I found a number of spelling errors, so I have created a pull request on the 7.x-4.0 branch to fix them

Each of the loaders requires a number of CVterms installed on the site. For example, the featuremap loader requires the below cvterms

>Required cvterms
Error : Could not find cvterm : alias [cv_id = 21695].
Error : Could not find cvterm : analysis_method [cv_id = 21695].
Error : Could not find cvterm : software [cv_id = 21695].
Error : Could not find cvterm : map_type [cv_id = 21695].
Error : Could not find cvterm : population_type [cv_id = 21695].
Error : Could not find cvterm : population_size [cv_id = 21695].
Error : Could not find cvterm : source_url [cv_id = 21695].
Error : Could not find cvterm : comments [cv_id = 21695].
Error : Could not find cvterm : genome_group [cv_id = 21695].

Is there a separate module or command that sets up this site CV with all the terms the loader expects? Should they have been inserted on installing this module?

I can otherwise insert the terms manually as I get the errors. I see you have a nice drush command that automatically inserts the term into the right CV, ie , drush mcl-add-cvterm comments

I've created a test template excel file of genotype_snp type which is comprised of db, dataset, stock and genotype_snp sheets. When I uploaded the excel with MCL, it failed with error logs like this:

Error Logs
[stock]

row 2 --------------
(name) = () not found in db
Invalid stock type : cultivar

For the first error, does it mean the stock name should exist in the db sheet ? But I can't find this header in db.
For the second error, is stock type same as germplasm_type? Shouldn't I select from the choices given in the header description?

Thanks

Currently, the MCL pub loader will handle a missing value in the 'citation' column of the excel sheet by generating a citation, appropriate for the publication type.

However, this citation is only used to populate the 'uniquename' ('Unique Local Identifier') attribute (tripal field data__identifier), the actual citation remains blank (tripal field tpub__citation).

I propose to also use this same generated value to populate this citation field (stored in pubprop with type_id from cv tripal_pub, cvterm Citation)

Nevermind, I should be at the gitlab repository

Dear all
I'm using marker search module (ver.2) and attempting to use location search tool in that module.
However, I could not find the column headings for locations in the marker template downloaded.
Is there any way to upload location informations and use location search tool?

Best,

Dear Sir
I'm using mcl ver.2.
However, I could not download template files.
Hence, I uploded the template file using supplementary data of the journal ( https://academic.oup.com/database/article/doi/10.1093/database/bax092/4718480), as shown below, however, I could not find log files.
I also could not find marker type on mainlab_chado_search.
Two warnings were found as shown below.
Is there any way to solve these problems?

*marker_name | marker_type | *genus | *species|
XXXXXXXXXXX |YYYYYYYYYYY|ZZZZZZ|QQQQQ|

Warning: ZipArchive::close(): Invalid or uninitialized Zip object in mcl_download_log() (line 203 of /var/www/html/sites/all/modules/mcl/includes/mcl.inc).
Warning: readfile(/var/www/html/sites/default/files/mcl/user/administrator/1/mcl-1-logs.zip): failed to open stream: No such file or directory in mcl_download_log() (line 208 of /var/www/html/sites/all/modules/mcl/includes/mcl.inc).

which section is the hyperlink in?

7.x-5.0
Either the following should be added to "templates/mcl_template_marker.class.inc" after line 123
$cvterms['sequence']['marker_locus'] = -1;

or

includes/class/mcl_chado_class/mcl_chado_feature.class.inc
line 1134 should be changed from
$locus = MCL_CHADO_FEATURE::addFeature($mcl_tmpl, $locus_name, $locus_name, $cvterms['sequence']['marker_locus'], $this->getOrganismID());
to
$locus = MCL_CHADO_FEATURE::addFeature($mcl_tmpl, $locus_name, $locus_name, $cvterms['MAIN']['marker_locus'], $this->getOrganismID());

I suspect the latter because the tripal_map materialized view references MAIN->marker_locus

Hi,

I'd like to configure the Search Trait Evaluation. However, I do not know which kind of MCL data should I use. I supposed that the data should contains trait value for each sample, but I have viewed the template data formats in MCL Data Template List, and still can't figure out which one (or ones) of the MCL Template was needed for Search Trait Evaluation.

Are there detailed manual or examples on how to configure the Search Trait Evaluation tools?

Any suggestion would be grateful.

Best wishes,

Songtao Gui

Hello,
I'm attempting to use your loader. I have created a simple db upload job from the db template file:

I create a job using the UI and run it using drush mcl-run. It runs with no feedback:

drush mcl-run
    Running uploading job in queue..

    Processing job : db_test [6].

    Processing job : test5 [5].

    DONE.

The job status page is updated to failed (see below).

Downloading the log file returns a zip file that is 0 bytes and cannot be unzipped:

$ unzip mcl-6-logs.zip
Archive:  mcl-6-logs.zip
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of mcl-6-logs.zip or
        mcl-6-logs.zip.zip, and cannot find mcl-6-logs.zip.ZIP, period.

$ ls -l mcl-6-logs.zip
-rw-r--r--@ 1 chet  staff  0 Jun 21 10:51 mcl-6-logs.zip

to be clear: the db was not loaded:

select * from chado.db where name='mainlab';
drupal=>

Any thoughts on how to proceed?

Thank you

Bradford