The heatmap cannot be displayed, and the expression data cannot be downloaded.

[guichenzhu]

I have installed the module and loaded biological sample information as well as expression data according to the tutorial. I checked my tripal version and there are no conflicts with the module. However, when I enter genes on the heatmap page and click "display expression heatmap", there is no heatmap displayed and no error message either. When I click "Download expression data for these features", there is an error message: "Warning: fopen(): Filename cannot be empty in analysis_expression_data_downloader->write() (line 174 of /var/www/html/sites/all/modules/tripal_analysis_expression/tripal_analysis_expression/includes/analysis_expression_data_downloader.inc). Exception: Cannot open collection file: sites/default/files/tripal/tripal_analysis_expression_download/expression_data_64215243ae50f.csv in analysis_expression_data_downloader->write() (line 176 of /var/www/html/sites/all/modules/tripal_analysis_expression/tripal_analysis_expression/includes/analysis_expression_data_downloader.inc)." Can you please advise me on how to solve this problem?

[dsenalik]

That is odd that there is no error message. If the gene names are correct you should see a heatmap, and if the genes are incorrect, you should see an error There is no expression data available for the features you entered.

Can you check the logs to see if there are any errors shown there? /admin/reports/dblog

Can you try entering invalid genes and see if you see an error message then?

I suspect the download error is just because there is no data to download.

[dsenalik]

Are you using the 7.x-3.0 version or the latest version from GitHub? The last released version is from 2017 so it is also possible that there are changes made since then that may help you.

And I think I found an error in the download, I will fix that. Pull #431

[guichenzhu]

Dear Douglas Senalik:   I am very happy to receive your reply.   I installed version 7.x-3.0, which is the latest version released in 2017. Following your instructions, I entered invalid gene ID and received an error message saying "There is no expression data available for the features you entered." When I clicked "Display Expression Heatmap" only, there were no error messages in the log report. However, when I selected "Download expression data for these features" there were errors reported in the log. I have attached several pictures: one showing the result with a correct gene ID, one showing the result with an incorrect gene ID, and two showing the log report.   I have been troubled by this issue for a long time and I really appreciate your help!

------------------ 原始邮件 ------------------ 发件人: "tripal/tripal_analysis_expression" @.>; 发送时间: 2023年3月27日(星期一) 晚上10:54 @.>; @.**@.>; 主题: Re: [tripal/tripal_analysis_expression] The heatmap cannot be displayed, and the expression data cannot be downloaded. (Issue #430)

Are you using the 7.x-3.0 version or the latest version from GitHub? The last released version is from 2017 so it is also possible that there are changes made since then that may help you.

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[dsenalik]

Thank you for the update, but unfortunately the attachments did not make it here to the GitHub issue. Maybe you can upload the images directly here. There have been a very large number of changes and bug fixes since the 7.x-1.0 release! can you download the current version of the module and try that? You can do that with git clone or you can just download a zip from https://github.com/tripal/tripal_analysis_expression/archive/refs/heads/master.zip

If this works for you, we should create a new released version.

[guichenzhu]

I uninstalled the previous version and reinstalled the version you sent me. Currently, my expression data can be downloaded normally, but the heatmap still cannot be displayed. There is no response when I enter the correct gene ID, and there is an error message when I enter an incorrect gene ID, which reads "There is no expression data available for the features you entered."

[guichenzhu]

And I have found an issue that the two blocks related to heatmap display mentioned in the readme document are "tripal_analysis_expression features form for heatmap" and "tripal_elasticsearch block for search form: blast_merged_transcripts". However, the blocks I have on my site are "tripal_analysis_expression features form for heatmap" and "tripal_analysis_expression heatmap display". Could this be related to the issue that my heatmap cannot be displayed?

[guichenzhu]

Hello, you didn't reply to my question yesterday, and I'm worried that maybe I didn't send the email properly and you didn't receive my request for help. If it was because you were too busy and didn't see it, I'm sorry to bother you again, but I hope you can take a moment to reply to my question if you see this message. Thank you very much.

------------------ 原始邮件 ------------------ 发件人: "tripal/tripal_analysis_expression" @.>; 发送时间: 2023年3月29日(星期三) 晚上9:48 @.>; @.**@.>; 主题: Re: [tripal/tripal_analysis_expression] The heatmap cannot be displayed, and the expression data cannot be downloaded. (Issue #430)

Thank you for the update, but unfortunately the attachments did not make it here to the GitHub issue. Maybe you can upload the images directly here. There have been a very large number of changes and bug fixes since the 7.x-1.0 release! can you download the current version of the module and try that? You can do that with git clone or you can just download a zip from https://github.com/tripal/tripal_analysis_expression/archive/refs/heads/master.zip

If this works for you, we should create a new released version.

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[dsenalik]

Yes I was distracted by other things. On our site the heatmap blocks are exactly the same as yours, and there is not "tripal_elasticsearch block for search form: blast_merged_transcripts" - so I do not think this is your issue.

The SQL query used to get the data is quite complicated, and there are many INNER JOINs, which means that if any of the tables does not have a correct entry, nothing will be returned.

    $sql = "SELECT ER.signal,
                   F.feature_id AS feature_id,
                   F.uniquename AS feature_uniquename,
                   B.name AS biomaterial_name,
                   B.biomaterial_id,
                   B.description AS biomaterial_description,
                   AN.analysis_id,
                   AN.name AS analysis_name,
                   C.name AS contact_name
            FROM {elementresult} ER
            INNER JOIN {element} E ON E.element_id = ER.element_id
            INNER JOIN {feature} F ON F.feature_id = E.feature_id
            INNER JOIN {quantification} Q ON Q.quantification_id = ER.quantification_id
            INNER JOIN {acquisition} AQ ON AQ.acquisition_id = Q.acquisition_id
            INNER JOIN {assay} A ON A.assay_id = AQ.assay_id
            INNER JOIN {assay_biomaterial} AB ON AB.assay_id = A.assay_id
            INNER JOIN {biomaterial} B ON B.biomaterial_id = AB.biomaterial_id
            INNER JOIN {analysis} AN ON AN.analysis_id = Q.analysis_id
            LEFT JOIN {contact} C ON B.biosourceprovider_id = C.contact_id
            WHERE F.uniquename IN ('AfUnG041300')";

Are you comfortable doing some SQL queries to verify that all of these tables have data?

select * from element;
select * from quantification;
select * from acquisition;
select * from assay;
select * from assay_biomaterial;
select * from biomaterial;

[guichenzhu]

I have performed the SQL queries as you instructed, and the results show that these tables do not exist in the database. I also checked all the tables currently present in the database and have taken a screenshot of the results, which I have sent to you. I hope you can provide me with some assistance.

------------------ 原始邮件 ------------------ 发件人: "tripal/tripal_analysis_expression" @.>; 发送时间: 2023年3月31日(星期五) 晚上11:51 @.>; @.**@.>; 主题: Re: [tripal/tripal_analysis_expression] The heatmap cannot be displayed, and the expression data cannot be downloaded. (Issue #430)

Yes I was distracted by other things. On our site the heatmap blocks are exactly the same as yours, and there is not "tripal_elasticsearch block for search form: blast_merged_transcripts" - so I do not think this is your issue.

The SQL query used to get the data is quite complicated, and there are many INNER JOINs, which means that if any of the tables does not have a correct entry, nothing will be returned. $sql = "SELECT ER.signal, F.feature_id AS feature_id, F.uniquename AS feature_uniquename, B.name AS biomaterial_name, B.biomaterial_id, B.description AS biomaterial_description, AN.analysis_id, AN.name AS analysis_name, C.name AS contact_name FROM {elementresult} ER INNER JOIN {element} E ON E.element_id = ER.element_id INNER JOIN {feature} F ON F.feature_id = E.feature_id INNER JOIN {quantification} Q ON Q.quantification_id = ER.quantification_id INNER JOIN {acquisition} AQ ON AQ.acquisition_id = Q.acquisition_id INNER JOIN {assay} A ON A.assay_id = AQ.assay_id INNER JOIN {assay_biomaterial} AB ON AB.assay_id = A.assay_id INNER JOIN {biomaterial} B ON B.biomaterial_id = AB.biomaterial_id INNER JOIN {analysis} AN ON AN.analysis_id = Q.analysis_id LEFT JOIN {contact} C ON B.biosourceprovider_id = C.contact_id WHERE F.uniquename IN ('AfUnG041300')";
Are you comfortable doing some SQL queries to verify that all of these tables have data? select from element; select from quantification; select from acquisition; select from assay; select from assay_biomaterial; select from biomaterial;
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[dsenalik]

Sorry, I forgot the prefix

select * from chado.element;
select * from chado.quantification;
select * from chado.acquisition;
select * from chado.assay;
select * from chado.assay_biomaterial;
select * from chado.biomaterial;

[guichenzhu]

I have performed the query according to the command you provided earlier, and the final result is shown in the figure. Since I am not very familiar with this area, my interpretation of the result may not be very accurate. Does this result indicate that some tables have data while others do not? And does my expression data exist in the database？Thank you again for your help in spite of your busy schedule. I am deeply grateful.

------------------ 原始邮件 ------------------ 发件人: "tripal/tripal_analysis_expression" @.>; 发送时间: 2023年4月1日(星期六) 凌晨1:18 @.>; @.**@.>; 主题: Re: [tripal/tripal_analysis_expression] The heatmap cannot be displayed, and the expression data cannot be downloaded. (Issue #430)

Sorry, I forgot the prefix select from chado.element; select from chado.quantification; select from chado.acquisition; select from chado.assay; select from chado.assay_biomaterial; select from chado.biomaterial;
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[dsenalik]

I don't see the figure, you may have to upload it here https://github.com/tripal/tripal_analysis_expression/issues/430

[guichenzhu]

[dsenalik]

Let's do some remote debugging. Can you run each of these queries and report the results, I will use AfUnG041300 - make sure that name is correct!

SELECT * from chado.feature F WHERE F.uniquename = 'AfUnG041300';

This makes sure the feature exists. You should get something for this. Next try

SELECT COUNT(*) FROM chado.elementresult ER
INNER JOIN chado.element E ON E.element_id = ER.element_id
INNER JOIN chado.feature F ON F.feature_id = E.feature_id
WHERE F.uniquename = 'AfUnG041300';

You should get a non-zero number. If zero, we'll try something else. If not zero, continue with

SELECT COUNT(*) FROM chado.elementresult ER
INNER JOIN chado.element E ON E.element_id = ER.element_id
INNER JOIN chado.feature F ON F.feature_id = E.feature_id
INNER JOIN chado.quantification Q ON Q.quantification_id = ER.quantification_id
WHERE F.uniquename = 'AfUnG041300';

SELECT COUNT(*) FROM chado.elementresult ER
INNER JOIN chado.element E ON E.element_id = ER.element_id
INNER JOIN chado.feature F ON F.feature_id = E.feature_id
INNER JOIN chado.quantification Q ON Q.quantification_id = ER.quantification_id
INNER JOIN chado.acquisition AQ ON AQ.acquisition_id = Q.acquisition_id
WHERE F.uniquename = 'AfUnG041300';

SELECT COUNT(*) FROM chado.elementresult ER
INNER JOIN chado.element E ON E.element_id = ER.element_id
INNER JOIN chado.feature F ON F.feature_id = E.feature_id
INNER JOIN chado.quantification Q ON Q.quantification_id = ER.quantification_id
INNER JOIN chado.acquisition AQ ON AQ.acquisition_id = Q.acquisition_id
INNER JOIN chado.assay A ON A.assay_id = AQ.assay_id
WHERE F.uniquename = 'AfUnG041300';

SELECT COUNT(*) FROM chado.elementresult ER
INNER JOIN chado.element E ON E.element_id = ER.element_id
INNER JOIN chado.feature F ON F.feature_id = E.feature_id
INNER JOIN chado.quantification Q ON Q.quantification_id = ER.quantification_id
INNER JOIN chado.acquisition AQ ON AQ.acquisition_id = Q.acquisition_id
INNER JOIN chado.assay A ON A.assay_id = AQ.assay_id
INNER JOIN chado.assay_biomaterial AB ON AB.assay_id = A.assay_id
WHERE F.uniquename = 'AfUnG041300';

SELECT COUNT(*) FROM chado.elementresult ER
INNER JOIN chado.element E ON E.element_id = ER.element_id
INNER JOIN chado.feature F ON F.feature_id = E.feature_id
INNER JOIN chado.quantification Q ON Q.quantification_id = ER.quantification_id
INNER JOIN chado.acquisition AQ ON AQ.acquisition_id = Q.acquisition_id
INNER JOIN chado.assay A ON A.assay_id = AQ.assay_id
INNER JOIN chado.assay_biomaterial AB ON AB.assay_id = A.assay_id
INNER JOIN chado.biomaterial B ON B.biomaterial_id = AB.biomaterial_id
WHERE F.uniquename = 'AfUnG041300';

SELECT COUNT(*) FROM chado.elementresult ER
INNER JOIN chado.element E ON E.element_id = ER.element_id
INNER JOIN chado.feature F ON F.feature_id = E.feature_id
INNER JOIN chado.quantification Q ON Q.quantification_id = ER.quantification_id
INNER JOIN chado.acquisition AQ ON AQ.acquisition_id = Q.acquisition_id
INNER JOIN chado.assay A ON A.assay_id = AQ.assay_id
INNER JOIN chado.assay_biomaterial AB ON AB.assay_id = A.assay_id
INNER JOIN chado.biomaterial B ON B.biomaterial_id = AB.biomaterial_id
INNER JOIN chado.analysis AN ON AN.analysis_id = Q.analysis_id
WHERE F.uniquename = 'AfUnG041300';

[guichenzhu]

[dsenalik]

Thank you for running these. Did the very last one return a count, it is not shown. But today I remembered you said that you could download data, so this all confirms the data is present, and something else is wrong.

Could you try viewing again, and immediately after check for any errors at the end of the apache log file? tail -n 20 /var/log/apache2/error.log

[guichenzhu]

Thank you very much for your free help. I hope I didn't interrupt your work too much. I followed your instructions and took a screenshot of the last query result. However, I couldn't find error.log in the /var/log/apache2/ directory, but I found it in the /var/log/httpd/ directory. There were error messages at the end of the file, and I have taken a screenshot of them.

------------------ 原始邮件 ------------------ 发件人: "tripal/tripal_analysis_expression" @.>; 发送时间: 2023年4月2日(星期天) 晚上10:01 @.>; @.**@.>; 主题: Re: [tripal/tripal_analysis_expression] The heatmap cannot be displayed, and the expression data cannot be downloaded. (Issue #430)

Thank you for running these. Did the very last one return a count, it is not shown. But today I remembered you said that you could download data, so this all confirms the data is present, and something else is wrong.

Could you try viewing again, and immediately after check for any errors at the end of the apache log file? tail -n 20 /var/log/apache2/error.log

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[guichenzhu]

[dsenalik]

It looks like you are running on tripal 2.x, is that correct? I have no experience with this version. I tried the link in your log file and was able to get to the heatmap page and get the same error as you have reported. I was able to download the data, but I noticed it is maybe not correct? There are 10 columns with data, and five more without anything. It is as if the "rep3" should be attached to "preanthesis_stage" for example, and so on, then there would be 10 columns of headers and of data. I am wondering if the data was loaded into the db with some problems because of spaces in the treatment names, for example preanthesis_stage rep1 was interpreted as two separate columns. This would not be easy to fix, you might have to reload the experiment after removing spaces in names. It is also possible this is a problem in the module, I will try to check that later.

    preanthesis_stage    rep3   preanthesis_stage    rep1   anthesis_stage   rep3   anthesis_stage   rep2   anthesis_stage   rep1   preanthesis_rep3    preanthesis_rep1    anthesis_rep3   anthesis_rep2   anthesis_rep1
AfUnG041300 0   0   0   0   0   0   0   0   0   0                   
AfUnG041200 0   0   0   0   0   0   0   0   0   0                   

[dsenalik]

Do one more SQL query for me please and report the results.

SELECT ER.signal,
F.feature_id AS feature_id,
F.uniquename AS feature_uniquename,
B.name AS biomaterial_name,
B.biomaterial_id,
B.description AS biomaterial_description,
AN.analysis_id,
AN.name AS analysis_name,
C.name AS contact_name
FROM chado.elementresult ER
INNER JOIN chado.element E ON E.element_id = ER.element_id
INNER JOIN chado.feature F ON F.feature_id = E.feature_id
INNER JOIN chado.quantification Q ON Q.quantification_id = ER.quantification_id
INNER JOIN chado.acquisition AQ ON AQ.acquisition_id = Q.acquisition_id
INNER JOIN chado.assay A ON A.assay_id = AQ.assay_id
INNER JOIN chado.assay_biomaterial AB ON AB.assay_id = A.assay_id
INNER JOIN chado.biomaterial B ON B.biomaterial_id = AB.biomaterial_id
INNER JOIN chado.analysis AN ON AN.analysis_id = Q.analysis_id
LEFT JOIN chado.contact C ON B.biosourceprovider_id = C.contact_id
WHERE F.uniquename IN ('AfUnG041300', 'AfUnG041200')";

[guichenzhu]

I am using the tripal 3.x version. Due to my mistake in naming the Biosamples for the species Aristolochia fimbriata earlier, there were issues with downloading data. However, my other species Annona glaba does not have this problem because I only loaded one Biosample for this species and the downloaded data has values. However, the heatmap display still fails for this species, so I think you don't need to consider the issue you mentioned for now. You can verify it using the species Annona glaba later.

------------------ 原始邮件 ------------------ 发件人: "tripal/tripal_analysis_expression" @.>; 发送时间: 2023年4月3日(星期一) 凌晨1:18 @.>; @.**@.>; 主题: Re: [tripal/tripal_analysis_expression] The heatmap cannot be displayed, and the expression data cannot be downloaded. (Issue #430)

It looks like you are running on tripal 2.x, is that correct? I have no experience with this version. I tried the link in your log file and was able to get to the heatmap page and get the same error as you have reported. I was able to download the data, but I noticed it is maybe not correct? There are 10 columns with data, and five more without anything. It is as if the "rep3" should be attached to "preanthesis_stage" for example, and so on, then there would be 10 columns of headers and of data. I am wondering if the data was loaded into the db with some problems because of spaces in the treatment names, for example preanthesis_stage rep1 was interpreted as two separate columns. This would not be easy to fix, you might have to reload the experiment after removing spaces in names. It is also possible this is a problem in the module, I will try to check that later. preanthesis_stage rep3 preanthesis_stage rep1 anthesis_stage rep3 anthesis_stage rep2 anthesis_stage rep1 preanthesis_rep3 preanthesis_rep1 anthesis_rep3 anthesis_rep2 anthesis_rep1 AfUnG041300 0 0 0 0 0 0 0 0 0 0 AfUnG041200 0 0 0 0 0 0 0 0 0 0
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[guichenzhu]

[dsenalik]

I just looked at the source code of the heatmap page, and all of the data is there. It is just not rendering into an image for some reason. Unfortunately this is something to do with javascript, which I don't know so much about. On the firefox inspector page I see this error, which must mean something, it does not occur on our site.

[guichenzhu]

I think I have seen this issue before, but I don't remember where. The main point now is to solve the problem of calling the plotly library, right? I am also trying to solve this problem, but I still hope to get your help.

------------------ 原始邮件 ------------------ 发件人: "tripal/tripal_analysis_expression" @.>; 发送时间: 2023年4月3日(星期一) 凌晨3:08 @.>; @.**@.>; 主题: Re: [tripal/tripal_analysis_expression] The heatmap cannot be displayed, and the expression data cannot be downloaded. (Issue #430)

I just looked at the source code of the heatmap page, and all of the data is there. It is just not rendering into an image for some reason. Unfortunately this is something to do with javascript, which I don't know so much about. On the firefox inspector page I see this error, which must mean something, it does not occur on our site.

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[guichenzhu]

[dsenalik]

Thank you for posting the SQL output. This shows a bug in the module's data export! I created issue #434 to fix this. Fixed with merged pull #435

[dsenalik]

And as far as the plotly library, it appears that it is loaded, but for some reason isn't available. I have no idea why.

[guichenzhu]

I looked into it today and it seems that the code that loads the plotly library in this module is causing the issue. I was wondering where this code is located so I could try to make some modifications.

[guichenzhu]

Hello, I still haven't solved this problem. I have consulted some front-end web designers, but they couldn't solve the problem either. So I really have no choice. You mentioned that you're not very familiar with JS, can you please pass my problem to other members of your team? I have been stuck on this issue for a long time, and I really hope to solve it. Thank you very much.

------------------ 原始邮件 ------------------ 发件人: "tripal/tripal_analysis_expression" @.>; 发送时间: 2023年4月3日(星期一) 凌晨5:27 @.>; @.**@.>; 主题: Re: [tripal/tripal_analysis_expression] The heatmap cannot be displayed, and the expression data cannot be downloaded. (Issue #430)

And as far as the plotly library, it appears that it is loaded, but for some reason isn't available. I have no idea why.

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[dsenalik]

I have passed it along

[dsenalik]

Here are some comments that I hope can help

Lacey-Anne Sanderson Hi @Douglas Senalik I don't have time to dig very deep but her are my quick thoughts: Plotly is being added to the page here: https://github.com/tripal/tripal_analysis_expression/blob/d20d540e587b88c0f69bdd7b[…]a3/tripal_analysis_expression/tripal_analysis_expression.module I wonder if it's the order it's added to the page as Drupal aggregates calls like this and not always in the same order (it's consistent with a site but not between). If it is this problem it can be fixed by making sure plotly has a heavier weight then the heatmap script and that both are heavier than jquery. On a side note, best practice is to not include external libraries in your repo. Rather the libraries api should have been used, plotly should have been added to the libraries folder and then added to the page using the libraries api. This respects ownership of scripts :upside_down_face:

Lacey-Anne Sanderson If they check this doc where is says weight it describes this a bit more: https://api.drupal.org/api/drupal/includes!common.inc/function/drupal_add_js/7.x

[dsenalik]

Can you please make these changes and see if it helps? In file tripal_analysis_expression/tripal_analysis_expression.module starting at line 512 add these weights. After doing this clear all caches with drush cache-clear all or at /admin/config/development/performance

      drupal_add_js(drupal_get_path('module',
          'tripal_analysis_expression') . '/theme/js/plotly-latest.min.js',
        ['weight' => -999]);
      drupal_add_js(['tripal_analysis_expression' => ['data' => $heatmap]],
        ['type' => 'setting', 'weight' => -998]);
      drupal_add_js(['tripal_analysis_expression' => ['baseURL' => $base_url]],
        ['type' => 'setting', 'weight' => -997]);
      drupal_add_js(drupal_get_path('module',
          'tripal_analysis_expression') . '/theme/js/heatmap.js',
        ['weight' => -996]);

[dsenalik]

Because Firefox shows that plotly is for some reason loaded last

[guichenzhu]

Thank you and your team very much, I did it! After adding the weight, the heatmap was successfully displayed. I would like to express my heartfelt thanks to you for your help during this time, patiently answering my questions and even asking your team members when encountering areas where you are not proficient. I sincerely wish you all the best in the future!

------------------ 原始邮件 ------------------ 发件人: "tripal/tripal_analysis_expression" @.>; 发送时间: 2023年4月14日(星期五) 凌晨5:32 @.>; @.**@.>; 主题: Re: [tripal/tripal_analysis_expression] The heatmap cannot be displayed, and the expression data cannot be downloaded. (Issue #430)

Can you please make these changes and see if it helps? In file tripal_analysis_expression/tripal_analysis_expression.module starting at line 512 add these weights. After doing this clear all caches with drush cache-clear all or at /admin/config/development/performance drupal_add_js(drupal_get_path('module', 'tripal_analysis_expression') . '/theme/js/plotly-latest.min.js', ['weight' => -999]); drupal_add_js(['tripal_analysis_expression' => ['data' => $heatmap]], ['type' => 'setting', 'weight' => -998]); drupal_add_js(['tripal_analysis_expression' => ['baseURL' => $base_url]], ['type' => 'setting', 'weight' => -997]); drupal_add_js(drupal_get_path('module', 'tripal_analysis_expression') . '/theme/js/heatmap.js', ['weight' => -996]);
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[dsenalik]

Great news @guichenzhu I'm glad we could solve this I will merge this fix into the module, and when that is done this issue will be closed.