PS updated to 2.0.15 & SG updated to 4.0.22 #570

CarlosHorro · 2021-03-11T13:37:25Z

No description provided.

SG updated to 4.0.22

bernt-matthias · 2021-03-12T20:42:59Z

Hey @CarlosHorro do you like to integrate my changes from here: #572? Or should be merge them separately?

For this PR it seems that only an assertion needs to be adapted.

CarlosHorro · 2021-03-14T21:34:43Z

Hi @bernt-matthias We may integrate them here, how do I do that?

Hey @CarlosHorro do you like to integrate my changes from here: #572? Or should be merge them separately?

For this PR it seems that only an assertion needs to be adapted.

bernt-matthias · 2021-03-15T08:48:06Z

We may integrate them here, how do I do that?

Should be simply: git cherry-pick edef57be5ff2a0a1c93d3ee4858eab01516fa88c

1. remove stderr redirection in case of ``` command 2>> $temp_stderr && .... && cat $temp_stderr 2>&1; ``` stderr is swallowed if command fails. this was the case for PS, FC, and IP in case of ``` command 2>> $temp_stderr && .... ; cat $temp_stderr 2>&1; ``` the last cat is executed even if the command fails. the exit code of the command line is then the exit code of the cat, i.e. the tool will always be counted successful, even if everything fails. 2. fix peptideshaker find exec constructs Galaxy removes the last ';' from the generated command line. thus we need to make sure that the last `find ... -exec ... \;` is not the last command. 3. remove some unnecessay parentheses

bernt-matthias · 2021-03-15T09:56:24Z

tools/peptideshaker/peptide_shaker.xml

@@ -12,8 +12,7 @@
    </requirements>
    <expand macro="stdio" />

-    <command><![CDATA[
-    ## When supporting more advanced Galaxy versions:    command use_shared_home="false"
+    <command use_shared_home="false"><![CDATA[


I think it would be better to increase the profile of the tools to something greater than or equal to 18.01.

See https://github.com/galaxyproject/galaxy/blob/ce23f963e036722865ecd27fda509f173406ab61/lib/galaxy/tool_util/parser/xml.py#L169

I would suggest at least 20.01

Yes, you are right @bernt-matthias, thank you. That was something I wanted to do some time ago but I didn't remember to include it...

CarlosHorro · 2021-03-15T10:30:27Z

Great, I think we have included enough stuff here :-)

bernt-matthias · 2021-03-15T10:41:18Z

Great, I think we have included enough stuff here :-)

I think we should append log_folder/*.log to the stderr. See here compomics/searchgui#288 (comment)

bernt-matthias · 2021-03-15T11:05:32Z

Maybe like this: If you include this in the first line of the shell script:

trap ">&2 cat log_folder/*.log" EXIT;

CarlosHorro · 2021-03-15T11:40:34Z

Maybe like this: If you include this in the first line of the shell script:
trap ">&2 cat log_folder/*.log" EXIT;

Yep, it seems to work nicely, I will add it :-)

bernt-matthias · 2021-03-15T12:08:00Z

One more thing: CarlosHorro#2

bernt-matthias · 2021-03-15T12:09:15Z

Interesting new tool errors...

CarlosHorro · 2021-03-15T12:22:55Z

Interesting new tool errors...

Well, the error seems related to trying to write into a system-related's folder:

_
java.lang.RuntimeException: java.io.FileNotFoundException: /usr/local/share/peptide-shaker-2.0.15-0/resources/conf/paths.txt (Permission denied)
at com.compomics.util.io.flat.SimpleFileWriter.(SimpleFileWriter.java:59)
at eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.writeConfigurationToFile(PeptideShakerPathParameters.java:391)
at eu.isas.peptideshaker.cmd.PathSettingsCLI.setPathSettings(PathSettingsCLI.java:110)
at eu.isas.peptideshaker.cmd.PathSettingsCLI.extractAndUpdatePathOptions(PathSettingsCLI.java:269)
at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1366)
Caused by: java.io.FileNotFoundException: /usr/local/share/peptide-shaker-2.0.15-0/resources/conf/paths.txt (Permission denied)
at java.base/java.io.FileOutputStream.open0(Native Method)
at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298)
at java.base/java.io.FileOutputStream.(FileOutputStream.java:237)
at java.base/java.io.FileOutputStream.(FileOutputStream.java:187)
at java.base/java.io.FileWriter.(FileWriter.java:96)
at com.compomics.util.io.flat.SimpleFileWriter.(SimpleFileWriter.java:53)
... 4 more
_

But I don't understand why this happens now and not just right after I included "command use_shared_home="false" in PS...

bernt-matthias · 2021-03-15T12:25:02Z

But I don't understand why this happens now and not just right after I included "command use_shared_home="false" in PS...

Maybe because we did not see the exception until the trap has been included.

You can simply try to revert the profile and set command use_shared_home="false" again

CarlosHorro · 2021-03-15T12:35:02Z

But I don't understand why this happens now and not just right after I included "command use_shared_home="false" in PS...

Maybe because we did not see the exception until the trap has been included.

You can simply try to revert the profile and set command use_shared_home="false" again

I will check if it is feasible to write that file in the temp folder. I will undo the profile otherwise...

detect oom errors as fatal_oom and not fatal

CarlosHorro · 2021-03-15T21:06:05Z

But I don't understand why this happens now and not just right after I included "command use_shared_home="false" in PS...

Maybe because we did not see the exception until the trap has been included.

You can simply try to revert the profile and set command use_shared_home="false" again

I've seen that this is not immediate to solve. There is even another problem :

java.io.FileNotFoundException: /tmp/tmprrb5ssna/job_working_directory/000/6/working/PeptideShakerCLI/exportFactory.json (No such file or directory)
	at java.base/java.io.FileInputStream.open0(Native Method)
	at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
	at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
	at com.compomics.util.io.json.JsonMarshaller.getJsonStringFromFile(JsonMarshaller.java:227)
	at com.compomics.util.io.json.JsonMarshaller.fromJson(JsonMarshaller.java:142)
	at eu.isas.peptideshaker.export.PSExportFactory.loadFromFile(PSExportFactory.java:158)
	at eu.isas.peptideshaker.export.PSExportFactory.getInstance(PSExportFactory.java:99)
	at eu.isas.peptideshaker.cmd.ReportCLIParams.<clinit>(ReportCLIParams.java:17)
	at eu.isas.peptideshaker.cmd.PeptideShakerCLIParams.createOptionsCLI(PeptideShakerCLIParams.java:76)
	at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1370)

So I will undo the last changes until these issues are solved in the app itself.

CarlosHorro · 2021-03-16T11:11:33Z

So, I guess we can merge this like it is and afterwards when PS app itself manages the paths in a better way we can create another PR.

bernt-matthias · 2021-03-16T11:14:46Z

So, I guess we can merge this like it is and afterwards when PS app itself manages the paths in a better way we can create another PR.

Agreed. Was just thinking if we can have profile="20.01" for fasta_cli and ident_params?

Have you opened an issue at the PS repo?

bernt-matthias · 2021-03-16T11:18:15Z

I still do not understand how the two error relate to the use of a shared home / a more recent profile.

Or are the two exceptions non-critical? Then we could be more specific in the stdio regular expressions...

CarlosHorro · 2021-03-16T11:40:52Z

So, I guess we can merge this like it is and afterwards when PS app itself manages the paths in a better way we can create another PR.

Agreed. Was just thinking if we can have profile="20.01" for fasta_cli and ident_params?

Trying it...

Have you opened an issue at the PS repo?

Yes, just did it:
compomics/peptide-shaker#445

CarlosHorro · 2021-03-16T11:43:25Z

I still do not understand how the two error relate to the use of a shared home / a more recent profile.

Or are the two exceptions non-critical? Then we could be more specific in the stdio regular expressions...

Not sure either; however, 1) they don't look critical as PS has been working well without taking care of them, and 2) I think we need to move this forward and manage that all in the future PR.

bernt-matthias · 2021-03-16T13:35:06Z

I think we need to move this forward and manage that all in the future PR.

Agreed. But please also enable the newer profile for peptide_shaker. The profile is not the source of the problem, but the trap which appends the exception traces from the log files to stderr which is then caught by our stdio regular expressions, in particular

tools-galaxyp/tools/peptideshaker/macros_basic.xml

Line 6 in bbe7a74

I already verified this locally.

bernt-matthias

I will merge as soon as the CI passes

PS updated to 2.0.14

17491b3

SG updated to 4.0.22

bernt-matthias mentioned this pull request Mar 12, 2021

some fixes for searchgui and peptideshaker #572

Closed

1 task

Removed wrong result in test (removed from PS after last update).

7700dc1

CarlosHorro and others added 2 commits March 14, 2021 23:01

Merge branch 'master' into sg_4022_ps_2014

e9a71c4

PS updated to 2.0.15

a254773

CarlosHorro changed the title ~~PS updated to 2.0.14 & SG updated to 4.0.22~~ PS updated to 2.0.15 & SG updated to 4.0.22 Mar 15, 2021

CarlosHorro and others added 2 commits March 15, 2021 10:05

use_shared_home="false"

a9e4f37

bernt-matthias reviewed Mar 15, 2021

View reviewed changes

Profile updated to 20.01

a6e9a89

CarlosHorro and others added 3 commits March 15, 2021 12:42

Added logs to stderr output.

ac36119

Added logs to PS stderr output.

d7c9057

detect oom errors as fatal_oom and not fatal

95736b3

CarlosHorro added 2 commits March 15, 2021 13:36

Merge pull request #2 from bernt-matthias/CarlosHorro_sg_4022_ps_2014

7416940

detect oom errors as fatal_oom and not fatal

Merge branch 'master' into sg_4022_ps_2014

fe669cf

CarlosHorro added 2 commits March 15, 2021 22:18

Undone some last features until app behaviour is fixed.

48797cf

Refreshing PR

2bc4ae3

Added profile 20.01 to fasta_cli and ident_params tools

bbe7a74

Readded PS 20.01 profile.

f921b21

bernt-matthias approved these changes Mar 16, 2021

View reviewed changes

bernt-matthias merged commit 44a2063 into galaxyproteomics:master Mar 16, 2021

bernt-matthias mentioned this pull request Mar 16, 2021

SearchGUI Error: Map failed compomics/searchgui#288

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PS updated to 2.0.15 & SG updated to 4.0.22 #570

PS updated to 2.0.15 & SG updated to 4.0.22 #570

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PS updated to 2.0.15 & SG updated to 4.0.22 #570

PS updated to 2.0.15 & SG updated to 4.0.22 #570

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