Open jarrodscott opened 6 years ago
oh, and let me know if you need the files and I can pass them along
Hey @jarrodscott, Thanks for the heads up. I have partly fixed this issue, the import error was coming from the server codebase. So now you can push projects with a collection. But there is another issue on anvi-server, it should load collection automatically and draw the tree but it does not. I will try to address that issue too. Thank you again for detailed error report!
Hi @ozcan sweet success! thanks for the fast fix.
except it never actually loads on https://anvi-server.org/
I can see it on My Projects
page and also download the data.
Hey @jarrodscott, you are right. I have inspected error logs and looked at the files and noticed couple issues.
anvi-export-table
exports all the contents of the table but sometimes those tables do not match the format anvi-server wants, for example in your state.json file there are columns for last_modified
and name
like in the table. but the server only needs one content
field.
In additional data file, the first column is entry_id
which is a just unique number for each record in the database but anvi-server does not want in that format. The first column needs to match with split/item names in your tree.
Easier solution would be opening your files with anvi-interactive --manual
flag on your machine. And using Upload to server button, Purpose of anvi-push
is more like automation.
Hi all,
In brief, I am using
anvi-push
to push pangenomic data toanviserver
and I get this error:Anvio Server Error: module 'anvio.dbops' has no attribute 'TablesForCollections'
The problem seems obvious?TablesForCollections
is not in 'anvio.dbops', which it is not. I tried amending the source code by addingfrom anvio.tables.collections import TablesForCollections
to 'anvio.dbops' but that did not work--worth a shotI did the following:
anvi-export-collection -p genomes_min_occ_2-PAN.db -C default -O genomes --include-unbinned
which generatedbins-info
&bins
files. thenanvi-export-table genomes_min_occ_2-PAN.db
to generate the rest of the needed files(gene_cluster_presence_absence.txt, layer_orders.txt,layer_additionaldata.txt,item_additional_data.txt)
finally:
anvi-push --user MYUSERNAME --api-url https://anvi-server.org/ -n Genomes_Pan -t newick.txt -d gene_cluster_presence_absence.txt -R layer_orders.txt -D layer_additional_data.txt --delete-if-exists -A item_additional_data.txt --bins genomes_bins.txt -s states.txt --bins-info genomes_bins-info.txt
and I get this: `Enter your password for the server:
But...if I leave off
--bins-info genomes_bins-info.txt` it runs just fine:`Enter your password for the server:
I do not see anything strange looking about
genomes_bins-info.txt
.Clade_I anvi-interactive #778899 Clade_II anvi-interactive #778899 Clade_III anvi-interactive #778899 Clades_II-V anvi-interactive #778899 Core anvi-interactive #778899 SCG anvi-interactive #924900 Core_22 anvi-interactive #778899 UNBINNED_ITEMS_BIN anvi-interactive #000000
System Specifics: (anvio-4) Js-MacBook-Pro-3:anvi-interactive-pan J$ python --version Python 3.6.3 :: Anaconda, Inc.`
Anvi'o version ...............................: 4-master Profile DB version ...........................: 23 Contigs DB version ...........................: 11 Pan DB version ...............................: 8 Genome data storage version ..................: 6 Auxiliary data storage version ...............: 2
mac osx 10.10.5