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python on knime server won't start

October 25, 2016, 7:43 am
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Hi

We are trying out KNIME Server 4.3, and have a problem getting python to start on the server. It runs when KNIME is running as the Analytic Platform. The error message from there server workflow is 

There are messages for workflow "QueryProducts 2016-10-25 15.31.12"
  Python Source 6:34:0:15 - ERROR: Execute failed: Could not start python kernel:
Could not detect python version
 

Python running interactively as the Analytic platform that is used by the server can start without a problem. 

We have exported the preference file from the Analytic Platform, and placed into the config directory in the knime server workflow repository as preferences.epf. This doesn't seem to help.

We are running python 2.7 with protobuf 3.1.0.post1

David

 

 

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Database read node and Neo4j

October 25, 2016, 8:31 am
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Hi

This is tantilisingly close to working with Neo4j, but just a step away!

We have installed the latest jdbc drivers from Neo4j, https://github.com/neo4j-contrib/neo4j-jdbc/releases/tag/3.0, and have used it to connect an instance of the graph database. This worked. We then try to pull some data out in a database reader node. The cypher query is

Match (p:product) return p

which should return all the nodes which are products.

it does return, but only the first node makes it to the output table. It returns as a string that can be turned into a json type. 

{"status":"YES","ID":"cornflakes","rules":"before 9am","uuid":"d4a00670-9a05-11e6-a0af-00155d68022d"}

 

We have a feeling it may be returning as separate result sets, and so the others may be dropped.

When we put more conditions on the query, we get an error 

ERROR Database Reader      4:55       Execute failed: Encountered duplicate row ID  "Row0" at row number 2

Can't really see what is creating it.

Has anyone any experience of what can be done? It would be great if the database nodes can work for Neo4j.

David

 

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Data Profiling in Knime

October 25, 2016, 9:22 am
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Kmeans and ANN integration

October 25, 2016, 12:49 pm
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Hi,

I want to create a workflow using kmeans results as one of the imputs of an ANN learner node. Is this possible in knime?

Best Regards

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Unable to connect to Workflow Server: publicserver.knime.org

October 25, 2016, 1:04 pm
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I have been trying to connect to Workflow Server: publicserver.knime.org to access the example file but unable to go it. Do I need to do anything different other than using windows ftp and using guest username and pwd.

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GC overhead limit issues when running the Topic Extractor Node

October 25, 2016, 5:45 pm
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Hi All,

I ran into a GC overhead limit while running the topic extractor (parallel LDA) node on ~600K documents.  Each document probably contains about 50 terms.  Is there a possible workaround to this problem.  

I have a macbook pro 2.6 GHz Intel Core i7 with 8GB RAM.

Appreciate any suggestions to help optimize the performance.

 

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Maximum row count problem

October 26, 2016, 1:24 am
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In my analysis I've created a table with almost 2.5 billion rows. After the Cross join I want to convert the strings to numbers, use a math formula on each row and convert the data into a pivot table. I've run across a limitation of the amount of rows I can use for the String to number node and solved it by splitting the 2.5 billion rows into five different rows (it's now running). Is there an alternative way of solving this problem?

The error I've come across: Execute failed: Row count is greater than 2147483647. The current node cannot handle more than this number. Please ask the vendor to update the implementation.

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Image Converter Node: Double to UnsignedByteType

October 26, 2016, 1:36 am
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Hi KNIP,

we are currently loading images (previously saved as DoubleType images using the Image Writer node in the KNIP toolbox) into KNIME using the image reader node. We would like to convert them to UnsignedByteType by scaling using the Imge Converter node, however this seems to be unsuccessful (i.e. the images just stay as double type).

Do you have any suggestions? (if required I can upload an example workflow as well, values in the double type images dont exceed 16bit)

Cheers and thanks in advance,

Ben

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Knime workflow execution error when I am running from the command line (Batch)

October 26, 2016, 1:38 am
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Hi,

I am trying to run the workflow by command prompt and I executed following commands -

knime -consoleLog -nosplash -application org.knime.product.KNIME_BATCH_APPLICATION -workflowFile=""

knime.exe -consoleLog -noexit -reset -nosplash "--launcher.suppressErrors" -application org.knime.product.KNIME_BATCH_APPLICATION -workflowDir=""

(Of course I put the valid path for file and directory)

I am facing the issue with the following error message -

workflow is locked by another knime instance

There is no lock file I see and no KNIME process running already.

Please suggest how can I get rid of this problem.

 

Thank you in advance

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Trying to append data to a Table file

October 26, 2016, 2:35 am
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Hi,

I want to save data in a Table (using Table Writer) and then periodically append new data to it. The Table Writer node will either overwrite or fail if the table already exists (depending on configuration). My solution is to read in the table and then to concatenate new data and then save.

However, I have hit a snag. If the data table does not already exist, Table Reader fails with a Warning that the file does not exist. and the flow stops. I tried putting the Table Reader inside a Try-Catch, but that does not work becuse only a Warning is given if the file does not exist - it does not seem to fail badly enough to for the Try-Catch to deal with it. The flow simply stops at Table Reader.

Is there a way to check if a Table file exists before I use Table Reader to load it? Or is there some way to handle a Table file that does not exit.

Thanks,

Paul

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SAS7BDAT Node is truncating the decimal values

October 26, 2016, 5:19 am
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Hi 

I am trying to read the SAS Data set into knime and the decimal value is getting truncated.  Source value is 40.719535 and the output from the SAS7BDAT reader's out put is 40.719. Please help to resolve.

Thanks
Prasanna

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ODBC driver

October 26, 2016, 8:09 am
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'Hi

I'm trying to make a connection to an acces database (.accdb), but I don't see an ODBC driver when I try to configure a Database Reader or a Database Connector node. I only have JDBC drivers in the Databse Driver dropdown list.

Please help me get the ODBC driver in my Knime.

Thank you in advance

Ps. I have configured my database in the "ODBC data source administator" in Windows

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Can we run PySpark code thru Knime ?

October 26, 2016, 8:31 am
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Hi Team,

We have few PySpark scripts actually running on a Hadoop cluster.  We would like to know if we have facility to run PySpark scripts (which uses sql concepts of Pyspark) on Knime. Knime supports Spark connectors, but can we run Pyspark scripts ?

If yes, can you please forward use case documentation or any documentation, which are implemented using Spark and PySpark.

Thanks in advance.

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Openbabel optional parameters usage

October 26, 2016, 9:48 am
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Hello,

I'm new to KNIME and trying to use Openbabel to generate conformers and optimize geometry. What is the correct usage of this node? I tried putting --gen3d --conformer but it doesnt seem to work.

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Python Error

October 26, 2016, 1:22 pm
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Hi All,

I've got Python installed on my Windows machine (2.7.11) and now trying the Python nodes (I'm new to Python though so please bear with me).

I understand that I have to construct the RDKit bit vector object and tried this code below:


from rdkit import DataStructs
for fps in input_table['Fingerprint']:
	fp = DataStructs.CreateFromBitString(fps)

However, I got this error here:

Traceback (most recent call last):
  File "C:\Program Files\KNIME\plugins\org.knime.python_3.1.2.v201603040957\py\PythonKernel.py", line 282, in execute
    exec(source_code, _exec_env, _exec_env)
  File "<string>", line 6, in <module>
ArgumentError: Python argument types in
    rdkit.DataStructs.cDataStructs.CreateFromBitString(unicode)
did not match C++ signature:
    CreateFromBitString(class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >)

Does anyone know if there's anything that I did wrong with the installation?

Thanks.

LM.

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Is it possible to create in Knime some Noisy values ?

October 26, 2016, 2:08 pm
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I need to turn a Variable which is really overfittin, is it possible to turn in down knime with a node that creates some noise ?

 

 

Thank you 

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Pathway to occurences in different files

October 27, 2016, 12:19 am
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Dear contributors,

It is probably simple but I can't find the nodes to do that.

My need is as follow: I have a document containing a list of files (.txt). Each test file contains 2 coulumns x and y. In y there is only 2 values: 0 and 255 while x is an integer from 0 to 800 . I would like to develop a workflow that can tell me how much is the occurence of 255 in each text file.

Something like: list file --> extract x and y in each text file --> calculate 255 occurence --> get a table where in the first coloumn we have the name of the text file and in the second colomun the occurence number.

Thank you for your help,

Chakib,

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Database Writer Error

October 27, 2016, 4:24 am
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Hi 

When I am trying to write data from a joiner to Teradata database using Database Writer, the database chosen by Knime is not from the database URL : jdbc:teradata://10.89.XXX.XX/Database_name instead it is taking to default database to create the table. Please let me nkow what setting I need to tweak. Thank you.

Thanks and Regards
Prasanna 

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Searching for combinaison of data points in a table

October 27, 2016, 4:52 am
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Hi,

I have the following question: 

I have a table with a temperature column and many other columns with measurement of data points under different conditions – See Table A.

For each condition, I need to get the min value and its associated temperature.    This set of data is collected in a new table – See table B

Table A:

Row Id

Temperature

Condition A

Condition B

Condition C

….

1

25

33.2

25.6

5.6

 

2

36

52.6

65.1

56.4

 

3

40

15.8

14.5

25.6

 

…

32

26.1

10.2

40.5

 

…

 

 

 

 

 

 

Table B:

Condition

Min Value

Temperature

Condition A

15.8

40

Condition B

10.2

32

Condition C

5.6

5.6

…

 

 

 

Would you have any idea how I could implement this in Knime in an efficient way?

Thanks in advace for your help,

Cheers,

Cl

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Unzip password protected file

October 27, 2016, 7:37 am
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I have a zip file on my local drive which is password protected, when I try to unzip using knime I get this error message "Execute failed: unsupported feature encryption used in entry Filename.csv". I know the password for the zip file but i don't know how to use it in knime. Could someone suggest?

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