From 21d30a923f42813216b805ee6a53eefab8a73e91 Mon Sep 17 00:00:00 2001 From: Tobias O Date: Wed, 12 Nov 2025 22:47:10 +1300 Subject: [PATCH] [Refactor] Large scale formatting/linting (#193) All html files now prettier formatted and fixes for incompatible blocks applied Co-authored-by: Tim Lorsbach Reviewed-on: https://git.envipath.com/enviPath/enviPy/pulls/193 Co-authored-by: Tobias O Co-committed-by: Tobias O --- templates/actions/collections/compound.html | 11 +- .../collections/compound_structure.html | 15 +- templates/actions/collections/edge.html | 11 +- templates/actions/collections/group.html | 5 +- templates/actions/collections/model.html | 9 +- templates/actions/collections/node.html | 11 +- templates/actions/collections/package.html | 22 +- templates/actions/collections/reaction.html | 11 +- templates/actions/collections/rule.html | 9 +- templates/actions/collections/scenario.html | 11 +- templates/actions/collections/setting.html | 11 +- templates/actions/objects/compound.html | 67 +- .../actions/objects/compound_structure.html | 53 +- templates/actions/objects/edge.html | 27 +- templates/actions/objects/group.html | 18 +- templates/actions/objects/model.html | 38 +- templates/actions/objects/node.html | 36 +- templates/actions/objects/package.html | 60 +- templates/actions/objects/pathway.html | 143 ++-- templates/actions/objects/reaction.html | 58 +- templates/actions/objects/rule.html | 45 +- templates/actions/objects/scenario.html | 37 +- templates/actions/objects/user.html | 50 +- templates/admin.html | 54 +- templates/collections/joblog.html | 135 ++-- templates/collections/objects_list.html | 635 +++++++++------ templates/compare.html | 120 +-- templates/errors/400_bad_request.html | 19 +- templates/errors/403_access_denied.html | 21 +- templates/errors/404_not_found.html | 19 +- templates/errors/error.html | 14 +- templates/errors/user_account_inactive.html | 15 +- templates/framework.html | 4 +- templates/framework_modern.html | 6 +- templates/migration.html | 91 ++- templates/migration_detail.html | 106 ++- templates/modals/cite_modal.html | 75 +- .../import_legacy_package_modal.html | 102 ++- .../collections/import_package_modal.html | 102 ++- .../collections/new_compound_modal.html | 177 +++-- .../modals/collections/new_group_modal.html | 105 ++- .../modals/collections/new_model_modal.html | 426 ++++++---- .../modals/collections/new_package_modal.html | 120 +-- .../modals/collections/new_pathway_modal.html | 630 ++++++++------- .../new_prediction_setting_modal.html | 262 +++--- .../collections/new_reaction_modal.html | 125 ++- .../modals/collections/new_rule_modal.html | 160 ++-- .../collections/new_scenario_modal.html | 237 +++--- .../add_additional_information_modal.html | 133 ++-- .../objects/add_pathway_edge_modal.html | 281 ++++--- .../objects/add_pathway_node_modal.html | 177 +++-- .../modals/objects/add_structure_modal.html | 177 +++-- .../objects/delete_pathway_edge_modal.html | 131 +-- .../objects/delete_pathway_node_modal.html | 133 ++-- .../objects/download_pathway_csv_modal.html | 75 +- .../objects/download_pathway_image_modal.html | 61 +- .../modals/objects/edit_compound_modal.html | 103 ++- .../edit_compound_structure_modal.html | 100 ++- .../objects/edit_group_member_modal.html | 248 +++--- .../modals/objects/edit_model_modal.html | 102 ++- templates/modals/objects/edit_node_modal.html | 103 ++- .../modals/objects/edit_package_modal.html | 99 ++- .../edit_package_permissions_modal.html | 397 ++++++---- .../modals/objects/edit_password_modal.html | 112 ++- .../modals/objects/edit_pathway_modal.html | 100 ++- .../edit_prediction_setting_modal.html | 253 +++--- .../modals/objects/edit_reaction_modal.html | 98 ++- templates/modals/objects/edit_rule_modal.html | 98 ++- templates/modals/objects/edit_user_modal.html | 156 ++-- .../modals/objects/evaluate_model_modal.html | 146 ++-- .../modals/objects/export_package_modal.html | 75 +- .../objects/generic_copy_object_modal.html | 164 ++-- .../modals/objects/generic_delete_modal.html | 86 +- .../objects/generic_set_aliases_modal.html | 345 ++++---- .../generic_set_external_reference_modal.html | 142 ++-- .../objects/generic_set_scenario_modal.html | 97 ++- .../objects/identify_missing_rules_modal.html | 113 +-- .../objects/manage_api_token_modal.html | 188 +++-- .../modals/objects/publish_package_modal.html | 71 +- .../modals/objects/set_license_modal.html | 283 ++++--- ...scenario_additional_information_modal.html | 87 +- templates/modals/predict_modal.html | 273 ++++--- templates/objects/composite_rule.html | 277 ++++--- templates/objects/compound.html | 594 ++++++++------ templates/objects/compound_structure.html | 218 +++-- templates/objects/edge.html | 336 +++++--- templates/objects/enzymelink.html | 253 +++--- templates/objects/group.html | 117 +-- templates/objects/model.html | 14 +- templates/objects/node.html | 260 +++--- templates/objects/package.html | 107 ++- templates/objects/pathway.html | 746 ++++++++++-------- templates/objects/reaction.html | 562 ++++++++----- templates/objects/scenario.html | 188 +++-- templates/objects/simple_rule.html | 595 ++++++++------ templates/objects/user.html | 302 +++---- templates/pathway_playground.html | 17 +- templates/pathway_playground2.html | 133 ++-- templates/predict_pathway.html | 3 +- templates/static/about_us.html | 302 ++++--- templates/static/careers.html | 419 ++++++---- templates/static/cite.html | 413 ++++++---- templates/static/contact.html | 408 ++++++---- templates/static/cookie_policy.html | 320 +++++--- templates/static/legal.html | 320 +++++--- templates/static/login.html | 12 +- templates/static/login_base.html | 169 ++-- templates/static/password_reset_complete.html | 44 +- templates/static/password_reset_confirm.html | 181 +++-- templates/static/password_reset_done.html | 48 +- templates/static/password_reset_form.html | 50 +- templates/static/privacy_policy.html | 274 ++++--- templates/static/static_base.html | 102 +-- templates/static/terms_of_use.html | 184 +++-- 114 files changed, 10684 insertions(+), 7009 deletions(-) diff --git a/templates/actions/collections/compound.html b/templates/actions/collections/compound.html index 90551b07..417f30a8 100644 --- a/templates/actions/collections/compound.html +++ b/templates/actions/collections/compound.html @@ -1,6 +1,7 @@ {% if meta.can_edit %} -
  • - - New Compound -
    • -{% endif %} \ No newline at end of file +
  • + + New Compound +
    • +{% endif %} diff --git a/templates/actions/collections/compound_structure.html b/templates/actions/collections/compound_structure.html index 3e615cc1..3867a865 100644 --- a/templates/actions/collections/compound_structure.html +++ b/templates/actions/collections/compound_structure.html @@ -1,6 +1,11 @@ {% if meta.can_edit %} -
  • - - New Compound Structure -
    • -{% endif %} \ No newline at end of file +
  • + + New Compound Structure +
    • +{% endif %} diff --git a/templates/actions/collections/edge.html b/templates/actions/collections/edge.html index eb003dc1..efdccf98 100644 --- a/templates/actions/collections/edge.html +++ b/templates/actions/collections/edge.html @@ -1,6 +1,7 @@ {% if meta.can_edit %} -
  • - - New Edge -
    • -{% endif %} \ No newline at end of file +
  • + + New Edge +
    • +{% endif %} diff --git a/templates/actions/collections/group.html b/templates/actions/collections/group.html index dd9054cf..7146febc 100644 --- a/templates/actions/collections/group.html +++ b/templates/actions/collections/group.html @@ -1,4 +1,5 @@
  • - - New Group + + New Group
    • diff --git a/templates/actions/collections/model.html b/templates/actions/collections/model.html index 94d1a952..48be3ea9 100644 --- a/templates/actions/collections/model.html +++ b/templates/actions/collections/model.html @@ -1,6 +1,7 @@ {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %} -
  • - - New Model -
    • +
  • + + New Model +
    • {% endif %} diff --git a/templates/actions/collections/node.html b/templates/actions/collections/node.html index 968423f3..4835e16f 100644 --- a/templates/actions/collections/node.html +++ b/templates/actions/collections/node.html @@ -1,6 +1,7 @@ {% if meta.can_edit %} -
  • - - New Node -
    • -{% endif %} \ No newline at end of file +
  • + + New Node +
    • +{% endif %} diff --git a/templates/actions/collections/package.html b/templates/actions/collections/package.html index 1fdd80bf..edb3577b 100644 --- a/templates/actions/collections/package.html +++ b/templates/actions/collections/package.html @@ -1,12 +1,20 @@
  • - - New Package + + New Package
  • - - Import Package from JSON + + Import Package from JSON
  • - - Import Package from legacy JSON -
    • \ No newline at end of file + + Import Package from legacy + JSON + diff --git a/templates/actions/collections/reaction.html b/templates/actions/collections/reaction.html index 00d96f4f..62ebd8ed 100644 --- a/templates/actions/collections/reaction.html +++ b/templates/actions/collections/reaction.html @@ -1,6 +1,7 @@ {% if meta.can_edit %} -
  • - - New Reaction -
    • -{% endif %} \ No newline at end of file +
  • + + New Reaction +
    • +{% endif %} diff --git a/templates/actions/collections/rule.html b/templates/actions/collections/rule.html index dbef29da..a3dcbbcd 100644 --- a/templates/actions/collections/rule.html +++ b/templates/actions/collections/rule.html @@ -1,6 +1,7 @@ {% if meta.can_edit %} -
  • - - New Rule -
    • +
  • + + New Rule +
    • {% endif %} diff --git a/templates/actions/collections/scenario.html b/templates/actions/collections/scenario.html index 25b46b7f..92521924 100644 --- a/templates/actions/collections/scenario.html +++ b/templates/actions/collections/scenario.html @@ -1,6 +1,7 @@ {% if meta.can_edit %} -
  • - - New Scenario -
    • -{% endif %} \ No newline at end of file +
  • + + New Scenario +
    • +{% endif %} diff --git a/templates/actions/collections/setting.html b/templates/actions/collections/setting.html index db8b95dc..4d7eb345 100644 --- a/templates/actions/collections/setting.html +++ b/templates/actions/collections/setting.html @@ -1,6 +1,7 @@ {% if meta.can_edit %} -
  • - - New Setting -
    • -{% endif %} \ No newline at end of file +
  • + + New Setting +
    • +{% endif %} diff --git a/templates/actions/objects/compound.html b/templates/actions/objects/compound.html index c56918b5..ff34041b 100644 --- a/templates/actions/objects/compound.html +++ b/templates/actions/objects/compound.html @@ -1,32 +1,43 @@ {% if meta.can_edit %} -
  • - - Edit Compound -
    • -
  • - - Set Aliases -
    • -
  • - - Add Structure -
    • -
  • - - Set Scenarios -
    • -
  • - - Set External Reference -
    • +
  • + + Edit Compound +
    • +
  • + + Set Aliases +
    • +
  • + + Add Structure +
    • +
  • + + Set Scenarios +
    • +
  • + + Set External Reference +
    • {% endif %} -
  • - - Copy -
    • +
  • + + Copy +
    • {% if meta.can_edit %} -
  • - - Delete Compound -
    • +
  • + + Delete Compound +
    • {% endif %} diff --git a/templates/actions/objects/compound_structure.html b/templates/actions/objects/compound_structure.html index 45647405..cfe3a57b 100644 --- a/templates/actions/objects/compound_structure.html +++ b/templates/actions/objects/compound_structure.html @@ -1,22 +1,35 @@ {% if meta.can_edit %} -
  • - - Edit Compound Structure -
    • -
  • - - Set Aliases -
    • -
  • - - Set Scenarios -
    • -
  • - - Set External Reference -
    • -
  • - - Delete Compound Structure -
    • +
  • + + Edit Compound Structure +
    • +
  • + + Set Aliases +
    • +
  • + + Set Scenarios +
    • +
  • + + Set External Reference +
    • +
  • + + Delete Compound Structure +
    • {% endif %} diff --git a/templates/actions/objects/edge.html b/templates/actions/objects/edge.html index e595a248..c36d7dd2 100644 --- a/templates/actions/objects/edge.html +++ b/templates/actions/objects/edge.html @@ -1,14 +1,17 @@ {% if meta.can_edit %} -
  • - - Set Aliases -
    • -
  • - - Set Scenarios -
    • -
  • - - Delete Edge -
    • +
  • + + Set Aliases +
    • +
  • + + Set Scenarios +
    • +
  • + + Delete Edge +
    • {% endif %} diff --git a/templates/actions/objects/group.html b/templates/actions/objects/group.html index b7fdbeb3..fdeeb76b 100644 --- a/templates/actions/objects/group.html +++ b/templates/actions/objects/group.html @@ -1,10 +1,12 @@ {% if meta.can_edit %} -
  • +
  • - Add/Remove Member -
    • -
  • - - Delete Group -
    • -{% endif %} \ No newline at end of file + Add/Remove Member + +
  • + + Delete Group +
    • +{% endif %} diff --git a/templates/actions/objects/model.html b/templates/actions/objects/model.html index acff9f23..b84d7f67 100644 --- a/templates/actions/objects/model.html +++ b/templates/actions/objects/model.html @@ -1,18 +1,22 @@ {% if meta.can_edit %} -
  • - - Edit Model -
    • -
  • - - Evaluate Model -
    • -
  • - - Retrain Model -
    • -
  • - - Delete Model -
    • -{% endif %} \ No newline at end of file +
  • + + Edit Model +
    • +
  • + + Evaluate Model +
    • +
  • + + Retrain Model +
    • +
  • + + Delete Model +
    • +{% endif %} diff --git a/templates/actions/objects/node.html b/templates/actions/objects/node.html index 605cacf6..787132eb 100644 --- a/templates/actions/objects/node.html +++ b/templates/actions/objects/node.html @@ -1,18 +1,22 @@ {% if meta.can_edit %} -
  • - - Edit Node -
    • -
  • - - Set Aliases -
    • -
  • - - Set Scenarios -
    • -
  • - - Delete Node -
    • +
  • + + Edit Node +
    • +
  • + + Set Aliases +
    • +
  • + + Set Scenarios +
    • +
  • + + Delete Node +
    • {% endif %} diff --git a/templates/actions/objects/package.html b/templates/actions/objects/package.html index 22a56421..fb489d37 100644 --- a/templates/actions/objects/package.html +++ b/templates/actions/objects/package.html @@ -1,26 +1,36 @@ {% if meta.can_edit %} -
  • - - Edit Package -
    • -
  • - - Edit Permissions -
    • -
  • - - Publish Package -
    • -
  • - - Export Package as JSON -
    • -
  • - - License -
    • -
  • - - Delete Package -
    • -{% endif %} \ No newline at end of file +
  • + + Edit Package +
    • +
  • + + Edit Permissions +
    • +
  • + + Publish Package +
    • +
  • + + Export Package as JSON +
    • +
  • + + License +
    • +
  • + + Delete Package +
    • +{% endif %} diff --git a/templates/actions/objects/pathway.html b/templates/actions/objects/pathway.html index 785f6213..760557b9 100644 --- a/templates/actions/objects/pathway.html +++ b/templates/actions/objects/pathway.html @@ -1,59 +1,92 @@ {% if meta.can_edit %} -
  • - - Add Compound -
    • -
  • - - Add Reaction -
    • - +
  • + + Add Compound +
    • +
  • + + Add Reaction +
    • + {% endif %} -
  • - - Copy -
    • -
  • - - Download Pathway as CSV -
    • -
  • - - Download Pathway as Image -
    • +
  • + + Copy +
    • +
  • + + Download Pathway as CSV +
    • +
  • + + Download Pathway as Image +
    • {% if meta.can_edit %} -
  • - - Identify Missing Rules -
    • - -
  • - - Edit Pathway -
    • -
  • - - Set Scenarios -
    • -
  • - - Set Aliases -
    • - {#
  • #} - {# #} - {# Calculate Compound Properties#} - {#
    • #} - -
  • - - Delete Compound -
    • -
  • - - Delete Reaction -
    • -
  • - - Delete Pathway -
    • +
  • + + Identify Missing + Rules +
    • + +
  • + + Edit Pathway +
    • +
  • + + Set Scenarios +
    • +
  • + + Set Aliases +
    • + {#
  • #} + {# #} + {# Calculate Compound Properties#} + {#
    • #} + +
  • + + Delete Compound +
    • +
  • + + Delete Reaction +
    • +
  • + + Delete Pathway +
    • {% endif %} diff --git a/templates/actions/objects/reaction.html b/templates/actions/objects/reaction.html index 73484600..1bf3d953 100644 --- a/templates/actions/objects/reaction.html +++ b/templates/actions/objects/reaction.html @@ -1,28 +1,38 @@ {% if meta.can_edit %} -
  • - - Edit Reaction -
    • -
  • - - Set Aliases -
    • -
  • - - Set Scenarios -
    • -
  • - - Set External Reference -
    • +
  • + + Edit Reaction +
    • +
  • + + Set Aliases +
    • +
  • + + Set Scenarios +
    • +
  • + + Set External Reference +
    • {% endif %} -
  • - - Copy -
    • +
  • + + Copy +
    • {% if meta.can_edit %} -
  • - - Delete Reaction -
    • +
  • + + Delete Reaction +
    • {% endif %} diff --git a/templates/actions/objects/rule.html b/templates/actions/objects/rule.html index 1b7b85c3..4c9e0282 100644 --- a/templates/actions/objects/rule.html +++ b/templates/actions/objects/rule.html @@ -1,24 +1,29 @@ {% if meta.can_edit %} -
  • - - Edit Rule -
    • -
  • - - Set Aliases -
    • -
  • - - Set Scenarios -
    • +
  • + + Edit Rule +
    • +
  • + + Set Aliases +
    • +
  • + + Set Scenarios +
    • {% endif %} -
  • - - Copy -
    • +
  • + + Copy +
    • {% if meta.can_edit %} -
  • - - Delete Rule -
    • +
  • + + Delete Rule +
    • {% endif %} diff --git a/templates/actions/objects/scenario.html b/templates/actions/objects/scenario.html index ddc79ed4..33e9f999 100644 --- a/templates/actions/objects/scenario.html +++ b/templates/actions/objects/scenario.html @@ -1,14 +1,25 @@ {% if meta.can_edit %} -
  • - - Add Additional Information -
    • -
  • - - Set Additional Information -
    • -
  • - - Delete Scenario -
    • -{% endif %} \ No newline at end of file +
  • + + Add Additional Information +
    • +
  • + + Set Additional Information +
    • +
  • + + Delete Scenario +
    • +{% endif %} diff --git a/templates/actions/objects/user.html b/templates/actions/objects/user.html index e1d832f1..9404c57c 100644 --- a/templates/actions/objects/user.html +++ b/templates/actions/objects/user.html @@ -1,22 +1,30 @@ {% if meta.can_edit %} -
  • - - Update -
    • -
  • - - Update Password -
    • -
  • - - New Prediction Setting -
    • -{#
  • #} -{# #} -{# Manage API Token#} -{#
    • #} -
  • - - Delete Account -
    • -{% endif %} \ No newline at end of file +
  • + + Update +
    • +
  • + + Update Password +
    • +
  • + + New Prediction Setting +
    • + {#
  • #} + {# #} + {# Manage API Token#} + {#
    • #} +
  • + + Delete Account +
    • +{% endif %} diff --git a/templates/admin.html b/templates/admin.html index b50f8922..bdc622dd 100644 --- a/templates/admin.html +++ b/templates/admin.html @@ -1,12 +1,17 @@ {% extends "framework.html" %} {% load static %} {% block content %} - -
    +
    -
    - - -
    - + +
    +

    -
    -
    -
    -
    - - - + {% endblock content %} diff --git a/templates/collections/joblog.html b/templates/collections/joblog.html index 07e15e71..56261c53 100644 --- a/templates/collections/joblog.html +++ b/templates/collections/joblog.html @@ -1,70 +1,79 @@ {% extends "framework.html" %} {% load static %} {% block content %} +
    +
    +
    + Jobs +
    +
    +

    Job Logs Desc

    +
    -
    -
    -
    - Jobs -
    -
    -

    - Job Logs Desc -

    - -
    - -
    -

    - - Jobs - -

    -
    -
    -
    - - - - - - - - - - - {% for job in jobs %} - - - - - - - {% if job.task_result and job.task_result|is_url == True %} - - {% elif job.task_result %} - - {% else %} - - {% endif %} - - {% endfor %} - -
    IDNameStatusQueuedDoneResult
    {{ job.task_id }}{{ job.job_name }}{{ job.status }}{{ job.created }}{{ job.done_at }}Result{{ job.task_result|slice:"40" }}...Empty
    -
    -
    - - - +
    +

    + + Jobs + +

    +
    +
    +
    + + + + + + + + + + + {% for job in jobs %} + + + + + + + {% if job.task_result and job.task_result|is_url == True %} + + {% elif job.task_result %} + + {% else %} + + {% endif %} + + {% endfor %} + +
    IDNameStatusQueuedDoneResult
    {{ job.task_id }}{{ job.job_name }}{{ job.status }}{{ job.created }}{{ job.done_at }}Result{{ job.task_result|slice:"40" }}...Empty
    +
    + + +
    +
    {% endblock content %} diff --git a/templates/collections/objects_list.html b/templates/collections/objects_list.html index 34519ab4..bd214465 100644 --- a/templates/collections/objects_list.html +++ b/templates/collections/objects_list.html @@ -2,269 +2,427 @@ {% load static %} {% block content %} - {% if object_type != 'package' %} -
    - - - -

    + {% if object_type != 'package' %} +
    + + + +

    +
    + {% endif %} + + {% block action_modals %} + {% if object_type == 'package' %} + {% include "modals/collections/new_package_modal.html" %} + {% include "modals/collections/import_package_modal.html" %} + {% include "modals/collections/import_legacy_package_modal.html" %} + {% elif object_type == 'compound' %} + {% include "modals/collections/new_compound_modal.html" %} + {% elif object_type == 'rule' %} + {% include "modals/collections/new_rule_modal.html" %} + {% elif object_type == 'reaction' %} + {% include "modals/collections/new_reaction_modal.html" %} + {% elif object_type == 'pathway' %} + {# {% include "modals/collections/new_pathway_modal.html" %} #} + {% elif object_type == 'node' %} + {% include "modals/collections/new_node_modal.html" %} + {% elif object_type == 'edge' %} + {% include "modals/collections/new_edge_modal.html" %} + {% elif object_type == 'scenario' %} + {% include "modals/collections/new_scenario_modal.html" %} + {% elif object_type == 'model' %} + {% include "modals/collections/new_model_modal.html" %} + {% elif object_type == 'setting' %} + {#{% include "modals/collections/new_setting_modal.html" %}#} + {% elif object_type == 'user' %} +
    + {% elif object_type == 'group' %} + {% include "modals/collections/new_group_modal.html" %} {% endif %} + {% endblock action_modals %} - {% block action_modals %} - {% if object_type == 'package' %} - {% include "modals/collections/new_package_modal.html" %} - {% include "modals/collections/import_package_modal.html" %} - {% include "modals/collections/import_legacy_package_modal.html" %} - {% elif object_type == 'compound' %} - {% include "modals/collections/new_compound_modal.html" %} - {% elif object_type == 'rule' %} - {% include "modals/collections/new_rule_modal.html" %} - {% elif object_type == 'reaction' %} - {% include "modals/collections/new_reaction_modal.html" %} - {% elif object_type == 'pathway' %} - {# {% include "modals/collections/new_pathway_modal.html" %} #} - {% elif object_type == 'node' %} - {% include "modals/collections/new_node_modal.html" %} - {% elif object_type == 'edge' %} - {% include "modals/collections/new_edge_modal.html" %} - {% elif object_type == 'scenario' %} - {% include "modals/collections/new_scenario_modal.html" %} - {% elif object_type == 'model' %} - {% include "modals/collections/new_model_modal.html" %} - {% elif object_type == 'setting' %} - {#{% include "modals/collections/new_setting_modal.html" %}#} - {% elif object_type == 'user' %} -
    - {% elif object_type == 'group' %} - {% include "modals/collections/new_group_modal.html" %} - {% endif %} - {% endblock action_modals %} - -
    +
    -
    - {% if object_type == 'package' %} - Packages - {% elif object_type == 'compound' %} - Compounds - {% elif object_type == 'structure' %} - Compound structures - {% elif object_type == 'rule' %} - Rules - {% elif object_type == 'reaction' %} - Reactions - {% elif object_type == 'pathway' %} - Pathways - {% elif object_type == 'node' %} - Nodes - {% elif object_type == 'edge' %} - Edges - {% elif object_type == 'scenario' %} - Scenarios - {% elif object_type == 'model' %} - Model - {% elif object_type == 'setting' %} - Settings - {% elif object_type == 'user' %} - Users - {% elif object_type == 'group' %} - Groups - {% endif %} - +
    + {% if object_type == 'package' %} + Packages + {% elif object_type == 'compound' %} + Compounds + {% elif object_type == 'structure' %} + Compound structures + {% elif object_type == 'rule' %} + Rules + {% elif object_type == 'reaction' %} + Reactions + {% elif object_type == 'pathway' %} + Pathways + {% elif object_type == 'node' %} + Nodes + {% elif object_type == 'edge' %} + Edges + {% elif object_type == 'scenario' %} + Scenarios + {% elif object_type == 'model' %} + Model + {% elif object_type == 'setting' %} + Settings + {% elif object_type == 'user' %} + Users + {% elif object_type == 'group' %} + Groups + {% endif %} + -
    - - {% if object_type == 'package' %} -

    A package contains pathways, rules, etc. and can reflect specific experimental - conditions. Learn - more >>

    - {% elif object_type == 'compound' %} -

    A compound stores the structure of a molecule and can include meta-information. - Learn more - >>

    - {% elif object_type == 'structure' %} -

    The structures stored in this compound - Learn more - >>

    - {% elif object_type == 'rule' %} -

    A rule describes a biotransformation reaction template that is defined as SMIRKS. - Learn more - >>

    - {% elif object_type == 'reaction' %} -

    A reaction is a specific biotransformation from educt compounds to product compounds. - Learn more - >>

    - {% elif object_type == 'pathway' %} -

    A pathway displays the (predicted) biodegradation of a compound as graph. - Learn more - >>

    - {% elif object_type == 'node' %} -

    Nodes represent the (predicted) compounds in a graph. - Learn more - >>

    - {% elif object_type == 'edge' %} -

    Edges represent the links between Nodes in a graph - Learn more - >>

    - {% elif object_type == 'scenario' %} -

    A scenario contains meta-information that can be attached to other data (compounds, rules, ..). - Learn more - >>

    - {% elif object_type == 'model' %} -

    A model applies machine learning to limit the combinatorial explosion. - Learn - more - >>

    - {% elif object_type == 'setting' %} -

    A setting includes configuration parameters for pathway predictions. - Learn more - >>

    - {% elif object_type == 'user' %} -

    Register now to create own packages and to submit and manage your data. - Learn more - >>

    - {% elif object_type == 'group' %} -

    Users can team up in groups to share packages. - Learn more - >>

    - {% endif %} +
    +
    + + {% if object_type == 'package' %} +

    + A package contains pathways, rules, etc. and can reflect specific + experimental conditions. + Learn more >> +

    + {% elif object_type == 'compound' %} +

    + A compound stores the structure of a molecule and can include + meta-information. + Learn more >> +

    + {% elif object_type == 'structure' %} +

    + The structures stored in this compound + Learn more >> +

    + {% elif object_type == 'rule' %} +

    + A rule describes a biotransformation reaction template that is + defined as SMIRKS. + Learn more >> +

    + {% elif object_type == 'reaction' %} +

    + A reaction is a specific biotransformation from educt compounds to + product compounds. + Learn more >> +

    + {% elif object_type == 'pathway' %} +

    + A pathway displays the (predicted) biodegradation of a compound as + graph. + Learn more >> +

    + {% elif object_type == 'node' %} +

    + Nodes represent the (predicted) compounds in a graph. + Learn more >> +

    + {% elif object_type == 'edge' %} +

    + Edges represent the links between Nodes in a graph + Learn more >> +

    + {% elif object_type == 'scenario' %} +

    + A scenario contains meta-information that can be attached to other + data (compounds, rules, ..). + Learn more >> +

    + {% elif object_type == 'model' %} +

    + A model applies machine learning to limit the combinatorial + explosion. + Learn more >> +

    + {% elif object_type == 'setting' %} +

    + A setting includes configuration parameters for pathway predictions. + Learn more >> +

    + {% elif object_type == 'user' %} +

    + Register now to create own packages and to submit and manage your + data. + Learn more >> +

    + {% elif object_type == 'group' %} +

    + Users can team up in groups to share packages. + Learn more >> +

    + {% endif %} - - {% if reviewed_objects and unreviewed_objects %} - {% if reviewed_objects|length == 0 and unreviewed_objects|length == 0 %} -

    Nothing found. There are two possible reasons:

    1. There is no content yet.
    2. You have no - reading permissions.

    Please be sure you have at least reading permissions.

    - {% endif %} - {% endif %} -
    - {% if reviewed_objects %} + + {% if reviewed_objects and unreviewed_objects %} + {% if reviewed_objects|length == 0 and unreviewed_objects|length == 0 %} +

    + Nothing found. There are two possible reasons:

    1. + There is no content yet.
    2. You have no reading + permissions.

    Please be sure you have at least reading + permissions. +

    + {% endif %} + {% endif %} +
    + {% if reviewed_objects %} {% if reviewed_objects|length > 0 %} -
    +

    - Reviewed + Reviewed

    -
    -
    +
    +
    - {% if object_type == 'package' %} + {% if object_type == 'package' %} {% for obj in reviewed_objects %} - {{ obj.name|safe }} - - + {{ obj.name|safe }} + + {% endfor %} - {% else %} + {% else %} {% for obj in reviewed_objects|slice:":50" %} - {{ obj.name|safe }}{# ({{ obj.package.name }}) #} - - + {{ obj.name|safe }}{# ({{ obj.package.name }}) #} + + {% endfor %} - {% endif %} + {% endif %}
    +
    + {% endif %} + {% endif %} + {% if unreviewed_objects %} +
    +

    + Unreviewed +

    - {% endif %} - {% endif %} - {% if unreviewed_objects %} -

    Unreviewed

    -
    -
    - {% if object_type == 'package' %} - {% for obj in unreviewed_objects %} - {{ obj.name|safe }} - {% endfor %} - {% else %} - {% for obj in unreviewed_objects|slice:":50" %} - {{ obj.name|safe }} - {% endfor %} - {% endif %} -
    -
    - {% endif %} - {% if objects %} - -
    - -
    +
    + {# prettier-ignore-start #} + {# prettier-ignore-end #} {% endblock content %} diff --git a/templates/compare.html b/templates/compare.html index db42eb7e..0b9f0dfc 100644 --- a/templates/compare.html +++ b/templates/compare.html @@ -1,55 +1,75 @@ {% extends "framework.html" %} {% block content %} -
    -
    - {% csrf_token %} - - - -
    -
    - {% if result %} - {{ smiles }}

    -
    -

    - {% if rule %} - {{ smirks }} -

    - {{ rule.reactants_smarts }} -

    - {{ rule.products_smarts }} -

    -
    - {{ rule.as_svg|safe }} -
    - {% endif %} -

    Diff

    - {% if diff %} - {% for d in diff %} - {{ d }} - {% endfor %} - {% else %} - {{ "No diff" }} - {% endif %} -
    -
    -

    Ambit

    - {% for p in ambit_res %} - {{ p }}
    -
    - {% endfor %} -
    - -
    -

    RDKit

    - {% for p in rdkit_res %} - {{ p }}
    -
    - {% endfor %} -
    -
    +
    +
    + {% csrf_token %} + + + +
    +
    + {% if result %} + {{ smiles }} +

    +
    +

    + {% if rule %} + {{ smirks }} +

    + {{ rule.reactants_smarts }} +

    + {{ rule.products_smarts }} +

    +
    {{ rule.as_svg|safe }}
    {% endif %} +

    Diff

    + {% if diff %} + {% for d in diff %} + {{ d }} + {% endfor %} + {% else %} + {{ "No diff" }} + {% endif %} +
    +
    +

    Ambit

    + {% for p in ambit_res %} + {{ p }}
    +
    + {% endfor %} +
    + +
    +

    RDKit

    + {% for p in rdkit_res %} + {{ p }}
    +
    + {% endfor %} +
    +
    + {% endif %} {% endblock content %} diff --git a/templates/errors/400_bad_request.html b/templates/errors/400_bad_request.html index f580c722..0848847d 100644 --- a/templates/errors/400_bad_request.html +++ b/templates/errors/400_bad_request.html @@ -1,15 +1,18 @@ {% extends "framework.html" %} {% load static %} {% block content %} - - {% endblock content %} diff --git a/templates/errors/403_access_denied.html b/templates/errors/403_access_denied.html index dd05368c..392e3dad 100644 --- a/templates/errors/403_access_denied.html +++ b/templates/errors/403_access_denied.html @@ -1,15 +1,18 @@ {% extends "framework.html" %} {% load static %} {% block content %} - - {% endblock content %} diff --git a/templates/errors/404_not_found.html b/templates/errors/404_not_found.html index 7191d985..d2e17a3f 100644 --- a/templates/errors/404_not_found.html +++ b/templates/errors/404_not_found.html @@ -1,15 +1,18 @@ {% extends "framework.html" %} {% load static %} {% block content %} - - {% endblock content %} diff --git a/templates/errors/error.html b/templates/errors/error.html index 11a35e03..77915bc7 100644 --- a/templates/errors/error.html +++ b/templates/errors/error.html @@ -1,13 +1,9 @@ {% extends "framework.html" %} {% load static %} {% block content %} - - - + {% endblock content %} diff --git a/templates/errors/user_account_inactive.html b/templates/errors/user_account_inactive.html index 3b656b77..727286e9 100644 --- a/templates/errors/user_account_inactive.html +++ b/templates/errors/user_account_inactive.html @@ -1,12 +1,11 @@ {% extends "framework.html" %} {% load static %} {% block content %} - - - + {% endblock content %} diff --git a/templates/framework.html b/templates/framework.html index ecedc8fc..a9e5fec3 100644 --- a/templates/framework.html +++ b/templates/framework.html @@ -124,7 +124,7 @@
    -
    +
    diff --git a/templates/framework_modern.html b/templates/framework_modern.html index ba9b28a0..bb089f1f 100644 --- a/templates/framework_modern.html +++ b/templates/framework_modern.html @@ -80,7 +80,7 @@ {% block main_content %} {# Breadcrumbs - outside main content, optional #} {% if breadcrumbs %} -
    +
      {% for elem in breadcrumbs %} @@ -113,7 +113,7 @@ {# License - inside paper if present #} {% if meta.url_contains_package and meta.current_package.license %} -
      +
      License
      @@ -137,7 +137,7 @@ {# Floating Help Tab #} {% if not public_mode %} -
      +
      +
      -
      - Migration Status BT Rules -
      -
      -

      Rules with Error: {{ error }}/{{ total }}

      -

      Rules without Error: {{ success }}/{{ total }}

      -
      +
      + Migration Status BT Rules +
      +
      +

      Rules with Error: {{ error }}/{{ total }}

      +

      Rules without Error: {{ success }}/{{ total }}

      +
      - {% for obj in results %} -
      - {% if obj.status %} -
      + {% if obj.status %} + - {% else %} -

      - {{ obj.name|safe }} -

      + {% endif %} +

      + {{ obj.name|safe }} +

      - -
      +
      - + {% endblock content %} diff --git a/templates/migration_detail.html b/templates/migration_detail.html index 240ffea8..9a989a5b 100644 --- a/templates/migration_detail.html +++ b/templates/migration_detail.html @@ -1,45 +1,77 @@ {% extends "framework.html" %} {% block content %} -
      -
      -
      - Migration Status for {{ bt_rule_name }} -
      -
      -

      A package contains pathways, rules, etc. and can reflect specific experimental - conditions. Learn - more >>

      -
      +
      +
      +
      + Migration Status for {{ bt_rule_name }} +
      +
      +

      + A package contains pathways, rules, etc. and can reflect specific + experimental conditions. + Learn more >> +

      +
      - {% for obj in results %} -
      - {% if obj.status %} - - {% else %} - - {% endif %} -

      - {{ obj.name|safe }} -

      -
      -
      -
      - 
      {{ obj.detail }}
      -
      -
      - {% endfor %} + {% for obj in results %} +
      + {% if obj.status %} + + {% else %} + + {% endif %} +

      + {{ obj.name|safe }} +

      +
      +
      + 
      {{ obj.detail }}
      +
      +
      + {% endfor %}
      +
      - + {% endblock content %} diff --git a/templates/modals/cite_modal.html b/templates/modals/cite_modal.html index d7b10945..9cdc26b3 100644 --- a/templates/modals/cite_modal.html +++ b/templates/modals/cite_modal.html @@ -1,31 +1,48 @@ -