Today the Vernalis nodes have been updated to version 1.8.0 on the nightly build.  this update includes most of the imminent-release nodes discussed at the recent KNIME Cheminformatics SIG (see links below).  This is a major new release encompassing 31 new nodes.

From the change log:

• 'Speedy SMILES' nodes (16 nodes) added for fast high-throughput pre-processing of SMILES strings (see slides from 5th Cheminformatics SIG for details)
• Benchmarking nodes with memory monitoring (6 nodes) added to Testing -> Benchmarking
• Memory Use node added to Testing
• Empty Column Checker node added to Testing - node ensures table columns have at least one non-missing cell in test cases
• Multi-file reader source nodes added to IO folder (Load Local ... Files - currently 7 nodes - CDXML, Mol, Mol2, PDB, RXN XML and text)  NB These nodes will accept a single flow variable for multiple files. From the node documentation, "Alternatively, a flow variable can be specified, containing one or more filenames separated by ';'"
• Many existing nodes are now streamable (more will become streamable in due course)

We anticipate moving this release to the stable builds in the coming weeks - please let us know of any issues asap with these new nodes.

Steve

Hi everyone,

I am creating a JS KNIME node and found out this bug when trying to deserialize a table from JSON. My custom node is similar to the Javascript Table View but  is deserializing the table as well.

When serializing, the JSONDataTableSpec constructor in the line 195 is saving the names of the column types (not the actual enum values).

if (!Arrays.asList(excludeColumns).contains(colName)) {
    colNames.add(colName);
    orgTypes.add(spec.getColumnSpec(i).getType().getName());
    DataType colType = spec.getColumnSpec(i).getType();
    colTypes.add(getJSONType(colType).name);
    numColumns++;
}

Yet later when I tried to deserialize the JSONDataTable to a regular BufferedDataTable with the method JSONDataTable#createBufferedDataTable, the JSONDataTableSpec#createDataTableSpec in the line 215 is trying to get the enum values from the name properties of the enum JSTypes instead of the actual string representation.

for (int i = 0; i < m_numColumns; i++) {
    JSTypes type = JSTypes.valueOf(m_colTypes.get(i));
    DataType dataType = null;
    switch (type) {
         case BOOLEAN:

The JSTypes enum is using uppercase for its values and lowercase for its name property. For example I cannot access with a "boolean" column type a column of type JSType.BOOLEAN. The valueOf is failing here.

        BOOLEAN("boolean"),
        NUMBER("number"),
        STRING("string"),
        /** @since 2.10 */
        PNG("png"),
        /** @since 2.10 */
        SVG("svg"),
        /** @since 2.11 */
        DATE_TIME("dateTime"),
        UNDEFINED("undefined");

As a result deserializing a toy table with string columns produces this exception.

ERROR JavaScript Editable Table 0:77       Execute failed: No enum constant org.knime.js.core.JSONDataTableSpec.JSTypes.string

Best regards and happy coding,

Miguel

I'm not sure what the issue is here, I'm posting here rather than at Chemaxon because it seems to specifically affect the library within KNIME rather than Marvin itself.

I use the Chemaxon functions to output a series of structures in SMILES format, such as this 

O=C(Nc1ccncc1)c1ncnc1C(=O)OC1CCCCC1

Now this is actually invalid, because of the ambiguity around the five memebred ring, but I can't seem to find a combination of functions that will let me fix this.

The reason I bring it up here is that if you were to import this string into MarvinSketch a valid structure is produced, and indeed Chemaxon renders it, but copying the SMILES from that gives O=C(Nc1ccncc1)c1[nH]cnc1C(=O)OC1CCCCC1, which is perfectly valid.

Is there a snippet of code or something that can be done to clean this up within a node, I've tried the various options of MolImporter to copy the structure into a new Molecule instance, but the invalid form remains.

I would have thought that one of the dearomaize/aromatize combinations would be enough to clear it, but it seems to get 'stuck' in an ambigous state.

ICQ 661116561 Sell dumps pin skim atm plastic card track1 track2 cvv fullz info
Contact :
ICQ : 661116561
Gmail : addytran1987@gmail.com
Sell dumps, dumps track2, sell dumps pin, dumps 101, dumps 201, sell track 1&2, sell track1 track2, sell track2, track1 track2, sell cvv, sell cvv2, cvv fullz, cvv fullz info, dead fullz, Clone emv, clone chip, clone Card, clone credit card,uk full, CA full, US full, cvv UK full, dead full, cloning emv, emv Software, emv encode,
Price list:
**Dumps pin track 1 track 2 track 1 2 :
--classic 65$ per one
--gold 75$ per one
--platinum 85$ per one

Bluetooth Skimmer (NCR, Diebold, Wincor and others) - 800 USD
Pin Pad (Bluetooth) - 800 USD
MSR 606 (+20 free white blank cards) - 400 USD
GSM Skimmer + Pin Pad (Bluetooth) - 1300 USD (POPULAR)
Full kit: Bluetooth Skimmer + Pin Pad (Bluetooth) + MSR 606 (20 free white blank cards) - 1600 USD

GSM Skimmer (NCR, Diebold, Wincor and others) - 900 USD
Pin Pad (GSM) - 900 USD
MSR 606 (+20 free white blank cards) - 400 USD
GSM Skimmer + Pin Pad (GSM) - 1500 USD (POPULAR)
Full kit: Bluetooth Skimmer + Pin Pad (Bluetooth) + MSR 606 (20 free white blank cards) - 1800 USD

SELLING : 
Sell EMV Sofware Clone Encode
SELL Dumps with pin
SELL dumps pin
Sell track1 track2 with pin
Sell track 1&2 with pin
Sell track2 with pin
Sell cvv2 full info
Sell cc
Sell UK full
Sell cvv UK full
Sell CA full
Sell cvv CA full
Sell US full
Sell cvv US full
Sell Dead full
Tag : sell cvv2, sell dumps, sell fullz, sell track2, sell track1/2, dumps track2, emv software, dead fullz, cvv fullz,

hotkey search : MSR605, MSR606, MCR200, skim dumps, card dumps, skimming, cashout, cashout money, 
Clone card, dumps 101, dumps 201, Duplique chip, sell cvv, Sell dumps, sell dumps pin, sell track 1 2, sell track 1, sell track 2,
cvv fullz, fullz info, cvv vbv, cvv non vbv, dumps with pin, dumps pin, track 1, track 2, 
track 1 2, track 1 track 2, withdraw, withdraw money,card writer,EMV CHIP, CHIP EMV,Skim atm, Veriphone vx670, 
skimmer, Atm skimmer, skimming device, forking, atm forking, Verifone offine, verifone software,

Sell dumps track 1/2 pin ICQ$660702361 sell cvv fullz info

Dumps store - cvv store - dumps 101 track1&2 - Sell cvv good 
Sell DUmps - Transfer WU
Cards dumps - Skim dumps - clone credit - dumps with pin
Contact : 
Gmail : biggirl21091@gmail.com    
ICQ : 660702361

Sell DUMPS :
*** Usa :101

- Visa Classic, MasterCard Standart =55$
- Visa Gold | Platinum | Business, MasterCard Gold | Platinum = 60$
- American Express = $70 ( WITHOUT SID )
- Discover = $80

*** Canada: 101 201

- Visa Classic, MasterCard Standart = 60$
- Visa Gold | Platinum | Business, MasterCard Gold | Platinum = 70$

*** EU, UK: 101 201

- Classic/Standart = 60$
- Gold/Platinum = 70$as
- Business/Signature/Purchase/Corporate/World = 100$

*** Other countries: 101 201

- MasterCard| Visa Classic = 50$
- Visa Gold|Platinum|Corporate|Signature|Business = 70$

*** ASIA/AUSTRALIA/Exotic: 101 201 121

- MasterCard| Visa Classic = $50
- Visa Gold|Platinum|Corporate|Signature|Business = $70

-----------------------------------------
- Sell cvv Us (Visa,Master) = 5$ per 1
- Sell cvv Us (Amex,Dis) = 7$ per 1
- Sell cvv Us vbv ( non vbv ) = 8$/1
- Sell cvv Us Bin 10$ , US Dob 15$
- Sell cvv Us fullz info = 25$ per 1
--------------------------------
- Sell cvv Uk (Visa,Master) = 10$ per 1
- Sell cvv Uk (Amex,Dis) = 12$ per 1
- Sell cvv Uk Bin 15$ , UK Dob 20$
- Sell cvv Uk fullz info = 30$ per 1
--------------------------------
- Sell cvv Ca (Visa,Master) = 10$ per 1
- Sell cvv Ca (Amex,Dis) = 12$ per 1
- Sell cvv Ca Bin 15$ , CA Dob 20$
- Sell cvv Ca fullz info = 30$ per 1
--------------------------------
- Sell cvv Au (Visa,Master) = 12$ per 1
- Sell cvv Au (Amex,Dis) = 15$ per 1
- Sell cvv Au Bin 17$ , AU Dob 20$
- Sell cvv Au fullz info = 30$ per 1
--------------------------------
- Sell cvv Eu (Visa,Master) = 20$ per 1
- Sell cvv Eu (Amex,Dis) = 23$ per 1
- Sell cvv Eu Bin 25$ , EU Dob 30$
- Sell cvv Eu fullz info = 40$ per 1
- Sell cvv Jcb : 22$/1

- Selling Dead Fullz info 180$/1k
[ Name | DOB | Zipcode | State | City | Address | Phone | Mail | SSN | ]

- Sell account paypal verified : 2$/1

I need a long time customer so if you are serious customer, contact me.
Thanks.

hotkey search : sell cvv,sell ccv, sell cvc , sell cc , sell credit card , transfer western union to indian , transfer western union to nigeria , sell dumps pin atm

, sell dumps card , sell clone card ,track 1 , track 2 , sell paypal account , paypal verified have bank card balance , gift card , egift , egift

card , mail pass checked fresh , full info reg bank , transfer money wu , wu transfer cheap fee , rdp , vps buy cvv , buy ccv, buy credit card , debit card , buy dumps card pin atm , egift walmart , egift ebay , ebay amazon , egift besbuy , gift card , egift card gift intunes , egift intunes , gift card intunes cvv , dumps , track , western union , egift

Sell Dumps 101 201 ICQ#671352786 Sell cvv2 Fullz Sell track 1 track 2 with pin EMV Software

ICQ : 671352786
Gmail : Bredteam2002@gmail.com
Skype : Bredteam2002

SELLING : 
Sell EMV Sofware Clone Encode
SELL Dumps with pin
SELL dumps pin
Sell track1 track2 with pin
Sell track 1&2 with pin
Sell track2 with pin
Sell cvv2 full info
Sell cc
Sell UK full
Sell cvv UK full
Sell CA full
Sell cvv CA full
Sell US full
Sell cvv US full
Sell Dead full

How to use MSR606 or MCR200 for write atm card and cashout money.
Clone credit card. use verifone software offine - decrypt card infomation - Clone EMV Chip ( EMV Software )
Sell Dumps 101 - Dumps 201 - Track 2 - Track1 track2 with pin - Track 1/2 with pin
Sell cvv Fullz info.

Verifone offine software = 460$
Clone emv chip software : 1200$

**Dumps pin track 1 track 2 track 1 2 :

--classic 65$ per one
--gold 75$ per one
--platinum 85$ per one

Tag : sell cvv2, sell dumps, sell fullz, sell track2, sell track1/2, dumps track2, emv software, dead fullz, cvv fullz,

hotkey search : MSR605, MSR606, MCR200, skim dumps, card dumps, skimming, cashout, cashout money, 
Clone card, dumps 101, dumps 201, Duplique chip, sell cvv, Sell dumps, sell dumps pin, sell track 1 2, sell track 1, sell track 2,
cvv fullz, fullz info, cvv vbv, cvv non vbv, dumps with pin, dumps pin, track 1, track 2, 
track 1 2, track 1 track 2, withdraw, withdraw money,card writer,EMV CHIP, CHIP EMV,Skim atm, Veriphone vx670, 
skimmer, Atm skimmer, skimming device, forking, atm forking, Verifone offine, verifone software,

carding-market.com Best Shop dumps pin cvv2 fullz online
carding-market.com Sell Dumps track 1/2 with pin Sell cvv2 fullz info 
http://carding-market.com/
Shop cvv online
Shop Dumps online
Cvv Store online
Dumps Store online
Shop track2 online
Buy dumps online
Buy Track2 online
Buy cvv UK FULLZ
Buy cvv US Fullz
BUY cvv EU Fullz
Buy cvv Japan
Sell cvv2 fullz info
Sell Dumps pin
Sell Dumps with pin
Sell track 2 with pin
Sell track1 track2 with pin
Sell track 1&2 with pin
Sell Dumps Us Dumps pin
Sell Dumps UK dumps pin
Sell Dumps EU Dumps pin
Sell DUmps RU Dumps pin
Sell cvv US Fullz info
Sell cvv UK Fullz info
Sell cvv CA Fullz info
Sell cvv AU Fullz info
Sell cvv EU Fullz info
Sell cvv JAPAN Fullz info
Buy Dumps US
BUy Dumps UK
Buy Dumps CA
Buy dumps EU
Buy dumps France
Tag : sell cvv2, sell dumps, sell fullz, sell track2, sell track1/2, dumps track2, emv software, dead fullz, cvv fullz,

hotkey search : MSR605, MSR606, MCR200, skim dumps, card dumps, skimming, cashout, cashout money, 
Clone card, dumps 101, dumps 201, Duplique chip, sell cvv, Sell dumps, sell dumps pin, sell track 1 2, sell track 1, sell track 2,
cvv fullz, fullz info, cvv vbv, cvv non vbv, dumps with pin, dumps pin, track 1, track 2, 
track 1 2, track 1 track 2, withdraw, withdraw money,card writer,EMV CHIP, CHIP EMV,Skim atm, Veriphone vx670, 
skimmer, Atm skimmer, skimming device, forking, atm forking, Verifone offine, verifone software,
Buy Dumps UK
Sell dumps 101
Sell dumps 201

Hi

I have a table generate dby the node Scorer-The Accuracy value apears only on the third row. I want to copy this value to the first and second row.

For  example output of Scorer is:

Roo ID    TruePositive..........Accuracy    Cohenen

No           1559                         ?                   ?

Yes         1131                         ?                   ?

Overall    ?                             0.941           0.878

I want the value of the third row of Accuracy apears on the first two rows as well.

How i should do that?

Malik

Hi

 have a table generate dby the node Scorer-The Accuracy value apears only on the third row. I want to copy this value to the first and second row.

For  example output of Scorer is:

Roo ID    TruePositive..........Accuracy    Cohenen

No           1559                         ?                   ?

Yes         1131                         ?                   ?

Overall    ?                             0.941           0.878

I want the value of the third row of Accuracy apears on the first two rows as well.

How i should do that?

Malik

Hello, I am stuck on a rather "simple issue". We are loading in a 2 GB Datafile. It is in multi line format:

product/productId: B00006HAXW
product/title: Rock Rhythm & Doo Wop: Greatest Early Rock
product/price: unknown
review/userId: A1RSDE90N6RSZF
review/profileName: Joseph M. Kotow
review/helpfulness: 9/9
review/score: 5.0
review/time: 1042502400
review/summary: Pittsburgh - Home of the OLDIES
review/text: I have all of the doo wop DVD's and this one is as good or 

I am parsing it usually with Python:

pyOut = {}

for str in kIn['Col0']:
    tokens = str.split(':', 1)
    if len(tokens):
        if tokens[0] in pyOut:
            column = pyOut[tokens[0]]
        else:
            column = []
        column.append(tokens[1].strip())
        pyOut.update({tokens[0] : column})

And it works fine, but when I am trying to load larger sizes ~32GB. I get this error:
ERROR Python Snippet       0:325:5    Execute failed: java.lang.RuntimeException: java.io.IOException: Cannot run program "python": CreateProcess error=2, The system cannot find the file specified

I would rather just skip python.. given the above data, any recomendations for a native node to transform it?

Thank you

Hi Knimers!

After select some columns to my script, the name of columns change to Knime.in.XXXXX.

Why is that and How can I fix it?

Tks again!

Hi everybody I am trying to calculate the Jaccard string similarity between two pairs of column names using the Java Snippet node using this library, which was added in the Additional Libraries tab. 

By calculate the Jaccard index I mean to add a column. 

I am aware of the string similarity node that comes with the Palladian package, but I still want to use the Jaccard index. 

This is the code that I am using in the node which is slightly modified form this GitHub code

I beg if someone can help me running this code.

// Your custom imports:

import info.debatty.java.stringsimilarity.interfaces.MetricStringDistance;
import info.debatty.java.stringsimilarity.interfaces.NormalizedStringSimilarity;
import info.debatty.java.stringsimilarity.interfaces.NormalizedStringDistance;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import net.jcip.annotations.Immutable;

// system variables
public class JSnippet extends AbstractJSnippet {
  // Fields for input columns
/** Input column: "NAMES TWO" */
  public String c_NAMESTWO;
/** Input column: "NAMES ONE" */
  public String c_NAMESONE;

  // Fields for output columns
/** Output column: "Jaccard" */
  public Double out_Jaccard;

// Your custom variables:

// expression start
    public void snippet() throws TypeException, ColumnException, Abort {
// Enter your code here:

public class Jaccard extends ShingleBased implements
        MetricStringDistance, NormalizedStringDistance,
        NormalizedStringSimilarity {

    /**
     * The strings are first transformed into sets of k-shingles (sequences of k
     * characters), then Jaccard index is computed as |A inter B| / |A union B|.
     * The default value of k is 3.
     *
     * @param k
     */
    public Jaccard(final int k) {
        super(k);
    }

    /**
     * The strings are first transformed into sets of k-shingles (sequences of k
     * characters), then Jaccard index is computed as |A inter B| / |A union B|.
     * The default value of k is 3.
     */
    public Jaccard() {
        super();
    }

    /**
     * Compute jaccard index: |A inter B| / |A union B|.
     * @param s1
     * @param s2
     * @return
     */
    public final double similarity(final String c_NAMESTWO, final String c_NAMESONE) {
        Map<String, Integer> profile1 = getProfile(c_NAMESTWO);
        Map<String, Integer> profile2 = getProfile(c_NAMESONE);

        Set<String> union = new HashSet<String>();
        union.addAll(profile1.keySet());
        union.addAll(profile2.keySet());

        int inter = 0;

        for (String key : union) {
            if (profile1.containsKey(key) && profile2.containsKey(key)) {
                inter++;
            }
        }

        return 1.0 * inter / union.size();
    }


    /**
     * Distance is computed as 1 - similarity.
     * @param s1
     * @param s2
     * @return
     */
    public final double distance(final String c_NAMESTWO, final String c_NAMESONE) {
        out_Jaccard = return 1.0 - similarity(c_NAMESTWO, c_NAMESONE);
    }
}

I am also attaching the workflow.

Best Regards

How do I use the Selenium Nodes to scroll the browser window and ensure an element is visible?

I often encounter the Selenium error "Element is not clickable at point(x,y). Other element would receive the click".

Some research suggests that I first need to ensure that the element is visible on the screen before it can be clicked. The sample JavaScript I've found looks like this:

((JavascriptExecutor)driver).executeScript("window.scrollTo(0,"+elementToClick.getLocation().x+")

... and ...

WebElement element = driver.findElement(By.id("id_of_element"));
((JavascriptExecutor) driver).executeScript("arguments[0].scrollIntoView(true);", element);
Thread.sleep(500); 

But I'm having trouble dropping this code into the Execute JavaScript Selenium node.

Even this simple script throws a "window.ScrollTo is not a function" error:

window.ScrollTo(0, 1000);

I'm using Firefox but have also encountered the same issue in Chrome. Any advice?

Hi All,

I'm using an XLS Reader node as input data file in my workflow.  I need to check if a sheet name exists and trap the error if the sheet is not present.  Is it possible to do that in Knime?  If yes, how?

Thanks in advance for your help,

Cheers,

Claire

Hello

I have a workflow that saves images from small molecules (Renderer to Image> Image Column Writer) with the output name that is based on the row number (i.e. "Row0.png" to "Row200.png" if I have 201 molecules).

If possible, I would like to save the images using the name of the small molecule that is contained in another column of my input table.

I am relatively new to KNIME (I have put my current workflow together doing online searches) and I seem unable to come up with the correct Google querry that will put me in the right direction.

I look forward to hearing from more advanced users.

Cheers

Charles

Hi there,

I would like to ask you about new functionalities in KNIME 3.2.1.

We have moved our Random Forest workflow for data analysis from Knime2 to Knime3. We were using Weka's Random Forest node and were getting good results. Now, after moving to Knime3 we decided to give it a try with the new Random Forest Learner/Predictor nodes for our classification task. Not only was your node way faster in our workflow (we only exchanged the RF nodes), but it seems that the classification works better than with Weka's RF node. We are now trying to pinpoint the reason for this.

We are using information gain for splitting (although we get the same results with Gini and information gain ratio). We also use the same number of trees (500) and default numbers of features in both nodes.
Theoretically, using information gain should be equivalent to what Weka node was doing, right?. However, our data has a lot of missing values, ~30% in some rows. Weka was using surrogate splitting to handle missing values, while you point to XGBoost's github in your node description. Does it mean that you are using exactly XGBoost's approach to missing data instead of surrogate splitting?

Best regards,
Piotr

  In my Knime workflow I have used a Database Reader node to fetch data from a MySQL database. I have written SQL query to select the required data. But the node fails execution with below error message

"Database Reader 266:373:368 - ERROR: Execute failed: Error writing file '/tmp/MYv30nfW' (Errcode: 28)"

 What is the reason for this error? Why is a file being created?

Dear all,

I would like to thank you for the very useful PDB Connector node.

I notice something weird, or maybe I don't put the right ID.

I would like to find all structures corresponding to a particular UniprotID.

For example, P10827.

So I tried to put it in IDs and Keywords tab, as UniprotKB Accession Number(s) but it was unsuccessful.

If I put this ID in Text Search section, there are missing some structures.

Could you please help me?

Regards,

Emilie

Is there an example of how to pass data (table and variables) to a Call Local Workflow and a Call Remote Workflow node?

David

Hi,

Is there a way to keep the Knime instance (org.knime.product.KNIME_BATCH_APPLICATION)  in memory while running a series of Workflows in sequence using a script?

I currently have a series of calls to run Knime in batch mode but each time the entire instance is loaded and unloaded from memory which seems unnecessary. I only need it in memory for the duration of the entire batch run though (which runs abour 7 workflows in sequence).

Thanks,

JGP