Google Protocol Buffers ?