V6 => V7 Bench update error

Any idea why this error is happening?

INFO:bench.utils:updating bench
Already up-to-date.
Requirement already satisfied (use --upgrade to upgrade): Pillow in ./env/lib/python2.7/site-packages
INFO:bench.app:pulling frappe
From https://github.com/frappe/frappe
 * branch            master     -> FETCH_HEAD
Already up-to-date.
INFO:bench.app:pulling erpnext
From https://github.com/frappe/erpnext
 * branch            master     -> FETCH_HEAD
Already up-to-date.
Requirement already up-to-date: pip in ./env/lib/python2.7/site-packages
Command "/home/ubuntu/frappe-bench/env/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-FwR4Hi/cryptography/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-vgYw31-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/ubuntu/frappe-bench/env/include/site/python2.7/cryptography" failed with error code 1 in /tmp/pip-build-FwR4Hi/cryptography/
Traceback (most recent call last):
  File "/usr/local/bin/bench", line 9, in <module>
    load_entry_point('bench==2.0.0', 'console_scripts', 'bench')()
  File "/home/ubuntu/bench-repo/bench/cli.py", line 40, in cli
    bench_command()
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/home/ubuntu/bench-repo/bench/commands/update.py", line 60, in update
    _update(pull, patch, build, bench, auto, restart_supervisor, requirements, no_backup, upgrade, force=force)
  File "/home/ubuntu/bench-repo/bench/commands/update.py", line 79, in _update
    update_requirements(bench_path=bench_path)
  File "/home/ubuntu/bench-repo/bench/utils.py", line 375, in update_requirements
    install_requirements(pip, req_file)
  File "/home/ubuntu/bench-repo/bench/utils.py", line 379, in install_requirements
    exec_cmd("{pip} install -q -r {req_file}".format(pip=pip, req_file=req_file))
  File "/home/ubuntu/bench-repo/bench/utils.py", line 130, in exec_cmd
    raise CommandFailedError(cmd)
bench.utils.CommandFailedError: ./env/bin/pip install -q -r ./apps/frappe/requirements.txt

manage to correct my 1st trouble but then :

INFO:bench.utils:updating bench
Already up-to-date.
Requirement already satisfied (use --upgrade to upgrade): Pillow in ./env/lib/python2.7/site-packages
INFO:bench.app:pulling frappe
From https://github.com/frappe/frappe
 * branch            master     -> FETCH_HEAD
Already up-to-date.
INFO:bench.app:pulling erpnext
From https://github.com/frappe/erpnext
 * branch            master     -> FETCH_HEAD
Already up-to-date.
Requirement already up-to-date: pip in ./env/lib/python2.7/site-packages
Migrating site1.local
Executing erpnext.patches.v7_0.migrate_schools_to_erpnext in site1.local (1bd3e0294d)
/home/ubuntu/frappe-bench/apps/erpnext/erpnext/schools/doctype/examination/examination.json missing
Traceback (most recent call last):
  File "/usr/lib/python2.7/runpy.py", line 162, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/utils/bench_helper.py", line 79, in <module>
    main()
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/utils/bench_helper.py", line 16, in main
    click.Group(commands=commands)(prog_name='bench')
  File "/home/ubuntu/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/home/ubuntu/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/home/ubuntu/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/ubuntu/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/ubuntu/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/ubuntu/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/home/ubuntu/frappe-bench/env/local/lib/python2.7/site-packages/click/decorators.py", line 17, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/commands/__init__.py", line 24, in _func
    ret = f(frappe._dict(ctx.obj), *args, **kwargs)
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/commands/site.py", line 206, in migrate
    migrate(context.verbose, rebuild_website=rebuild_website)
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/migrate.py", line 27, in migrate
    frappe.modules.patch_handler.run_all()
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/modules/patch_handler.py", line 25, in run_all
    if not run_single(patchmodule = patch):
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/modules/patch_handler.py", line 52, in run_single
    return execute_patch(patchmodule, method, methodargs)
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/modules/patch_handler.py", line 68, in execute_patch
    frappe.get_attr(patchmodule.split()[0] + ".execute")()
  File "/home/ubuntu/frappe-bench/apps/erpnext/erpnext/patches/v7_0/migrate_schools_to_erpnext.py", line 26, in execute
    frappe.get_doc('Portal Settings', 'Portal Settings').sync_menu()
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/website/doctype/portal_settings/portal_settings.py", line 30, in sync_menu
    self.save()
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/model/document.py", line 242, in save
    return self._save(*args, **kwargs)
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/model/document.py", line 272, in _save
    self._validate()
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/model/document.py", line 388, in _validate
    self._validate_links()
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/model/document.py", line 630, in _validate_links
    frappe.LinkValidationError)
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/__init__.py", line 299, in throw
    msgprint(msg, raise_exception=exc, title=title, indicator='red')
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/__init__.py", line 292, in msgprint
    _raise_exception()
  File "/home/ubuntu/frappe-bench/apps/frappe/frappe/__init__.py", line 265, in _raise_exception
    raise raise_exception, encode(msg)
frappe.exceptions.LinkValidationError: Could not find Row #10: Reference Doctype: Assessment
Traceback (most recent call last):
  File "/usr/local/bin/bench", line 9, in <module>
    load_entry_point('bench==2.0.0', 'console_scripts', 'bench')()
  File "/home/ubuntu/bench-repo/bench/cli.py", line 40, in cli
    bench_command()
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/home/ubuntu/bench-repo/bench/commands/update.py", line 60, in update
    _update(pull, patch, build, bench, auto, restart_supervisor, requirements, no_backup, upgrade, force=force)
  File "/home/ubuntu/bench-repo/bench/commands/update.py", line 90, in _update
    patch_sites(bench_path=bench_path)
  File "/home/ubuntu/bench-repo/bench/utils.py", line 164, in patch_sites
    run_frappe_cmd('--site', 'all', 'migrate', bench_path=bench_path)
  File "/home/ubuntu/bench-repo/bench/utils.py", line 501, in run_frappe_cmd
    raise CommandFailedError(args)
bench.utils.CommandFailedError: ('--site', 'all', 'migrate')

Im having the same issue. Cannot upgrade.

frappe@erpnext:~/frappe-bench$ sudo bench retry-upgrade
INFO:bench.app:pulling frappe
From https://github.com/frappe/frappe
 * branch            master     -> FETCH_HEAD
Already up-to-date.
INFO:bench.app:pulling erpnext
From https://github.com/frappe/erpnext
 * branch            master     -> FETCH_HEAD
Already up-to-date.
INFO:bench.app:pulling erpnext_demo
From https://github.com/frappe/erpnext_demo
 * branch            master     -> FETCH_HEAD
Already up-to-date.
Migrating erpnext.vm
Executing erpnext.patches.v7_0.migrate_schools_to_erpnext in erpnext.vm (d56cb677ea)
/home/frappe/frappe-bench/apps/erpnext/erpnext/schools/doctype/examination/examination.json missing
Traceback (most recent call last):
  File "/usr/lib/python2.7/runpy.py", line 162, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/frappe/frappe-bench/apps/frappe/frappe/utils/bench_helper.py", line 79, in <module>
    main()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/utils/bench_helper.py", line 16, in main
    click.Group(commands=commands)(prog_name='bench')
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/decorators.py", line 17, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/commands/__init__.py", line 24, in _func
    ret = f(frappe._dict(ctx.obj), *args, **kwargs)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/commands/site.py", line 206, in migrate
    migrate(context.verbose, rebuild_website=rebuild_website)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/migrate.py", line 27, in migrate
    frappe.modules.patch_handler.run_all()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/patch_handler.py", line 25, in run_all
    if not run_single(patchmodule = patch):
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/patch_handler.py", line 52, in run_single
    return execute_patch(patchmodule, method, methodargs)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/patch_handler.py", line 68, in execute_patch
    frappe.get_attr(patchmodule.split()[0] + ".execute")()
  File "/home/frappe/frappe-bench/apps/erpnext/erpnext/patches/v7_0/migrate_schools_to_erpnext.py", line 26, in execute
    frappe.get_doc('Portal Settings', 'Portal Settings').sync_menu()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/website/doctype/portal_settings/portal_settings.py", line 30, in sync_menu
    self.save()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/model/document.py", line 242, in save
    return self._save(*args, **kwargs)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/model/document.py", line 272, in _save
    self._validate()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/model/document.py", line 388, in _validate
    self._validate_links()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/model/document.py", line 630, in _validate_links
    frappe.LinkValidationError)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/__init__.py", line 299, in throw
    msgprint(msg, raise_exception=exc, title=title, indicator='red')
  File "/home/frappe/frappe-bench/apps/frappe/frappe/__init__.py", line 292, in msgprint
    _raise_exception()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/__init__.py", line 265, in _raise_exception
    raise raise_exception, encode(msg)
frappe.exceptions.LinkValidationError: Could not find Row #10: Reference Doctype: Assessment
Traceback (most recent call last):
  File "/usr/local/bin/bench", line 9, in <module>
    load_entry_point('bench', 'console_scripts', 'bench')()
  File "/home/frappe/bench-repo/bench/cli.py", line 40, in cli
    bench_command()
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/home/frappe/bench-repo/bench/commands/update.py", line 107, in retry_upgrade
    patch_sites()
  File "/home/frappe/bench-repo/bench/utils.py", line 164, in patch_sites
    run_frappe_cmd('--site', 'all', 'migrate', bench_path=bench_path)
  File "/home/frappe/bench-repo/bench/utils.py", line 501, in run_frappe_cmd
    raise CommandFailedError(args)
bench.utils.CommandFailedError: ('--site', 'all', 'migrate')

Pushed a fix.

Thank you @rmehta It is now working perfectly thanks to you!

I applied a manual fix from another thread and got it working in the meantime, but another instance i just tried to update this morning fail for another reason.

Traceback (most recent call last):
  File "/usr/lib/python2.7/runpy.py", line 162, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/frappe/frappe-bench/apps/frappe/frappe/utils/bench_helper.py", line 79, in <module>
    main()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/utils/bench_helper.py", line 16, in main
    click.Group(commands=commands)(prog_name='bench')
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/decorators.py", line 17, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/commands/__init__.py", line 24, in _func
    ret = f(frappe._dict(ctx.obj), *args, **kwargs)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/commands/site.py", line 206, in migrate
    migrate(context.verbose, rebuild_website=rebuild_website)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/migrate.py", line 27, in migrate
    frappe.modules.patch_handler.run_all()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/patch_handler.py", line 25, in run_all
    if not run_single(patchmodule = patch):
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/patch_handler.py", line 52, in run_single
    return execute_patch(patchmodule, method, methodargs)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/patch_handler.py", line 68, in execute_patch
    frappe.get_attr(patchmodule.split()[0] + ".execute")()
  File "/home/frappe/frappe-bench/apps/erpnext/erpnext/patches/v7_0/fix_duplicate_icons.py", line 11, in execute
    sync_desktop_icons()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/desk/doctype/desktop_icon/desktop_icon.py", line 281, in sync_desktop_icons
    sync_from_app(app)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/desk/doctype/desktop_icon/desktop_icon.py", line 317, in sync_from_app
    desktop_icon.save()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/model/document.py", line 242, in save
    return self._save(*args, **kwargs)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/model/document.py", line 259, in _save
    self.insert()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/model/document.py", line 213, in insert
    self._validate()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/model/document.py", line 388, in _validate
    self._validate_links()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/model/document.py", line 630, in _validate_links
    frappe.LinkValidationError)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/__init__.py", line 299, in throw
    msgprint(msg, raise_exception=exc, title=title, indicator='red')
  File "/home/frappe/frappe-bench/apps/frappe/frappe/__init__.py", line 292, in msgprint
    _raise_exception()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/__init__.py", line 265, in _raise_exception
    raise raise_exception, encode(msg)
frappe.exceptions.LinkValidationError: Could not find _doctype: Student
Traceback (most recent call last):
  File "/usr/local/bin/bench", line 9, in <module>
    load_entry_point('bench', 'console_scripts', 'bench')()
  File "/home/frappe/bench-repo/bench/cli.py", line 40, in cli
    bench_command()
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/home/frappe/bench-repo/bench/commands/update.py", line 60, in update
    _update(pull, patch, build, bench, auto, restart_supervisor, requirements, no_backup, upgrade, force=force)
  File "/home/frappe/bench-repo/bench/commands/update.py", line 90, in _update
    patch_sites(bench_path=bench_path)
  File "/home/frappe/bench-repo/bench/utils.py", line 164, in patch_sites
    run_frappe_cmd('--site', 'all', 'migrate', bench_path=bench_path)
  File "/home/frappe/bench-repo/bench/utils.py", line 504, in run_frappe_cmd
    raise CommandFailedError(args)
bench.utils.CommandFailedError: ('--site', 'all', 'migrate')
frappe@erpnext:~/frappe-bench$

Resolved this issue manually. Had to reload docs manually first for some reason.

bench --force reload-doc schools doctype student 
bench --force reload-doc schools doctype student_group 
bench --force reload-doc schools doctype course_schedule 
bench --force reload-doc schools doctype student_attendance 
bench --force reload-doc schools doctype course
bench --force reload-doc schools doctype program 
bench --force reload-doc schools doctype student_applicant 
bench --force reload-doc schools doctype examination 
bench --force reload-doc schools doctype fees 
bench --force reload-doc schools doctype instructor 
bench --force reload-doc schools doctype room

Sorry - pushed another fix.

Thanks! Will test original system later!