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Opencloning docs#47

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NicolasCARPi merged 9 commits intoelabftw:nextfrom
manulera:opencloning-docs
Jun 17, 2025
Merged

Opencloning docs#47
NicolasCARPi merged 9 commits intoelabftw:nextfrom
manulera:opencloning-docs

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@manulera
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As discussed, this PR includes documentation for the following:

  • What you need to load a sequence (must have a sequence file as an attachment)
  • What you need to load a primer (must have a resource entry with a field
    "sequence")
  • What happens when you save a sequence (the files that are created)
  • What happens when you save a primer (a resource with field sequence is created)
  • What happens when you save a sequence with intermediates (sequences that will
    have no entry in the database but will be saved as part of the history)
  • What happens when you save a sequence that used unsaved primers (you will be
    asked if you want to save them), and where they end up if you don't save them to
    the database.
  • Some best practices on how to set up the resource types to support the
    representation of strains and cell lines. One should have the following resource
    types:
    • Plasmid
    • Allele
    • Locus
    • Strain / cell line

@NicolasCARPi NicolasCARPi requested a review from sjkoke June 11, 2025 10:48
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Haven't looked at it too much yet but you can already adress the compilation warnings:

/home/ktr/.dev/elabdoc/doc/addons.rst:128: WARNING: Title underline too short.

Creating resources from OpenCloning
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [docutils]
/home/ktr/.dev/elabdoc/doc/addons.rst:128: WARNING: Title underline too short.

Creating resources from OpenCloning
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [docutils]
/home/ktr/.dev/elabdoc/doc/addons.rst:168: WARNING: Title underline too short.

Creating a primer
"""""""""""""""" [docutils]
/home/ktr/.dev/elabdoc/doc/addons.rst:168: WARNING: Title underline too short.

Creating a primer
"""""""""""""""" [docutils]
/home/ktr/.dev/elabdoc/doc/addons.rst:177: WARNING: Title underline too short.

Removing resources from the session
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [docutils]
/home/ktr/.dev/elabdoc/doc/addons.rst:177: WARNING: Title underline too short.

Removing resources from the session
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [docutils]
/home/ktr/.dev/elabdoc/doc/addons.rst:182: WARNING: Title underline too short.

Sequencing data
^^^^^^^^^^^^^^ [docutils]
/home/ktr/.dev/elabdoc/doc/addons.rst:182: WARNING: Title underline too short.

Sequencing data
^^^^^^^^^^^^^^ [docutils]
/home/ktr/.dev/elabdoc/doc/addons.rst:199: WARNING: Title underline too short.

Resource type organization
^^^^^^^^^^^^^^^^^^^^^^^^ [docutils]
/home/ktr/.dev/elabdoc/doc/addons.rst:199: WARNING: Title underline too short.

Resource type organization
^^^^^^^^^^^^^^^^^^^^^^^^ [docutils]
/home/ktr/.dev/elabdoc/doc/addons.rst:240: WARNING: Title underline too short.

Creating strains and cell lines
"""""""""""""""""""""""""""""" [docutils]
/home/ktr/.dev/elabdoc/doc/addons.rst:240: WARNING: Title underline too short.

Creating strains and cell lines
"""""""""""""""""""""""""""""" [docutils]

manulera and others added 4 commits June 12, 2025 08:26
…anulera-opencloning-docs

* 'opencloning-docs' of github.com:manulera/elabdoc:
  fix warnings
  final edit
  complete docs
  some extra work on docs
  starting with docs
NicolasCARPi
NicolasCARPi previously approved these changes Jun 13, 2025
@manulera manulera dismissed NicolasCARPi’s stale review June 13, 2025 23:14

The merge-base changed after approval.

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@sjkoke sjkoke left a comment

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Made some edits for grammar, checked the basic workflow.

sjkoke
sjkoke previously approved these changes Jun 17, 2025
@manulera manulera dismissed sjkoke’s stale review June 17, 2025 12:27

The merge-base changed after approval.

@NicolasCARPi NicolasCARPi merged commit 7a406b3 into elabftw:next Jun 17, 2025
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@manulera
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Thanks @sjkoke

@manulera manulera deleted the opencloning-docs branch June 18, 2025 16:47
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3 participants