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tlubitz / SBtab

SBtab - Table format for Systems Biology:
www.sbtab.net
MIT License
6 stars 8 forks source link

SBML2SBtab converter #95

Closed liebermeister closed 3 years ago

liebermeister commented 3 years ago

Hi Timo,

I tried to convert the hynne.xml example file (from the Sbtab repo) to SBtab. Both the commandline converter and the online converter throw error messages. The SBML file seems to be valid (according to the online SBML validator). Can you check this?

Thank you!

Best, Wolf

tlubitz commented 3 years ago

Hi Wolf,

I could reproduce the problem with the online converter.

I could NOT reproduce it with the current version of the commandline converter sbtab_sbml2sbtab.py. Could you check whether you have the most current version and report back whether the problem persists?

I'll update the online converter soon, it's a bit behind in versioning.

Best Timo

Am So., 18. Okt. 2020 um 20:06 Uhr schrieb Wolfram Liebermeister < notifications@github.com>:

Hi Timo,

I tried to convert the hynne.xml example file (from the Sbtab repo) to SBtab. Both the commandline converter and the online converter throw error messages. The SBML file seems to be valid (according to the online SBML validator). Can you check this?

Thank you!

Best, Wolf

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tlubitz commented 3 years ago

Hi Wolf^2

the online converter should work fine again.

Please still report back because of the commandline converter..

Best Timo

liebermeister commented 3 years ago

Hallo Timo,

Vielen Dank!

Hier ist die Fehlermeldung vom Kommandozeilen-Konverter, vielleicht kannst Du Dir einen Reim drauf machen?

Danke!

wolfram@persephone|/tmp:python3 /home/wolfram/projekte/sbtab/github/SBtab/python/sbtab_sbtab2sbml.py /home/wolfram/projekte/sbtab/github/SBtab/sbtab_examples/hynne/hynne.xml Traceback (most recent call last): File "/home/wolfram/projekte/sbtab/github/SBtab/python/SBtab.py", line 1059, in add_sbtab_string sbtab = SBtabTable(sbtab_string, filename) File "/home/wolfram/projekte/sbtab/github/SBtab/python/SBtab.py", line 85, in init self.add_sbtab_string(table_string) File "/home/wolfram/projekte/sbtab/github/SBtab/python/SBtab.py", line 547, in add_sbtab_string self.table = self._cut_table_string(self.preprocess) File "/home/wolfram/projekte/sbtab/github/SBtab/python/SBtab.py", line 146, in _cut_table_string if row.replace(delimiter, '') != '' and row.replace(delimiter, '') != '[]': TypeError: replace() argument 1 must be str, not bool

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/wolfram/projekte/sbtab/github/SBtab/python/sbtab_sbtab2sbml.py", line 40, in converter_sbtab2sbml_wrapper sbtab_doc = SBtab.SBtabDocument('conversion_document', f, args.sbtab) File "/home/wolfram/projekte/sbtab/github/SBtab/python/SBtab.py", line 968, in init self.add_sbtab_string(sbtab_init, filename) File "/home/wolfram/projekte/sbtab/github/SBtab/python/SBtab.py", line 1063, in add_sbtab_string 'ated properly: ' + str(e)) SBtab.SBtabError: The SBtab Table object could not be created properly: replace() argument 1 must be str, not bool

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/wolfram/projekte/sbtab/github/SBtab/python/sbtab_sbtab2sbml.py", line 78, in converter_sbtab2sbml_wrapper(args) File "/home/wolfram/projekte/sbtab/github/SBtab/python/sbtab_sbtab2sbml.py", line 42, in converter_sbtab2sbml_wrapper raise SBtabError('SBtab Document %s could not be created.' % args.sbtab) main.SBtabError: SBtab Document /home/wolfram/projekte/sbtab/github/SBtab/sbtab_examples/hynne/hynne.xml could not be created.

tlubitz commented 3 years ago

Hi Wolf,

nur ganz kurz:

Du benutzt das Skript sbtab_sbtab2sbml.py, aber Du übergibst ein SBML-Modell. Du benötigst das Skript sbtab_sbml2sbtab.py

Schau mal, ob das das Problem eventuell schon behebt.

Liebe Grüße, Timo

Am Mo., 19. Okt. 2020 um 20:09 Uhr schrieb Wolfram Liebermeister < notifications@github.com>:

Hallo Timo,

Vielen Dank!

Hier ist die Fehlermeldung vom Kommandozeilen-Konverter, vielleicht kannst Du Dir einen Reim drauf machen?

Danke!

wolfram@persephone|/tmp:python3 /home/wolfram/projekte/sbtab/github/SBtab/python/sbtab_sbtab2sbml.py /home/wolfram/projekte/sbtab/github/SBtab/sbtab_examples/hynne/hynne.xml Traceback (most recent call last): File "/home/wolfram/projekte/sbtab/github/SBtab/python/SBtab.py", line 1059, in add_sbtab_string sbtab = SBtabTable(sbtab_string, filename) File "/home/wolfram/projekte/sbtab/github/SBtab/python/SBtab.py", line 85, in init self.add_sbtab_string(table_string) File "/home/wolfram/projekte/sbtab/github/SBtab/python/SBtab.py", line 547, in add_sbtab_string self.table = self._cut_table_string(self.preprocess) File "/home/wolfram/projekte/sbtab/github/SBtab/python/SBtab.py", line 146, in _cut_table_string if row.replace(delimiter, '') != '' and row.replace(delimiter, '') != '[]': TypeError: replace() argument 1 must be str, not bool

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/wolfram/projekte/sbtab/github/SBtab/python/sbtab_sbtab2sbml.py", line 40, in converter_sbtab2sbml_wrapper sbtab_doc = SBtab.SBtabDocument('conversion_document', f, args.sbtab) File "/home/wolfram/projekte/sbtab/github/SBtab/python/SBtab.py", line 968, in init self.add_sbtab_string(sbtab_init, filename) File "/home/wolfram/projekte/sbtab/github/SBtab/python/SBtab.py", line 1063, in add_sbtab_string 'ated properly: ' + str(e)) SBtab.SBtabError: The SBtab Table object could not be created properly: replace() argument 1 must be str, not bool

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/wolfram/projekte/sbtab/github/SBtab/python/sbtab_sbtab2sbml.py", line 78, in converter_sbtab2sbml_wrapper(args) File "/home/wolfram/projekte/sbtab/github/SBtab/python/sbtab_sbtab2sbml.py", line 42, in converter_sbtab2sbml_wrapper raise SBtabError('SBtab Document %s could not be created.' % args.sbtab) main.SBtabError: SBtab Document /home/wolfram/projekte/sbtab/github/SBtab/sbtab_examples/hynne/hynne.xml could not be created.

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liebermeister commented 3 years ago

Au weia, da hatte ich ja Tomaten auf den Augen!!

Vielen Dank für Deine Hilfe .. und sorry ... !

Liebe Grüße Wolf