# Uncategorized **URL:** https://forum.tiledb.com/c/uncategorized/1.md?page=2 [Latest](https://forum.tiledb.com/latest.md) · [Categories](https://forum.tiledb.com/categories.md) **Page:** 3 --- ## [Importing tiledb dataset created with tiledb-vcf into R](https://forum.tiledb.com/t/importing-tiledb-dataset-created-with-tiledb-vcf-into-r/605)
**Author:** [@gmauro](https://forum.tiledb.com/u/gmauro)\ **Replies:** 4\ **Last updated:** [August 9, 2023, 5:11pm UTC](https://forum.tiledb.com/t/importing-tiledb-dataset-created-with-tiledb-vcf-into-r/605 "2023-08-09T17:11:14Z")
Hi everybody, I have created a tiledb dataset using tiledb-vcf and now I am trying to import it in R # if needed: install.packages('tiledb') library(tiledb) gwasdb\_uri \<- "/datasets/blood\_traits/data" gwasdb \<- tiledb:… --- ## [Is vacuuming thread-safe?](https://forum.tiledb.com/t/is-vacuuming-thread-safe/608)
**Author:** [@llazze97](https://forum.tiledb.com/u/llazze97)\ **Replies:** 2\ **Last updated:** [August 7, 2023, 8:53am UTC](https://forum.tiledb.com/t/is-vacuuming-thread-safe/608 "2023-08-07T08:53:38Z")
Good day everyone, I wanted to ask a question because the documentation contradicts itself about vacuuming, and I can’t understand if it’s thread-safe like consolidation or not. These are the links in question. --- ## [Are files getting corrupted during dataset creation using tiledbvcf?](https://forum.tiledb.com/t/are-files-getting-corrupted-during-dataset-creation-using-tiledbvcf/597)
**Author:** [@Vibhorgupta31](https://forum.tiledb.com/u/Vibhorgupta31)\ **Replies:** 8\ **Last updated:** [July 19, 2023, 9:39pm UTC](https://forum.tiledb.com/t/are-files-getting-corrupted-during-dataset-creation-using-tiledbvcf/597 "2023-07-19T21:39:10Z")
Hello, I am using tiledbvcf to create a dataset. I have to ingest 1700 files in the dataset. When I started the dataset creation process, and I check for the files the process was going smoothly . I queried in between t… --- ## [What could affect array opening time?](https://forum.tiledb.com/t/what-could-affect-array-opening-time/594)
**Author:** [@ohana](https://forum.tiledb.com/u/ohana)\ **Replies:** 3\ **Last updated:** [July 18, 2023, 12:47pm UTC](https://forum.tiledb.com/t/what-could-affect-array-opening-time/594 "2023-07-18T12:47:43Z")
Hello, I have an array in S3 with ~96GB of data stored. The array contains ~660,604 objects. When I try to open the array, it hangs for minutes. Although, I can still read the schema. Does the number of fragments writte… --- ## [Recent blog posts!](https://forum.tiledb.com/t/recent-blog-posts/592)
**Author:** [@ihnorton](https://forum.tiledb.com/u/ihnorton)\ **Replies:** 0\ **Last updated:** [June 29, 2023, 6:10pm UTC](https://forum.tiledb.com/t/recent-blog-posts/592 "2023-06-29T18:10:45Z")
Hi all, we have released several blog posts recently which folks here might be interested in: Introduction to TileDB Cloud User-defined functions Introduction to TileDB Cloud Task graphs TileDB 101: Population Genomics … --- ## [Optimizing the reads for sparse arrays](https://forum.tiledb.com/t/optimizing-the-reads-for-sparse-arrays/582)
**Author:** [@Ak\_J](https://forum.tiledb.com/u/Ak_J)\ **Replies:** 9\ **Last updated:** [June 27, 2023, 2:13pm UTC](https://forum.tiledb.com/t/optimizing-the-reads-for-sparse-arrays/582 "2023-06-27T14:13:44Z")
Hi, I am exploring data storage in TileDB array using Python API and I am quite fascinated by its Time Travel feature. I am using the TileDB-core version 2.15.2 and TileDB-Py version 0.21.3 . I store a 2-D sparse data… --- ## [Performance on blobs stores with small arrays](https://forum.tiledb.com/t/performance-on-blobs-stores-with-small-arrays/588)
**Author:** [@p-yv](https://forum.tiledb.com/u/p-yv)\ **Replies:** 1\ **Last updated:** [June 27, 2023, 2:04pm UTC](https://forum.tiledb.com/t/performance-on-blobs-stores-with-small-arrays/588 "2023-06-27T14:04:03Z")
Hi, I am working with samples of heterogeneous data. One may consider a dict of arrays with various shapes. I am considering using a group represent my dict and then storing all of the different arrays independently. T… --- ## [Azure Blob storage backend](https://forum.tiledb.com/t/azure-blob-storage-backend/503)
**Author:** [@gruffaren](https://forum.tiledb.com/u/gruffaren)\ **Replies:** 2\ **Last updated:** [June 15, 2023, 1:30pm UTC](https://forum.tiledb.com/t/azure-blob-storage-backend/503 "2023-06-15T13:30:17Z")
Hi, As mentioned in other threads there is a bit of lacking documentation when it comes to using Azure and GCS as storage backends. While waiting for such documentation to be created, I’d like to share the problem I’m … --- ## [Overwriting at an index, vs duplication](https://forum.tiledb.com/t/overwriting-at-an-index-vs-duplication/583)
**Author:** [@Dave\_L](https://forum.tiledb.com/u/Dave_L)\ **Replies:** 0\ **Last updated:** [June 6, 2023, 8:21pm UTC](https://forum.tiledb.com/t/overwriting-at-an-index-vs-duplication/583 "2023-06-06T20:21:28Z")
I am using the from\_pandas function to write new data to an existing array. I am attempting to overwrite data at existing indices, but instead the array is growing by the number of items that I am trying to overwrite (ex… --- ## [Update / change the range of a dimension after array creation](https://forum.tiledb.com/t/update-change-the-range-of-a-dimension-after-array-creation/578)
**Author:** [@Dave\_L](https://forum.tiledb.com/u/Dave_L)\ **Replies:** 2\ **Last updated:** [May 31, 2023, 2:13pm UTC](https://forum.tiledb.com/t/update-change-the-range-of-a-dimension-after-array-creation/578 "2023-05-31T14:13:08Z")
I was wondering if there is a way to increase the range of a dimension once an array has been created. For example, if I have a “timestamp” dimension of type datetime64, and when I created the array the range of the dime… --- ## [How to write to a sparse array slice with a time dimension. Getting: ValueError: Could not convert object to NumPy datetime](https://forum.tiledb.com/t/how-to-write-to-a-sparse-array-slice-with-a-time-dimension-getting-valueerror-could-not-convert-object-to-numpy-datetime/579)
**Author:** [@Dave\_L](https://forum.tiledb.com/u/Dave_L)\ **Replies:** 0\ **Last updated:** [May 30, 2023, 6:36pm UTC](https://forum.tiledb.com/t/how-to-write-to-a-sparse-array-slice-with-a-time-dimension-getting-valueerror-could-not-convert-object-to-numpy-datetime/579 "2023-05-30T18:36:23Z")
I would like to update values of a particular attribute at a particular slice in a sparse array. I read on the tiledb docs that currently this is not supported; I have to write to all attributes when performing a write o… --- ## [Query vcf header usiung tiledbvcf](https://forum.tiledb.com/t/query-vcf-header-usiung-tiledbvcf/570)
**Author:** [@Vibhorgupta31](https://forum.tiledb.com/u/Vibhorgupta31)\ **Replies:** 2\ **Last updated:** [May 17, 2023, 2:31am UTC](https://forum.tiledb.com/t/query-vcf-header-usiung-tiledbvcf/570 "2023-05-17T02:31:13Z")
Hi, I am new to the tileDB, and I just started to use tileDBvcf for a project. I wanted to know, how can I use tileDBVCF to query the metadata / vcf header data of a vcf file for eg information about refrence genome, i… --- ## [Python GCS support on Mac](https://forum.tiledb.com/t/python-gcs-support-on-mac/567)
**Author:** [@kdmnancefp](https://forum.tiledb.com/u/kdmnancefp)\ **Replies:** 2\ **Last updated:** [May 10, 2023, 10:53pm UTC](https://forum.tiledb.com/t/python-gcs-support-on-mac/567 "2023-05-10T22:53:29Z")
Hello, I am on a Macbook Pro, running Ventura, and Python 3.11.3. I installed the Python tiledb library via pip from PyPI. It installed version 0.21.3, and more specifically this wheel: tiledb-0.21.3-cp311-cp311-macosx… --- ## [Integrating with a flask/Dash application (Python)](https://forum.tiledb.com/t/integrating-with-a-flask-dash-application-python/563)
**Author:** [@Dave\_L](https://forum.tiledb.com/u/Dave_L)\ **Replies:** 3\ **Last updated:** [May 2, 2023, 11:53am UTC](https://forum.tiledb.com/t/integrating-with-a-flask-dash-application-python/563 "2023-05-02T11:53:26Z")
If I wish to use tileDB as my primary database and have a Dash-plotly application visualize the data stored in the array, what is the best way to handle the following: 1.) Is there an existing callback in tileDB that in… --- ## [Deployment of Database](https://forum.tiledb.com/t/deployment-of-database/565)
**Author:** [@mdylan2](https://forum.tiledb.com/u/mdylan2)\ **Replies:** 1\ **Last updated:** [April 29, 2023, 1:53am UTC](https://forum.tiledb.com/t/deployment-of-database/565 "2023-04-29T01:53:22Z")
Hi I am building a backend API to serve my TileDB database, which has been built by a custom script. I want to use an API to abstract away the TileDB syntax from consumers. We want to have a highly performant (speed-wis… --- ## [Multi-value attributes and MariaDB](https://forum.tiledb.com/t/multi-value-attributes-and-mariadb/562)
**Author:** [@vkaramanis](https://forum.tiledb.com/u/vkaramanis)\ **Replies:** 6\ **Last updated:** [April 28, 2023, 9:16am UTC](https://forum.tiledb.com/t/multi-value-attributes-and-mariadb/562 "2023-04-28T09:16:51Z")
Hi, I have a TileDB array, initialized in python, which has a 3-value fixed-length attribute: dtype(“float32, float32, float32”) I have connected this array with a MariaDB server to run SQL queries, but when I am \* sel… --- ## [Tips on Consolidating Sparse Arrays \[Python\]](https://forum.tiledb.com/t/tips-on-consolidating-sparse-arrays-python/559)
**Author:** [@mdylan2](https://forum.tiledb.com/u/mdylan2)\ **Replies:** 4\ **Last updated:** [April 14, 2023, 10:32am UTC](https://forum.tiledb.com/t/tips-on-consolidating-sparse-arrays-python/559 "2023-04-14T10:32:43Z")
Hello, I’m trying to run consolidation using multi-processing. My EC2 instance consists of 8 cores, 16 vCPUs, and 128 GiB of memory (EC2 instance r5.4xlarge). I am interested in consolidating fragments for massive spars… --- ## [Non-empty domain after write in global layout](https://forum.tiledb.com/t/non-empty-domain-after-write-in-global-layout/556)
**Author:** [@fabian-na](https://forum.tiledb.com/u/fabian-na)\ **Replies:** 4\ **Last updated:** [April 4, 2023, 9:05pm UTC](https://forum.tiledb.com/t/non-empty-domain-after-write-in-global-layout/556 "2023-04-04T21:05:02Z")
We want to store dense chunked data in the tiledb format using the C++ API and the TILEDB\_GLOBAL\_ORDER layout for writing. For doing so, fill values are added to the data such that it fits the specified tiling. Writing t… --- ## [From\_pandas correct way to set nullable attributes](https://forum.tiledb.com/t/from-pandas-correct-way-to-set-nullable-attributes/557)
**Author:** [@Dave\_L](https://forum.tiledb.com/u/Dave_L)\ **Replies:** 2\ **Last updated:** [April 4, 2023, 2:16am UTC](https://forum.tiledb.com/t/from-pandas-correct-way-to-set-nullable-attributes/557 "2023-04-04T02:16:52Z")
Hi, When I look at the Array schema produced by calling the from\_pandas Data Import method on my dataframe, I see that nullable=false for all of my attributes. I am trying to create a Sparse Array, and would like to (fo… --- ## [Tiledb performance with sparse point cloud data](https://forum.tiledb.com/t/tiledb-performance-with-sparse-point-cloud-data/544)
**Author:** [@Jagge](https://forum.tiledb.com/u/Jagge)\ **Replies:** 8\ **Last updated:** [March 23, 2023, 6:16pm UTC](https://forum.tiledb.com/t/tiledb-performance-with-sparse-point-cloud-data/544 "2023-03-23T18:16:09Z")
We are currently testing if we could use tiledb in our project but are unhappy with the performance, namely slicing from point cloud data seems to take quite a bit of time. Our current test case consists of a point cloud… --- ## [Deleting coordinates from sparse array](https://forum.tiledb.com/t/deleting-coordinates-from-sparse-array/548)
**Author:** [@mdylan2](https://forum.tiledb.com/u/mdylan2)\ **Replies:** 2\ **Last updated:** [March 21, 2023, 5:52pm UTC](https://forum.tiledb.com/t/deleting-coordinates-from-sparse-array/548 "2023-03-21T17:52:28Z")
Hey, is there any way to delete coordinates from a sparse array? I noticed there is a “delete” mode on the docs - is that for the entire array or can I specify a sub-array? Asking because I get junk values when I run: … --- ## [Re-Indexing String Dimensions For Sparse Arrays](https://forum.tiledb.com/t/re-indexing-string-dimensions-for-sparse-arrays/549)
**Author:** [@Dave\_L](https://forum.tiledb.com/u/Dave_L)\ **Replies:** 2\ **Last updated:** [March 17, 2023, 1:51pm UTC](https://forum.tiledb.com/t/re-indexing-string-dimensions-for-sparse-arrays/549 "2023-03-17T13:51:23Z")
Hi I was wondering if re-indexing string dimensions (via a move like operation) on sparse arrays is possible. For example, If I collect data sequentially in time and I don’t yet have the value of a certain property (let’… --- ## [Debugging Segmentation Fault While Loading an Array](https://forum.tiledb.com/t/debugging-segmentation-fault-while-loading-an-array/546)
**Author:** [@af-gh](https://forum.tiledb.com/u/af-gh)\ **Replies:** 3\ **Last updated:** [March 14, 2023, 8:10pm UTC](https://forum.tiledb.com/t/debugging-segmentation-fault-while-loading-an-array/546 "2023-03-14T20:10:50Z")
The following code crashes with a seg fault: In \[1\]: import tiledb In \[2\]: loaded = tiledb.open('/path/to/my/data') In \[3\]: loaded.df\[:\] Segmentation fault (core dumped) Are there any suggested approaches to debuggin… --- ## [Confused by dimensions vs attributes need help designing backend for project](https://forum.tiledb.com/t/confused-by-dimensions-vs-attributes-need-help-designing-backend-for-project/541)
**Author:** [@Dave\_L](https://forum.tiledb.com/u/Dave_L)\ **Replies:** 5\ **Last updated:** [March 10, 2023, 9:04pm UTC](https://forum.tiledb.com/t/confused-by-dimensions-vs-attributes-need-help-designing-backend-for-project/541 "2023-03-10T21:04:56Z")
I am trying to understand when I should be using attributes or dimensions for storing 1-D arrays in time. I have a 1-D array with n elements representing an IR spectra. At different points in time (at the second level) … --- ## [Quickly get dimension Mapping for sparse array](https://forum.tiledb.com/t/quickly-get-dimension-mapping-for-sparse-array/532)
**Author:** [@mdylan2](https://forum.tiledb.com/u/mdylan2)\ **Replies:** 1\ **Last updated:** [March 6, 2023, 9:27pm UTC](https://forum.tiledb.com/t/quickly-get-dimension-mapping-for-sparse-array/532 "2023-03-06T21:27:21Z")
What’s the most efficient way to get a dimension mapping of the sparse array i.e. the dot product of the non\_empty\_domains? Context: I have a 3 dimensional array, where dimensions are called idx, dataset\_name, idx\_name.… --- ## [Tiledb cache management](https://forum.tiledb.com/t/tiledb-cache-management/320)
**Author:** [@tiphaineruy](https://forum.tiledb.com/u/tiphaineruy)\ **Replies:** 3\ **Last updated:** [March 6, 2023, 4:05pm UTC](https://forum.tiledb.com/t/tiledb-cache-management/320 "2023-03-06T16:05:21Z")
Hello ! I was wondering a bit on how to optimize tile fetching and caching on arrays. So from what I’ve gathered. The only way to cache a cloud array for now is by playing with the parameter sm.tile\_cache\_size. Which … --- ## [How to speedup reading form a sparse TileDB array](https://forum.tiledb.com/t/how-to-speedup-reading-form-a-sparse-tiledb-array/529)
**Author:** [@Johannes](https://forum.tiledb.com/u/Johannes)\ **Replies:** 3\ **Last updated:** [February 21, 2023, 9:29pm UTC](https://forum.tiledb.com/t/how-to-speedup-reading-form-a-sparse-tiledb-array/529 "2023-02-21T21:29:07Z")
Hello, we use TileDB to store GPR-Data (Ground Penetrating Radar) which is in our case voxel data. A typical Dataset has dimension of around 10000x10000x100, which we store as a sparse TileDB array. Writing to TileDB … --- ## [Geospatial Workflow Question](https://forum.tiledb.com/t/geospatial-workflow-question/527)
**Author:** [@diehl](https://forum.tiledb.com/u/diehl)\ **Replies:** 4\ **Last updated:** [February 7, 2023, 2:11am UTC](https://forum.tiledb.com/t/geospatial-workflow-question/527 "2023-02-07T02:11:08Z")
Hello all, I have a set of vector geometries representing land management conditions over the Western U.S. and I need to transform these vector layers into a multidimensional raster for further analysis. I would love to… --- ## [TileDB 2.14.0 Released](https://forum.tiledb.com/t/tiledb-2-14-0-released/525)
**Author:** [@ihnorton](https://forum.tiledb.com/u/ihnorton)\ **Replies:** 0\ **Last updated:** [January 23, 2023, 10:23pm UTC](https://forum.tiledb.com/t/tiledb-2-14-0-released/525 "2023-01-23T22:23:49Z")
Hello, We have released TileDB Embedded 2.14.0. Associated platform package updates for R, Python, C#, Java, and MariaDB are available. In addition to fixes and performance improvements, this release contains several ne… --- ## [\[TileDB::Filter\] Error: Error incorrect unfiltered tile size allocated](https://forum.tiledb.com/t/tiledb-filter-error-error-incorrect-unfiltered-tile-size-allocated/514)
**Author:** [@Hao](https://forum.tiledb.com/u/Hao)\ **Replies:** 3\ **Last updated:** [December 1, 2022, 12:11pm UTC](https://forum.tiledb.com/t/tiledb-filter-error-error-incorrect-unfiltered-tile-size-allocated/514 "2022-12-01T12:11:06Z")
Hallo everyone, I’m following the tutorial to read some arrays. It’s just: with tiledb.DenseArray(database\_path, mode=‘r’) as arr: \*\* data = arr\[:\]\*\* I got this error: \[TileDB::Filter\] Error: Error incorrect unfi… [Previous page](https://forum.tiledb.com/c/uncategorized/1.md?page=1) [Next page](https://forum.tiledb.com/c/uncategorized/1.md?page=3)