VESPA | scale Evolutionary and Selective Pressure Analyses | Awesome List library

 by   aewebb80 Perl Version: 1.0.1 License: GPL-3.0

kandi X-RAY | VESPA Summary

kandi X-RAY | VESPA Summary

VESPA is a Perl library typically used in Awesome, Awesome List applications. VESPA has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Thanks for taking an interest in our pipeline. We hope you find the resources we provide here useful in getting you set up to analyse and interpret your data. To reference VESPA: Documentation is now hosted on ReadTheDocs.
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              VESPA has a low active ecosystem.
              It has 8 star(s) with 7 fork(s). There are 3 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 14 open issues and 4 have been closed. On average issues are closed in 84 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of VESPA is 1.0.1

            kandi-Quality Quality

              VESPA has no bugs reported.

            kandi-Security Security

              VESPA has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              VESPA is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              VESPA releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of VESPA
            Get all kandi verified functions for this library.

            VESPA Key Features

            No Key Features are available at this moment for VESPA.

            VESPA Examples and Code Snippets

            copy iconCopy
            $ tar -xvzf VESPA.tar.gz
            $ cd VESPA
            $ chmod +x \*Codeml\*.pl
            $ sudo mv \*Codeml\*.pl /usr/local/bin
            $ sudo mv CodemlWrapper/ /Library/Perl/5.XX/
            Note: Replace “5.XX” in the following command to the version of perl used by your system. (perl –v)
              
            VESPA: Very large-scale Evolutionary and Selective Pressure Analyses,Installation
            Perldot img2Lines of Code : 4dot img2License : Strong Copyleft (GPL-3.0)
            copy iconCopy
            $ tar -xvzf VESPA.tar.gz
            $ cd VESPA
            $ chmod +x vespa.py
            $ sudo mv vespa.py /usr/local/bin
              

            Community Discussions

            QUESTION

            Command works inside a docker container but fails with docker exec
            Asked 2021-May-30 at 19:47

            I'm using containerized Vespa.ai DB, and I want to execute the following commands from the host:

            1. vespa-stop-services
            2. vespa-remove-index
            3. vespa-start-services

            If I execute the following vespa-stop-services && vespa-remove-index && vespa-start-services from my shell after I attach the container, it works fine. But when I use docker exec it fails.

            I tried the following commands:

            ...

            ANSWER

            Answered 2021-May-30 at 19:47

            You need to specify the location of these commands when running from the parent host system

            The following works/should work :

            Source https://stackoverflow.com/questions/67763017

            QUESTION

            How to provide OpenNLP model for tokenization in vespa?
            Asked 2021-May-20 at 16:25

            How do I provide an OpenNLP model for tokenization in vespa? This mentions that "The default linguistics module is OpenNlp". Is this what you are referring to? If yes, can I simply set the set_language index expression by referring to the doc? I did not find any relevant information on how to implement this feature in https://docs.vespa.ai/en/linguistics.html, could you please help me out with this?

            Required for CJK support.

            ...

            ANSWER

            Answered 2021-May-20 at 16:25

            Yes, the default tokenizer is OpenNLP and it works with no configuration needed. It will guess the language if you don't set it, but if you know the document language it is better to use set_language (and language=...) in queries, since language detection is unreliable on short text.

            However, OpenNLP tokenization (not detecting) only supports Danish, Dutch, Finnish, French, German, Hungarian, Irish, Italian, Norwegian, Portugese, Romanian, Russian, Spanish, Swedish, Turkish and English (where we use kstem instead). So, no CJK.

            To support CJK you need to plug in your own tokenizer as described in the linguistics doc, or else use ngram instead of tokenization, see https://docs.vespa.ai/documentation/reference/schema-reference.html#gram

            n-gram is often a good choice with Vespa because it doesn't suffer from the recall problems of CJK tokenization, and by using a ranking model which incorporates proximity (such as e.g nativeRank) you'l still get good relevancy.

            Source https://stackoverflow.com/questions/67623459

            QUESTION

            Does Vespa support field projection for selected retrieval?
            Asked 2021-May-17 at 08:07

            Does Vespa support field projection for selected retrieval? (Similar to https://www.elastic.co/guide/en/elasticsearch/reference/current/search-fields.html in Elastic search)

            Interested in:

            • select all fields except a,b
            • select fields *_name - [select all field names ending with _name]
            • exclude fields *_name - [exclude all field names ending with _name]
            ...

            ANSWER

            Answered 2021-May-17 at 08:07

            Vespa don't support this today but feature requests are welcome over at https://github.com/vespa-engine/vespa/issues

            You can configure summary classes which is also more efficient then resolving this at query time. See https://docs.vespa.ai/en/document-summaries.html

            Source https://stackoverflow.com/questions/67562204

            QUESTION

            Is there a way of performing a weighted elementSimilarity with Vespa?
            Asked 2021-Mar-22 at 20:33

            I having trouble dealing with multivalue query items and fields in terms of element similarity. For example, if we have an array of strings like such:

            ...

            ANSWER

            Answered 2021-Mar-22 at 20:15

            There are many ways to accomplish this but what is best depends on if you need free text style matching (linguistic processing of the string including tokenization and stemming) or not. It also depends on if this is just a ranking signal for documents that are already retrieved or used to retrieve documents.

            If you don't need free text style matching but instead can use exact matching without linguistics processing (e.g using a fixed vocabulary) and this color ranking is just another ranking signal you should consider looking at using tensor ranking instead. Tensors are useful for ranking documents that are retrieved by the query operators, you cannot retrieve using a tensor (except for dense single order tensors using approximate nearest neighbor search). See tensor guide https://docs.vespa.ai/en/tensor-user-guide.html.

            If you need free text style matching there are also several approaches. In the below example I assume that you want to have text style matching and that a query term 'purple' should match the document with 'black and purple'. See matching documentation https://docs.vespa.ai/en/reference/schema-reference.html#match

            If you define the field colors like this

            Source https://stackoverflow.com/questions/66751806

            QUESTION

            How to include a OneHot in an ONNX coming from PyTorch
            Asked 2021-Mar-22 at 13:05

            I'm using PyTorch to train neural-net and output them into ONNX. I use these models in a Vespa index, which loads ONNXs through TensorRT. I need one-hot-encoding for some features but this is really hard to achieve within the Vespa framework.

            Is it possible to embed a one-hot-encoding for some given features inside my ONNX net (e.g. before the network's representation) ? If so, how should I achieve this based on a PyTorch model ?

            I already noticed two things:

            EDIT 2021/03/11: Here is my workflow:

            • training learning-to-rank models via PyTorch
            • exporting them as ONNX
            • importing these ONNX into my Vespa index in order to rank any query's results thanks to the ONNX model. Under the hood, Vespa uses TensorRT for inference (so I use Vespa's ONNX model evaluation)
            ...

            ANSWER

            Answered 2021-Mar-10 at 08:27

            If PyTorch can't export the OneHot operator to ONNX I think your best option is to ask them to fix that?

            Or, if you can extract the conversion from your model, such that the one-hot-encoded tensor is an input to your network, you can do that conversion on the Vespa side by writing a function supplying the one-hot tensor by converting the source data to it, e.g

            Source https://stackoverflow.com/questions/66544994

            QUESTION

            Moving cell data to respective row based on numbers in another column
            Asked 2021-Mar-10 at 22:52

            I have a list of parts that have a part code. I need to align columns B-E to match the list of numbers in column A, leaving blanks where the data has moved down. The number in column B should match the number in column A.

            A simple sort will not do because ColumnB,D,E has fewer entries than ColumnA and some numbers in ColumnB are not in ColumnA.

            A B C D E '005023 5025 oil-filler-level-plug-genuine-005025 GENUINE PIAGGIO, OIL FILLER PLUG. 1.5 '005024 5027 rear-hub-cone-shim-lambretta-005027 LAMBRETTA REAR HUB CONE SHIM. 1.25 '005025 5031 piston-s2-s3-524mm-125cc-gol-005031 ITALIAN MADE BY GOL 46.5 '005027 5032 exhaust-simonini-px-125-black-005032 135 '005029 5036 floor-runner-kit-vespa-px-125-200-005036 GOOD QUALITY, ITALIAN MADE, COMLETE FLOOR RUNNER KIT 25 '005031 5037 rear-light-grey-top-for-vespa-rally-005037 5 '005032 5038 front-hub-back-plate-chrome-005038 Suitable for all Lambretta S1 S2 S3 models 45 '005033 5041 clutch-plates-surflex-cosa-vespa-px-005041 TOP QUALITY ITALIAN COSA CLUTCH PLATES MADE BY SURFLEX. 16 '005036 5044 points-ducati-style-lambretta-005044 TOP QUALITY,CONTACT BREAKER POINT FOR LAMBRETTA 10 '005037 5045 condensor-ducati-dansi-li-sx-tv-gp-005045 DUCATI TYPE CONDENSOR FOR MOST LAMBRETTAS. 9 '005038 5047 panel-handle-lock-mechanisms-s1-s2-005047 TOP QUALITY, LAMBRETTA SERIES 1 & 2 SIDE PANEL HANDLE MECHANISM KIT. 41 '005040 5049 fork-push-rods-pistons-s1-2-3-005049 TOP QUALITY LAMBRETTA FORK PUSH ROD PISTON SET. 12 '005041 5050 fuel-tank-vespa-gs-160-180ss-rally-005050 100 '005044 5051 wheel-rim-chrome-10-inch-vespa-005051 TOP QUALITY, CHROMED WHEEL RIMS ( 1 X WHEEL ) 38 '005045 5052 carb-box-top-carbon-look-pe-px-efl-005052 VBB SPRINT GT PX 22 '005047 5054 input-shaft-needle-rollers-px-21-005054 ITALIAN MADE SET OF 23 INPUT SHAFT NEEDLE ROLLER BEARINGS 5 '005049 5055 air-hose-clips-19mm-series-2-carb-005055 LAMBRETTA SERIES1 AND 2 AIR HOSE CLIPS FOR STANDARD 5 '005050 5056 air-hose-vespa-vna-005056 6.5 ...

            ANSWER

            Answered 2021-Mar-10 at 22:52

            Add a reference from the VBA editor (Tools -> References...) to Microsoft ActiveX Data Objects; choose the latest version, usually 6.1

            Then you could write VBA code like the following:

            Source https://stackoverflow.com/questions/66530748

            QUESTION

            Vespa.ai: How to make an array of floats handle null values?
            Asked 2020-Nov-30 at 12:48

            I am trying to make a simple Vespa application, where one of my data fields are an Array. However the array contains some null values. For instance an array like: [2.0,1.4,null,5.6,...].

            What can I use instead of float to represent elements in the array?

            ...

            ANSWER

            Answered 2020-Nov-30 at 12:48

            Seems like you want to use a sparse tensor field instead since some addresses does not have a value. x{} denotes a sparse tensor, x[128] is an example of a dense tensor. See https://docs.vespa.ai/documentation/tensor-user-guide.html for an intro to vespa tensor fields.

            Source https://stackoverflow.com/questions/65073713

            QUESTION

            How to properly invoke search from another component
            Asked 2020-Oct-27 at 12:50

            Hi I am trying to execute a search from within a processing chain. Currently I am creating the Execution in the following way

            ...

            ANSWER

            Answered 2020-Oct-27 at 12:50

            Yes, the stub returned by Execution.Context.createContextStub() is just for testing and doesn't provide all the information that is needed. Instead:

            1. Get a com.yahoo.search.searchchain.ExecutionFactory injected in your component (by declaring it as a parameter in the constructor).

            2. To get an execution, call executionFactory.newExecution(chain)

            Source https://stackoverflow.com/questions/64553746

            QUESTION

            Unable to setup Vespa container on multiple instances
            Asked 2020-Oct-15 at 20:15

            I have two instances where I have to deploy Vespa on a docker container. One container will act as a config cluster, container cluster, and content cluster while the other will act as a container cluster and content cluster.

            host.xml file for the application looks like:

            ...

            ANSWER

            Answered 2020-Oct-15 at 20:15

            To get this working you should avoid having underscores in the network name, use the fully qualified name for the config server and name the containers to get DNS working.

            Create the network on a manager swarm host:

            Source https://stackoverflow.com/questions/64371439

            QUESTION

            Recall returns nothing when querying rank-profile
            Asked 2020-Oct-12 at 18:14

            I have a sample Vespa instance and I want to train a lightgbm model from the rank-profile. https://docs.vespa.ai/documentation/learning-to-rank.html

            However, anytime I specify the recall with the docID, I get 0 hits. I'm using example code from here: https://github.com/vespa-engine/sample-apps/blob/master/text-search/src/python/collect_training_data.py

            ...

            ANSWER

            Answered 2020-Oct-12 at 18:14

            The collect script/function expects that there is a field called id in your document schema. If you alter the script to use the uri field instead you should be able to retrieve the documents.

            Source https://stackoverflow.com/questions/64322983

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install VESPA

            The main VESPA wrapper is written in Python, while the CodeML wrapper is written in Perl. To begin, we recommend downloading a versioned tarball from the releases page.
            This approach installs many but not all of the binary dependencies.
            Install Anaconda or Miniconda
            Download release, decompress and cd inside it
            Create the conda environment: conda env create -f vespa_conda.yml
            Activate it: source activate vespa27
            Run VESPA with python vespa.py

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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            gh repo clone aewebb80/VESPA

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            git@github.com:aewebb80/VESPA.git

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