Proteopedia:Openfox
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==Open Issues== | ==Open Issues== | ||
| - | + | ===A=== | |
| - | * (2) | + | * (2) Jaime & Itsik need speak about this as the email portion of this page is NOT working: [[Special:Contact]] --[[User:Jaime Prilusky|Jaime Prilusky]] 16:03, 7 April 2025 (UTC) |
| - | * (3) Jaime & Itsik need speak about this | + | * (3) Jaime & Itsik need speak about this one which is not working [[Special:SandboxReservation]] --[[User:Jaime Prilusky|Jaime Prilusky]] 16:09, 7 April 2025 (UTC) |
| - | * (4) | + | * (4) '''Mobile''': In the mobile view, the titles inside the scrolling text are not formatted properly, e.g. https://proteopedia.openfox.io/w/Hen_Egg-White_(HEW)_Lysozyme. Unexpectedly, when you minimize the section before the scrolling text, the Jmol window is hidden. I like that it is possible to minimize sections, though. I tried to adapt by moving the section header for the scrolling text outside of the scrolling section. Please compare to Production site: https://proteopedia.org/wiki/index.php/Hen_Egg-White_(HEW%29_Lysozyme --[[User:Karsten Theis|Karsten Theis]] 19:45, 29 March 2025 (UTC) |
| - | * | + | * (5) If problem (old 5) is solved (i.e., while in '''landscape view''', it should show left/right text/3D applet), this is not a problem and can then be ignored. The caret (^) on the left-hand side of the title should collapse only the applet. Now it collapses the applet plus text, leaving only the footer.--[[User:Jaime Prilusky|Jaime Prilusky]] |
| - | * | + | * (7) '''Tabs inside the SAT''' section have tiny text titles, smaller than the standard text in the page. Also, contrast is poor (blue text on pale blue background). I vote for larger font with better color contrast. --[[User:Angel Herraez|Angel_Herraez]] 11:25, 13 August 2025 (UTC) |
| - | * | + | * (8) '''Exiting the edit page option with "cancel" link/button''': This works ok, but when I have shown the SAT, then hide the SAT (no changes done), clicking on "cancel" brings the Firefox browser prompt "would you like to abandon the page?" -- this prompt should not happen; it does not in proteopedia.org. [[User:Angel Herraez|Angel_Herraez]] 11:48, 13 August 2025 (UTC) |
| - | + | ===B=== | |
| - | * | + | * (12) At https://proteopedia.openfox.io/w/SARS-CoV-2_spike_protein_fusion_transformation The green link An Alternate pathway is not working it yields the text in Jmol applet. [[User:Eric Martz|Eric Martz]] 19:23, 12 December 2025 (UTC) |
| + | :: This was a file not found error, due to trying to '''directly load a pdb file''' rather that a scene file; indeed, this is not done with a scene but with a jmolLink tag and a script sub-tag; the file is supposedly in a subfolder below /images/ (as per the setup of the legacy site) and maybe in this new site pdb files are located elsewhere. --[[User:Angel Herraez|Angel Herraez]] 14:42, 19 December 2025 (UTC) | ||
| + | :: '''Solution:''' pdb files (posibly other files inc. images) are not located at <code>/images/ </code> but at <code>/wiki/images/ </code>. I have fixed this particular page but it might happen in other pages. <span style="color:green;">Maybe some automatic redirection could be applied, i.e. the <code>/images/</code> folder be redirected to <code>/wiki/images/</code>?</span> | ||
| - | * | + | * (14) The '''Main Page''' needs to be formatted closer to the [https://bioinformatics.org/molvis/tmp/ppda-main-page/main-old.png old production version]. Here [https://bioinformatics.org/molvis/tmp/ppda-main-page/openfox-problems.png some problems are marked]. Here is a [https://bioinformatics.org/molvis/tmp/ppda-main-page/openfox-better.png better version in openfox] (comments were inserted) but still some problems are marked. |
| - | * | + | * (17) Applet '''popup window''' not working for some scenes -- [[User:Jaime Prilusky|Jaime Prilusky]] 08:33, 21 December 2025 (UTC) On page [[User:Jaime_Prilusky/Test/Simple]], popup for scene "cylinders" works fine while popup for scene "1acj with Tacrine" fails. |
| + | : Both are working correctly for me; Firefox Win11 --[[User:Angel Herraez|Angel Herraez]] 19:05, 25 December 2025 (UTC) <span style="color:green;">Can somebody else confirm?</span> | ||
| - | * | + | * (19) "Search Proteopedia" (upper right corner of page in openfox) defaults only to the Main namespace. This default will cause most user searches to fail because they won't notice and/or won't understand about '''namespaces'''. The default search should include all namespaces (but not, in my opinion, talk namespaces). [[User:Eric Martz|Eric Martz]] 16:10, 22 December 2025 (UTC) |
| - | + | ===C=== | |
| + | * (21) It is helpful to have '''search hits numbered''', as they are in old Proteopedia. [[User:Eric Martz|Eric Martz]] 16:28, 22 December 2025 (UTC) | ||
| - | + | * (22) Pages with "Workbench" in their titles should be readable only by their authors. They should have a tab "workbench" that allows the owner to enable reading and/or editing by other Users. See https://proteopedia.openfox.io/w/Proteopedia:Workbench | |
| - | ( | + | ** When I am logged in as Eric Martz, I can read the contents of https://proteopedia.openfox.io/w/User:Test_Account_2/Workbench <span style="color:#00b000;">Fixed √</span> --[[User:Angel Herraez|Angel Herraez]] 11:18, 29 December 2025 (UTC) |
| + | ** When I am logged in as "Test Account 2" there is no "workbench" tab there. [[User:Eric Martz|Eric Martz]] 00:08, 27 December 2025 (UTC) | ||
| - | * | + | * (23) The "Request Account" form needs a number of fixes, and it did not work when I requested a new account. Please see details at https://proteopedia.org/wiki/index.php/Proteopedia:Openfox_Request_Account [[User:Eric Martz|Eric Martz]] 00:08, 27 December 2025 (UTC) |
| - | * ''' | + | * (24) In all my testing so far, I was using the default '''JSmol version''' 14.31.8 which is very old and obsolete. It did not occur to me to use Preferences, Appearance, Advanced JSmol version until now. I strongly recommend that the current version of JSmol 16.3.41 (or 16.3.33 as is the default in old public Proteopedia) be the default in Openfox. {{Yelspan|Otherwise, much testing will have to be redone.}} [[User:Eric Martz|Eric Martz]] 00:08, 27 December 2025 (UTC) |
| - | * ''' | + | * (25) '''Sequence Tool help:''' In seeded pages, there is a [show sequence] link (green background) at top left hand side. Next to it there is a question mark icon. Clicking on it should open a pop-up window, but nothing happens. The target page is index.php?title=Seqtool&printable=yes |
| + | :: The link code is <nowiki><i id="seqtoolInfo" class="fas fa-question-circle" onclick="seqtoolInfo();" style="display: inline-block;"></i></nowiki> | ||
| + | :: The action gives an error in the browser JS console saying <nowiki>Uncaught TypeError: (intermediate value).seqtoolInfo is not a function</nowiki> | ||
| - | * | + | * (26) Seeded pages like [https://proteopedia.openfox.io/w/2ghi this one] that have evolutionary conservation data (ConSurf) include a toggle, a checkbox which right now is fully adjacent to previous and following text; space needs to be added on both sides: |
| - | https://proteopedia.openfox.io/w/ | + | :: <code>Check☐to colour</code> ==> <code>Check ☐ to colour</code> |
| - | + | ||
| - | * ''' | + | * (27) '''Main page''': The blue "i" icon (for info) overlaid at bottom-right on each of the 3 large images is displayed duplicated vertically. It seems to be CSS background-image that needs "no-repeat". |
| - | * ''' | + | * (28) The two checkboxes "[ ] Include only Seeded (Automatic) pages - [ ] only Human created pages" '''are missing''' when searching on the search slot on the top-right corner. They only appear after searching on the 'Search results' page. [[User:Jaime Prilusky|Jaime Prilusky]] 05:16, 30 December 2025 (UTC) |
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| - | * | + | * (29) Applet on pages in languages other than English is not working on Mobile - see [https://proteopedia.openfox.io/w/Myoglobin_(arabic) Arabic], [https://proteopedia.openfox.io/w/Hemoglobin_(Hebrew) Hebrew], [https://proteopedia.openfox.io/w/Lysozyme_(Arabic) Arabic] and [https://proteopedia.org/wiki/index.php/Lysozyme_(hebrew) Hebrew] [[User:Jaime Prilusky|Jaime Prilusky]] 06:10, 30 December 2025 (UTC) |
| - | https://proteopedia.openfox.io/w/ | + | |
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| - | https://proteopedia.org/wiki/index.php/ | + | |
| - | * | + | * (30) When a file has multiple structures (like [https://proteopedia.openfox.io/w/1o0l here]), a toggle is displayed under the JSmol panel to play or stop animation. When the pop-up is opened (large window with a duplicate of the structure), the animation toggle icon (right-pointing triangle within a circle) is very large; its size should be adjusted as it is in the calling page. |
| + | : <code>#animCont svg { vertical-align:bottom; width:1.3em; height:1.3em; margin-bottom:0.1em; }</code> | ||
| + | : Maybe this happens because the pop-up page, JSmolPopup.htm, is not calling Proteopedia.css, or it has the wrong version of this file. | ||
| - | + | ===D=== | |
| - | * | + | * (31) The JSmol pop-up menu in the SAT is not properly CSS formatted. Specifically, triangular arrowheads should be flushed right for each entry that has sub-menus, not left and below the entry. Compare with menu for JSmol in the page. |
| - | * The link 'or create this page', appearing when searching for a non-existing page, opens a new window. This leaves the report of non-existing page open, which is confusing. [[User:Jaime Prilusky|Jaime Prilusky]] 19:00, 20 May 2025 (UTC) | ||
| - | + | == Issues marked as '''to be made to work by the Weizmann Team''', after OpenFox becomes the production system== | |
| + | See [[Proteopedia:Openfox/Final Setup]] | ||
| - | * '''OK Fixed -''' The 2nd instance (near very bottom of page) of the '''JmolButton''' ''animation off'' does not appear on the page: https://proteopedia.openfox.io/w/Sandbox_I3DC_005, but if one looks at the identical page on the Proteopedia production system it appears, i.e. https://proteopedia.org/w/Journal:Acta_Cryst_D:S2059798324008210 20-May-2025 11:05. | ||
| - | + | == Issues marked as solved: see [[Proteopedia:Openfox/Solved]] == | |
| + | Moved to [[Proteopedia:Openfox/Solved]] | ||
| - | + | (Might need a quick additional verification before swapping sites) | |
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* The font used for the titles fails to distinguish zero from letter oh. This leads to serious confusion/errors. The title font in public proteopedia is not much better. This title font should be changed to one that has a line through zero to be unambiguous. Compare | * The font used for the titles fails to distinguish zero from letter oh. This leads to serious confusion/errors. The title font in public proteopedia is not much better. This title font should be changed to one that has a line through zero to be unambiguous. Compare | ||
| - | * https://proteopedia.openfox.io/w/7k0x | + | :* https://proteopedia.openfox.io/w/7k0x |
| - | * https://proteopedia.openfox.io/w/7kox | + | :* https://proteopedia.openfox.io/w/7kox |
| - | * https://proteopedia.openfox.io/w/7v0o | + | :* https://proteopedia.openfox.io/w/7v0o |
| - | * https://proteopedia.openfox.io/w/7vo0 | + | :* https://proteopedia.openfox.io/w/7vo0 |
| - | * [[User:Eric Martz|Eric Martz]] 17:36, 2 June 2025 (UTC) | + | :* [[User:Eric Martz|Eric Martz]] 17:36, 2 June 2025 (UTC) |
| + | :* And there is also the problem between number one and lowercase L. | ||
| + | :Maybe [https://www.BrailleInstitute.org/freefont/ Atkinson Hyperlegible Font]; it's SansSerif, not monospaced as most with dashed zeros are (not nice for regular text titles). [https://github.com/googlefonts/atkinson-hyperlegible Donwload web font]. <br>Another candidates: [https://www.fontsquirrel.com/fonts/go Go Font] [https://fonts.google.com/specimen/Finlandica?preview.text=abc%20oO0%20l1 Finlandica GoogleFont] <br> [[User:Angel Herraez|Angel_Herraez]] 16:58, 12 August 2025 (UTC) | ||
| + | : Current font is better, but not very good: [[Image:Linux Libertine sample.png]]--[[User:Angel Herraez|Angel Herraez]] 11:58, 30 December 2025 (UTC) | ||
Current revision
Contents |
Open Issues
A
- (2) Jaime & Itsik need speak about this as the email portion of this page is NOT working: Special:Contact --Jaime Prilusky 16:03, 7 April 2025 (UTC)
- (3) Jaime & Itsik need speak about this one which is not working Special:SandboxReservation --Jaime Prilusky 16:09, 7 April 2025 (UTC)
- (4) Mobile: In the mobile view, the titles inside the scrolling text are not formatted properly, e.g. https://proteopedia.openfox.io/w/Hen_Egg-White_(HEW)_Lysozyme. Unexpectedly, when you minimize the section before the scrolling text, the Jmol window is hidden. I like that it is possible to minimize sections, though. I tried to adapt by moving the section header for the scrolling text outside of the scrolling section. Please compare to Production site: https://proteopedia.org/wiki/index.php/Hen_Egg-White_(HEW%29_Lysozyme --Karsten Theis 19:45, 29 March 2025 (UTC)
- (5) If problem (old 5) is solved (i.e., while in landscape view, it should show left/right text/3D applet), this is not a problem and can then be ignored. The caret (^) on the left-hand side of the title should collapse only the applet. Now it collapses the applet plus text, leaving only the footer.--Jaime Prilusky
- (7) Tabs inside the SAT section have tiny text titles, smaller than the standard text in the page. Also, contrast is poor (blue text on pale blue background). I vote for larger font with better color contrast. --Angel_Herraez 11:25, 13 August 2025 (UTC)
- (8) Exiting the edit page option with "cancel" link/button: This works ok, but when I have shown the SAT, then hide the SAT (no changes done), clicking on "cancel" brings the Firefox browser prompt "would you like to abandon the page?" -- this prompt should not happen; it does not in proteopedia.org. Angel_Herraez 11:48, 13 August 2025 (UTC)
B
- (12) At https://proteopedia.openfox.io/w/SARS-CoV-2_spike_protein_fusion_transformation The green link An Alternate pathway is not working it yields the text in Jmol applet. Eric Martz 19:23, 12 December 2025 (UTC)
- This was a file not found error, due to trying to directly load a pdb file rather that a scene file; indeed, this is not done with a scene but with a jmolLink tag and a script sub-tag; the file is supposedly in a subfolder below /images/ (as per the setup of the legacy site) and maybe in this new site pdb files are located elsewhere. --Angel Herraez 14:42, 19 December 2025 (UTC)
- Solution: pdb files (posibly other files inc. images) are not located at
/images/but at/wiki/images/. I have fixed this particular page but it might happen in other pages. Maybe some automatic redirection could be applied, i.e. the/images/folder be redirected to/wiki/images/?
- (14) The Main Page needs to be formatted closer to the old production version. Here some problems are marked. Here is a better version in openfox (comments were inserted) but still some problems are marked.
- (17) Applet popup window not working for some scenes -- Jaime Prilusky 08:33, 21 December 2025 (UTC) On page User:Jaime_Prilusky/Test/Simple, popup for scene "cylinders" works fine while popup for scene "1acj with Tacrine" fails.
- Both are working correctly for me; Firefox Win11 --Angel Herraez 19:05, 25 December 2025 (UTC) Can somebody else confirm?
- (19) "Search Proteopedia" (upper right corner of page in openfox) defaults only to the Main namespace. This default will cause most user searches to fail because they won't notice and/or won't understand about namespaces. The default search should include all namespaces (but not, in my opinion, talk namespaces). Eric Martz 16:10, 22 December 2025 (UTC)
C
- (21) It is helpful to have search hits numbered, as they are in old Proteopedia. Eric Martz 16:28, 22 December 2025 (UTC)
- (22) Pages with "Workbench" in their titles should be readable only by their authors. They should have a tab "workbench" that allows the owner to enable reading and/or editing by other Users. See https://proteopedia.openfox.io/w/Proteopedia:Workbench
- When I am logged in as Eric Martz, I can read the contents of https://proteopedia.openfox.io/w/User:Test_Account_2/Workbench Fixed √ --Angel Herraez 11:18, 29 December 2025 (UTC)
- When I am logged in as "Test Account 2" there is no "workbench" tab there. Eric Martz 00:08, 27 December 2025 (UTC)
- (23) The "Request Account" form needs a number of fixes, and it did not work when I requested a new account. Please see details at https://proteopedia.org/wiki/index.php/Proteopedia:Openfox_Request_Account Eric Martz 00:08, 27 December 2025 (UTC)
- (24) In all my testing so far, I was using the default JSmol version 14.31.8 which is very old and obsolete. It did not occur to me to use Preferences, Appearance, Advanced JSmol version until now. I strongly recommend that the current version of JSmol 16.3.41 (or 16.3.33 as is the default in old public Proteopedia) be the default in Openfox. Otherwise, much testing will have to be redone. Eric Martz 00:08, 27 December 2025 (UTC)
- (25) Sequence Tool help: In seeded pages, there is a [show sequence] link (green background) at top left hand side. Next to it there is a question mark icon. Clicking on it should open a pop-up window, but nothing happens. The target page is index.php?title=Seqtool&printable=yes
- The link code is <i id="seqtoolInfo" class="fas fa-question-circle" onclick="seqtoolInfo();" style="display: inline-block;"></i>
- The action gives an error in the browser JS console saying Uncaught TypeError: (intermediate value).seqtoolInfo is not a function
- (26) Seeded pages like this one that have evolutionary conservation data (ConSurf) include a toggle, a checkbox which right now is fully adjacent to previous and following text; space needs to be added on both sides:
-
Check☐to colour==>Check ☐ to colour
-
- (27) Main page: The blue "i" icon (for info) overlaid at bottom-right on each of the 3 large images is displayed duplicated vertically. It seems to be CSS background-image that needs "no-repeat".
- (28) The two checkboxes "[ ] Include only Seeded (Automatic) pages - [ ] only Human created pages" are missing when searching on the search slot on the top-right corner. They only appear after searching on the 'Search results' page. Jaime Prilusky 05:16, 30 December 2025 (UTC)
- (29) Applet on pages in languages other than English is not working on Mobile - see Arabic, Hebrew, Arabic and Hebrew Jaime Prilusky 06:10, 30 December 2025 (UTC)
- (30) When a file has multiple structures (like here), a toggle is displayed under the JSmol panel to play or stop animation. When the pop-up is opened (large window with a duplicate of the structure), the animation toggle icon (right-pointing triangle within a circle) is very large; its size should be adjusted as it is in the calling page.
-
#animCont svg { vertical-align:bottom; width:1.3em; height:1.3em; margin-bottom:0.1em; } - Maybe this happens because the pop-up page, JSmolPopup.htm, is not calling Proteopedia.css, or it has the wrong version of this file.
D
- (31) The JSmol pop-up menu in the SAT is not properly CSS formatted. Specifically, triangular arrowheads should be flushed right for each entry that has sub-menus, not left and below the entry. Compare with menu for JSmol in the page.
Issues marked as to be made to work by the Weizmann Team, after OpenFox becomes the production system
See Proteopedia:Openfox/Final Setup
Issues marked as solved: see Proteopedia:Openfox/Solved
Moved to Proteopedia:Openfox/Solved
(Might need a quick additional verification before swapping sites)
Left Aside Issues
(solve these if possible)
- Is there a mechanism to prevent two users from editing the same page concurrently? This seems important to me, especially for collaborative student projects. Eric Martz 17:42, 29 March 2025 (UTC) Please put an answer here. Eric Martz 17:47, 2 June 2025 (UTC)
- The font used for the titles fails to distinguish zero from letter oh. This leads to serious confusion/errors. The title font in public proteopedia is not much better. This title font should be changed to one that has a line through zero to be unambiguous. Compare
- https://proteopedia.openfox.io/w/7k0x
- https://proteopedia.openfox.io/w/7kox
- https://proteopedia.openfox.io/w/7v0o
- https://proteopedia.openfox.io/w/7vo0
- Eric Martz 17:36, 2 June 2025 (UTC)
- And there is also the problem between number one and lowercase L.
- Maybe Atkinson Hyperlegible Font; it's SansSerif, not monospaced as most with dashed zeros are (not nice for regular text titles). Donwload web font.
Another candidates: Go Font Finlandica GoogleFont
Angel_Herraez 16:58, 12 August 2025 (UTC) - Current font is better, but not very good:
--Angel Herraez 11:58, 30 December 2025 (UTC)
Proteopedia Page Contributors and Editors (what is this?)
Joel L. Sussman, Angel Herraez, Eric Martz, Jaime Prilusky, Karsten Theis, Yitzhak Krumbein
