From acc6b84becab38bc2d86d2ebdb35d9700e5b79d9 Mon Sep 17 00:00:00 2001 From: codycbakerphd Date: Fri, 21 Jun 2024 16:08:36 -0400 Subject: [PATCH 01/91] fix subconverter stubbing --- .../manageNeuroconv/manage_neuroconv.py | 48 +++++++++++++------ 1 file changed, 34 insertions(+), 14 deletions(-) diff --git a/src/pyflask/manageNeuroconv/manage_neuroconv.py b/src/pyflask/manageNeuroconv/manage_neuroconv.py index 007491060..a277275dd 100644 --- a/src/pyflask/manageNeuroconv/manage_neuroconv.py +++ b/src/pyflask/manageNeuroconv/manage_neuroconv.py @@ -924,20 +924,40 @@ def update_conversion_progress(message): options = {interface: {} for interface in info["source_data"]} for interface in options: - available_opts = available_options.get("properties").get(interface).get("properties", {}) - - # Specify if stub test - if run_stub_test: - if available_opts.get("stub_test"): - options[interface]["stub_test"] = True - - # Specify if iterator options are available - elif available_opts.get("iterator_opts"): - options[interface]["iterator_opts"] = dict( - display_progress=True, - progress_bar_class=TQDMProgressSubscriber, - progress_bar_options=progress_bar_options, - ) + print(f"{interface} entered") + + options_per_interface_or_converter = available_options.get("properties").get(interface) + # Nested converters + if "properties" not in options_per_interface_or_converter: + for subinterface in options_per_interface_or_converter: + available_opts = options_per_interface_or_converter[subinterface].get("properties", {}) + options_to_update = options[interface][subinterface] + + if run_stub_test and "stub_test" in available_opts: + options_to_update["stub_test"] = True + + if "iterator_opts" in available_opts: + options_to_update["iterator_opts"] = dict( + display_progress=True, + progress_bar_class=TQDMProgressSubscriber, + progress_bar_options=progress_bar_options, + ) + + print(f"{interface} has been stubbed") + # Standard interface + else: + available_opts = options_per_interface_or_converter.get("properties", {}) + options_to_update = options[interface] + + if run_stub_test and "stub_test" in available_opts: + options_to_update["stub_test"] = True + + if "iterator_opts" in available_opts: + options_to_update["iterator_opts"] = dict( + display_progress=True, + progress_bar_class=TQDMProgressSubscriber, + progress_bar_options=progress_bar_options, + ) # Add GUIDE watermark package_json_file_path = resource_path("package.json" if is_packaged() else "../package.json") From 0f25ff442181e964222ab7e1c843a86346ab2a79 Mon Sep 17 00:00:00 2001 From: Cody Baker Date: Mon, 24 Jun 2024 19:09:31 -0400 Subject: [PATCH 02/91] fix scanimage build --- nwb-guide.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/nwb-guide.spec b/nwb-guide.spec index 0fb2d28f2..8d767edb0 100644 --- a/nwb-guide.spec +++ b/nwb-guide.spec @@ -39,6 +39,7 @@ modules_to_collect = [ 'ndx_pose', 'tzdata', 'elephant', + 'ScanImageTiffReader', ] for module_name in modules_to_collect: collection = collect_all(module_name) From 6a1aae445f9c2b8f35970cfeda7114aba17f27ec Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Wed, 26 Jun 2024 20:53:38 -0400 Subject: [PATCH 03/91] Update switcher for 1.0.2 --- docs/_static/switcher.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/_static/switcher.json b/docs/_static/switcher.json index 082d3fc8d..243fad936 100644 --- a/docs/_static/switcher.json +++ b/docs/_static/switcher.json @@ -4,6 +4,12 @@ "url": "https://nwb-guide.readthedocs.io/en/latest/", "preferred": false }, + { + "name": "1.0.2", + "version": "v1.0.2", + "url": "https://nwb-guide.readthedocs.io/en/v1.0.2/", + "preferred": true + }, { "name": "1.0.1", "version": "v1.0.1", From 2a416a2618b93c6eb8c204e51d4bdbccd693daca Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Fri, 28 Jun 2024 13:44:23 -0700 Subject: [PATCH 04/91] Update switcher.json --- docs/_static/switcher.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_static/switcher.json b/docs/_static/switcher.json index 243fad936..7d4841159 100644 --- a/docs/_static/switcher.json +++ b/docs/_static/switcher.json @@ -14,7 +14,7 @@ "name": "1.0.1", "version": "v1.0.1", "url": "https://nwb-guide.readthedocs.io/en/v1.0.1/", - "preferred": true + "preferred": false }, { "name": "1.0.0", From 0880cb78bcf04f3b3f1ff8857bfe139cc05c82e4 Mon Sep 17 00:00:00 2001 From: rly Date: Mon, 1 Jul 2024 16:47:27 -0700 Subject: [PATCH 05/91] Remove gap above version switcher dropdown --- docs/_static/css/custom.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css index f0baefd23..06fd446c1 100644 --- a/docs/_static/css/custom.css +++ b/docs/_static/css/custom.css @@ -11,7 +11,7 @@ button.btn.version-switcher__button { .version-switcher__container.dropdown:hover .dropdown-menu { display: block; left: 0; - margin-top: var(--bs-dropdown-spacer); + margin-top: 0; top: 100%; } From 7684ba7a28ac817e0372a659cbd7d192f163e7f6 Mon Sep 17 00:00:00 2001 From: rly Date: Mon, 1 Jul 2024 16:56:21 -0700 Subject: [PATCH 06/91] Fix css --- docs/_static/css/custom.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css index 06fd446c1..809ab5bfe 100644 --- a/docs/_static/css/custom.css +++ b/docs/_static/css/custom.css @@ -11,7 +11,7 @@ button.btn.version-switcher__button { .version-switcher__container.dropdown:hover .dropdown-menu { display: block; left: 0; - margin-top: 0; + margin-top: 0 !important; top: 100%; } From ee2c30e83f74d204c3fd9ea10fa6dec92091cf4d Mon Sep 17 00:00:00 2001 From: dhmjhu <166628128+dhmjhu@users.noreply.github.com> Date: Tue, 2 Jul 2024 16:34:46 -0400 Subject: [PATCH 07/91] escape HTML tags in error messages from server --- .../core/components/pages/guided-mode/data/GuidedSourceData.js | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/electron/frontend/core/components/pages/guided-mode/data/GuidedSourceData.js b/src/electron/frontend/core/components/pages/guided-mode/data/GuidedSourceData.js index e989e6652..e95c0dc94 100644 --- a/src/electron/frontend/core/components/pages/guided-mode/data/GuidedSourceData.js +++ b/src/electron/frontend/core/components/pages/guided-mode/data/GuidedSourceData.js @@ -121,13 +121,14 @@ export class GuidedSourceDataPage extends ManagedPage { if (result.message) { const [type, ...splitText] = result.message.split(":"); + const escapedType = type.replaceAll("<", "<").replaceAll(">", ">"); const text = splitText.length ? splitText.join(":").replaceAll("<", "<").replaceAll(">", ">") : result.traceback ? `
${result.traceback.trim().split("\n").slice(-2)[0].trim()}
` : ""; - const message = `

Request Failed

${type}

${text}

`; + const message = `

Request Failed

${escapedType}

${text}

`; this.notify(message, "error"); throw result; } From 07daf727b6610eea544aae8830068bedcd9c3354 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 18 Jul 2024 10:36:08 -0400 Subject: [PATCH 08/91] Update dataset_publication.rst --- docs/tutorials/dataset_publication.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorials/dataset_publication.rst b/docs/tutorials/dataset_publication.rst index fd99a2a20..db6de6bf2 100644 --- a/docs/tutorials/dataset_publication.rst +++ b/docs/tutorials/dataset_publication.rst @@ -1,7 +1,7 @@ Dataset Publication =================== -For this tutorial, we'll be adapting the previous :doc:`Multi-Session Tutorial ` to publish our data to the DANDI Archive. +For this tutorial, we'll publish the NWB files created in :doc:`Multi-Session Tutorial ` as a Dandiset on the DANDI Archive. This workflow works for any collection of NWB files (2.1+), whether they were created by NWB GUIDE or not. .. note:: Creating an account on DANDI requires approval from the archive administrators. Separate approval is required for both the main archive and the development server. From d9c524b6a1e6461db885c950a125875bbc15d100 Mon Sep 17 00:00:00 2001 From: Jeremy Magland Date: Thu, 25 Jul 2024 08:17:43 -0400 Subject: [PATCH 09/91] Update Neurosift URL --- src/electron/frontend/core/components/Neurosift.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/electron/frontend/core/components/Neurosift.js b/src/electron/frontend/core/components/Neurosift.js index 438107205..381e6dbca 100644 --- a/src/electron/frontend/core/components/Neurosift.js +++ b/src/electron/frontend/core/components/Neurosift.js @@ -86,7 +86,7 @@ export class Neurosift extends LitElement { ${this.fullscreen ? new FullScreenToggle({ target: this }) : ""}