GNU Health - Bugs: bug #64464, health_genetics export po file...

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bug #64464: health_genetics export po file error.

Submitter:	Feng Shu <tumashu>
Submitted:	Mon 24 Jul 2023 04:59:53 AM UTC


Category:	Programming / Tracebacks	Severity:	3 - Normal
Item Group:	None	Status:	Ready For Test
Privacy:	Public	Assigned to:	meanmicio
Open/Closed:	Open	Release:	4.3.0
Module:	health_genetics	Component:	Hospital Management

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Fri 11 Aug 2023 11:27:35 AM UTC, comment #6: Fixed on https://hg.savannah.gnu.org/hgweb/health/rev/8b02b17c3ef4	Luis Falcon <meanmicio>
Fri 11 Aug 2023 07:14:37 AM UTC, comment #5: Thanks, Feng! I'll check it out today.. don't recall seeing the traceback on a new DB.. Sometimes in the past I ran into similar issues because of the length of the model name... I'll double check today and let you know. Bests Luis	Luis Falcon <meanmicio>
Fri 11 Aug 2023 01:08:27 AM UTC, comment #4: I think it is health_genetics_uniprot' problem, feng@Tumashu ~/gnuhealth/tryton/server/trytond-6.0.33/bin $ ./trytond-admin -d gnuhealth -u health_genetics_uniprot Traceback (most recent call last): File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 458, in parse_xmlstream self.sax_parser.parse(source) File "/usr/lib/python3.11/xml/sax/expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "/usr/lib/python3.11/xml/sax/xmlreader.py", line 125, in parse self.feed(buffer) File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed self._parser.Parse(data, isFinal) File "../Modules/pyexpat.c", line 468, in EndElement File "/usr/lib/python3.11/xml/sax/expatreader.py", line 336, in end_element self._cont_handler.endElement(name) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 513, in endElement self.taghandler = self.taghandler.endElement(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 295, in endElement self.mh.import_record( File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 689, in import_record self.create_records(model, [values], [fs_id]) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 695, in create_records records = Model.create(vlist) ^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 159, in wrapper return func(cls, args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 614, in create cursor.execute(table.insert(insert_columns, File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/backend/postgresql/database.py", line 74, in execute cursor.execute(self, sql, args) psycopg2.errors.UndefinedColumn: 错误: 关系 "gnuhealth_protein_disease" 的 "create_uid" 字段不存在 LINE 1: INSERT INTO "gnuhealth_protein_disease" AS "a" ("create_uid"... ^ The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/bin/./trytond-admin", line 23, in <module> admin.run(options) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/admin.py", line 53, in run pool.init(update=options.update, lang=list(lang), File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/pool.py", line 164, in init restart = not load_modules( ^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 440, in load_modules _load_modules(update) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 408, in _load_modules load_module_graph(graph, pool, update, lang) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 252, in load_module_graph tryton_parser.parse_xmlstream(fp) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 460, in parse_xmlstream raise Exception("Error " + self.current_state()) from e Exception: Error In tag record model gnuhealth.protein.disease with id health_genetics_uniprot.DI-00001. feng@Tumashu ~/gnuhealth/tryton/server/trytond-6.0.33/bin $	Feng Shu <tumashu>
Thu 10 Aug 2023 07:40:58 AM UTC, comment #3: Hmm I ran po-export... The error seems to happen in here: psycopg2.errors.UndefinedColumn: column "create_uid" of relation "gnuhealth_protein_disease" does not exist LINE 1: INSERT INTO "gnuhealth_protein_disease" AS "a" ("create_uid"... psycopg2 complains about the create_uid column does not exist on table gnuhealth_protein_disease. It might be related to the length of the model, but I have not run into issues yet in other contexts, and the protein disease model has been there for some versions now... ... I'll run the export process from the client and let you know. Table "public.gnuhealth_protein_disease" Column \| Type \| Collation \| Nullable \| Default ---------------------+--------------------------------+-----------+----------+------------------------------------------------------- id \| integer \| \| not null \| nextval('gnuhealth_protein_disease_id_seq'::regclass) acronym \| character varying \| \| not null \| active \| boolean \| \| \| false create_date \| timestamp(6) without time zone \| \| \| create_uid \| integer \| \| \| description \| text \| \| \| ...	Luis Falcon <meanmicio>
Wed 09 Aug 2023 02:12:01 AM UTC, comment #2: raceback (most recent call last): File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 458, in parse_xmlstream self.sax_parser.parse(source) File "/usr/lib/python3.11/xml/sax/expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "/usr/lib/python3.11/xml/sax/xmlreader.py", line 125, in parse self.feed(buffer) File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed self._parser.Parse(data, isFinal) File "../Modules/pyexpat.c", line 468, in EndElement File "/usr/lib/python3.11/xml/sax/expatreader.py", line 336, in end_element self._cont_handler.endElement(name) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 513, in endElement self.taghandler = self.taghandler.endElement(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 295, in endElement self.mh.import_record( File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 689, in import_record self.create_records(model, [values], [fs_id]) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 695, in create_records records = Model.create(vlist) ^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 159, in wrapper return func(cls, args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 614, in create cursor.execute(table.insert(insert_columns, File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/backend/postgresql/database.py", line 74, in execute cursor.execute(self, sql, args) psycopg2.errors.UndefinedColumn: 错误: 关系 "gnuhealth_protein_disease" 的 "create_uid" 字段不存在 LINE 1: INSERT INTO "gnuhealth_protein_disease" AS "a" ("create_uid"... ^ The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/bin/trytond-admin", line 23, in <module> admin.run(options) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/admin.py", line 53, in run pool.init(update=options.update, lang=list(lang), File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/pool.py", line 164, in init restart = not load_modules( ^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 440, in load_modules _load_modules(update) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 408, in _load_modules load_module_graph(graph, pool, update, lang) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 252, in load_module_graph tryton_parser.parse_xmlstream(fp) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 460, in parse_xmlstream raise Exception("Error " + self.current_state()) from e Exception: Error In tag record model gnuhealth.protein.disease with id health_genetics_uniprot.DI-00001. ## Add Language to tryton ... Connecting to database 'po-export-db' with 'admin' ... /usr/lib/python3/dist-packages/passlib/utils/__init__.py:854: DeprecationWarning: 'crypt' is deprecated and slated for removal in Python 3.13 from crypt import crypt as _crypt ## Running trytond-admin command to update DB (3. Active language) ... Traceback (most recent call last): File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 458, in parse_xmlstream self.sax_parser.parse(source) File "/usr/lib/python3.11/xml/sax/expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "/usr/lib/python3.11/xml/sax/xmlreader.py", line 125, in parse self.feed(buffer) File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed self._parser.Parse(data, isFinal) File "../Modules/pyexpat.c", line 468, in EndElement File "/usr/lib/python3.11/xml/sax/expatreader.py", line 336, in end_element self._cont_handler.endElement(name) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 513, in endElement self.taghandler = self.taghandler.endElement(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 295, in endElement self.mh.import_record( File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 689, in import_record self.create_records(model, [values], [fs_id]) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 695, in create_records records = Model.create(vlist) ^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 159, in wrapper return func(cls, args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 614, in create cursor.execute(table.insert(insert_columns, File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/backend/postgresql/database.py", line 74, in execute cursor.execute(self, sql, args) psycopg2.errors.UndefinedColumn: 错误: 关系 "gnuhealth_protein_disease" 的 "create_uid" 字段不存在 LINE 1: INSERT INTO "gnuhealth_protein_disease" AS "a" ("create_uid"... ^ The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/bin/trytond-admin", line 23, in <module> admin.run(options) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/admin.py", line 53, in run pool.init(update=options.update, lang=list(lang), File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/pool.py", line 164, in init restart = not load_modules( ^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 440, in load_modules _load_modules(update) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 408, in _load_modules load_module_graph(graph, pool, update, lang) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 252, in load_module_graph tryton_parser.parse_xmlstream(fp) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 460, in parse_xmlstream raise Exception("Error " + self.current_state()) from e Exception: Error In tag record model gnuhealth.protein.disease with id health_genetics_uniprot.DI-00001.	Feng Shu <tumashu>
Mon 24 Jul 2023 08:41:17 AM UTC, comment #1: Hi, Feng The health_genetics packages and some of their models are being updated for in the default (development branch) for the upcoming 4.4. (see task task #16404: Update functionality in Health Genetics packages). The stable branch 4.2 is not affected. About the specific error, today I will be adding / updating datafiles and filling in the new primary key. Bests Luis	Luis Falcon <meanmicio>
Mon 24 Jul 2023 04:59:53 AM UTC, original submission: During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 458, in parse_xmlstream self.sax_parser.parse(source) File "/usr/lib/python3.11/xml/sax/expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "/usr/lib/python3.11/xml/sax/xmlreader.py", line 125, in parse self.feed(buffer) File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed self._parser.Parse(data, isFinal) File "../Modules/pyexpat.c", line 468, in EndElement File "/usr/lib/python3.11/xml/sax/expatreader.py", line 336, in end_element self._cont_handler.endElement(name) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 513, in endElement self.taghandler = self.taghandler.endElement(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 295, in endElement self.mh.import_record( File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 689, in import_record self.create_records(model, [values], [fs_id]) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 695, in create_records records = Model.create(vlist) ^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 159, in wrapper return func(cls, args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 634, in create cls.__raise_integrity_error( File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 352, in __raise_integrity_error raise RequiredValidationError( trytond.model.modelstorage.RequiredValidationError: A value is required for field "aliases" in "gnuhealth.gene". - The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/bin/trytond-admin", line 23, in <module> admin.run(options) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/admin.py", line 53, in run pool.init(update=options.update, lang=list(lang), File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/pool.py", line 164, in init restart = not load_modules( ^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 440, in load_modules _load_modules(update) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 408, in _load_modules load_module_graph(graph, pool, update, lang) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 252, in load_module_graph tryton_parser.parse_xmlstream(fp) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 460, in parse_xmlstream raise Exception("Error " + self.current_state()) from e Exception: Error In tag record model gnuhealth.gene with id health_genetics.A2BP1. ## Add Language to tryton ... Connecting to database 'po-export-db' with 'admin' ... /usr/lib/python3/dist-packages/passlib/utils/__init__.py:854: DeprecationWarning: 'crypt' is deprecated and slated for removal in Python 3.13 from crypt import crypt as _crypt ## Running trytond-admin command to update DB (3. Active language) ... Traceback (most recent call last): File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 614, in create cursor.execute(table.insert(insert_columns, File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/backend/postgresql/database.py", line 74, in execute cursor.execute(self, sql, args) psycopg2.errors.NotNullViolation: 错误: null value in column "aliases" of relation "gnuhealth_gene" violates not-null constraint DETAIL: 失败, 行包含(1, null, 16, 2023-07-24 04:57:44.862633, 0, null, null, null, mutations , 16p13, ataxin 2-binding protein 1, A2BP1, null, null, null). During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 458, in parse_xmlstream self.sax_parser.parse(source) File "/usr/lib/python3.11/xml/sax/expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "/usr/lib/python3.11/xml/sax/xmlreader.py", line 125, in parse self.feed(buffer) File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed self._parser.Parse(data, isFinal) File "../Modules/pyexpat.c", line 468, in EndElement File "/usr/lib/python3.11/xml/sax/expatreader.py", line 336, in end_element self._cont_handler.endElement(name) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 513, in endElement self.taghandler = self.taghandler.endElement(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 295, in endElement self.mh.import_record( File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 689, in import_record self.create_records(model, [values], [fs_id]) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 695, in create_records records = Model.create(vlist) ^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 159, in wrapper return func(cls, args, *kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 634, in create cls.__raise_integrity_error( File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/model/modelsql.py", line 352, in __raise_integrity_error raise RequiredValidationError( trytond.model.modelstorage.RequiredValidationError: A value is required for field "aliases" in "gnuhealth.gene". - The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/bin/trytond-admin", line 23, in <module> admin.run(options) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/admin.py", line 53, in run pool.init(update=options.update, lang=list(lang), File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/pool.py", line 164, in init restart = not load_modules( ^^^^^^^^^^^^^ File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 440, in load_modules _load_modules(update) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 408, in _load_modules load_module_graph(graph, pool, update, lang) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/modules/__init__.py", line 252, in load_module_graph tryton_parser.parse_xmlstream(fp) File "/home/feng/gnuhealth/tryton/server/trytond-6.0.33/trytond/convert.py", line 460, in parse_xmlstream raise Exception("Error " + self.current_state()) from e Exception: Error In tag record model gnuhealth.gene with id health_genetics.A2BP1.	Feng Shu <tumashu>

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Follow 6 latest changes.

Date	Changed by	Updated Field	Previous Value	Replaced by
2023-08-11	meanmicio	Status	Confirmed	Ready For Test
2023-08-10	meanmicio	Status	In Progress	Confirmed
2023-07-24	meanmicio	Category	None	Programming / Tracebacks
		Status	None	In Progress
		Assigned to	None	meanmicio
		Release	None	4.3.0

GNU Health - Bugs: bug #64464, health_genetics export po file...

bug #64464: health_genetics export po file error.

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