From 94be8e10d5f41ac3a928c9ba35399a7e483f6ff1 Mon Sep 17 00:00:00 2001 From: Samuel Wein Date: Thu, 31 Oct 2024 16:52:23 +0100 Subject: [PATCH] more fixes --- app.py | 2 +- slit_venv/share/man/man1/ttx.1 | 225 +++++++++++++++++++++++++++++++++ src/Workflow.py | 6 +- 3 files changed, 229 insertions(+), 4 deletions(-) create mode 100644 slit_venv/share/man/man1/ttx.1 diff --git a/app.py b/app.py index 8f641df..61a4b26 100644 --- a/app.py +++ b/app.py @@ -3,7 +3,7 @@ from src.common.captcha_ import captcha_control from src.common.common import page_setup, save_params - +import sys params = page_setup(page="main") diff --git a/slit_venv/share/man/man1/ttx.1 b/slit_venv/share/man/man1/ttx.1 new file mode 100644 index 0000000..bba23b5 --- /dev/null +++ b/slit_venv/share/man/man1/ttx.1 @@ -0,0 +1,225 @@ +.Dd May 18, 2004 +.\" ttx is not specific to any OS, but contrary to what groff_mdoc(7) +.\" seems to imply, entirely omitting the .Os macro causes 'BSD' to +.\" be used, so I give a zero-width space as its argument. +.Os \& +.\" The "FontTools Manual" argument apparently has no effect in +.\" groff 1.18.1. I think it is a bug in the -mdoc groff package. +.Dt TTX 1 "FontTools Manual" +.Sh NAME +.Nm ttx +.Nd tool for manipulating TrueType and OpenType fonts +.Sh SYNOPSIS +.Nm +.Bk +.Op Ar option ... +.Ek +.Bk +.Ar file ... +.Ek +.Sh DESCRIPTION +.Nm +is a tool for manipulating TrueType and OpenType fonts. It can convert +TrueType and OpenType fonts to and from an +.Tn XML Ns -based format called +.Tn TTX . +.Tn TTX +files have a +.Ql .ttx +extension. +.Pp +For each +.Ar file +argument it is given, +.Nm +detects whether it is a +.Ql .ttf , +.Ql .otf +or +.Ql .ttx +file and acts accordingly: if it is a +.Ql .ttf +or +.Ql .otf +file, it generates a +.Ql .ttx +file; if it is a +.Ql .ttx +file, it generates a +.Ql .ttf +or +.Ql .otf +file. +.Pp +By default, every output file is created in the same directory as the +corresponding input file and with the same name except for the +extension, which is substituted appropriately. +.Nm +never overwrites existing files; if necessary, it appends a suffix to +the output file name before the extension, as in +.Pa Arial#1.ttf . +.Ss "General options" +.Bl -tag -width ".Fl t Ar table" +.It Fl h +Display usage information. +.It Fl d Ar dir +Write the output files to directory +.Ar dir +instead of writing every output file to the same directory as the +corresponding input file. +.It Fl o Ar file +Write the output to +.Ar file +instead of writing it to the same directory as the +corresponding input file. +.It Fl v +Be verbose. Write more messages to the standard output describing what +is being done. +.It Fl a +Allow virtual glyphs ID's on compile or decompile. +.El +.Ss "Dump options" +The following options control the process of dumping font files +(TrueType or OpenType) to +.Tn TTX +files. +.Bl -tag -width ".Fl t Ar table" +.It Fl l +List table information. Instead of dumping the font to a +.Tn TTX +file, display minimal information about each table. +.It Fl t Ar table +Dump table +.Ar table . +This option may be given multiple times to dump several tables at +once. When not specified, all tables are dumped. +.It Fl x Ar table +Exclude table +.Ar table +from the list of tables to dump. This option may be given multiple +times to exclude several tables from the dump. The +.Fl t +and +.Fl x +options are mutually exclusive. +.It Fl s +Split tables. Dump each table to a separate +.Tn TTX +file and write (under the name that would have been used for the output +file if the +.Fl s +option had not been given) one small +.Tn TTX +file containing references to the individual table dump files. This +file can be used as input to +.Nm +as long as the referenced files can be found in the same directory. +.It Fl i +.\" XXX: I suppose OpenType programs (exist and) are also affected. +Don't disassemble TrueType instructions. When this option is specified, +all TrueType programs (glyph programs, the font program and the +pre-program) are written to the +.Tn TTX +file as hexadecimal data instead of +assembly. This saves some time and results in smaller +.Tn TTX +files. +.It Fl y Ar n +When decompiling a TrueType Collection (TTC) file, +decompile font number +.Ar n , +starting from 0. +.El +.Ss "Compilation options" +The following options control the process of compiling +.Tn TTX +files into font files (TrueType or OpenType): +.Bl -tag -width ".Fl t Ar table" +.It Fl m Ar fontfile +Merge the input +.Tn TTX +file +.Ar file +with +.Ar fontfile . +No more than one +.Ar file +argument can be specified when this option is used. +.It Fl b +Don't recalculate glyph bounding boxes. Use the values in the +.Tn TTX +file as is. +.El +.Sh "THE TTX FILE FORMAT" +You can find some information about the +.Tn TTX +file format in +.Pa documentation.html . +In particular, you will find in that file the list of tables understood by +.Nm +and the relations between TrueType GlyphIDs and the glyph names used in +.Tn TTX +files. +.Sh EXAMPLES +In the following examples, all files are read from and written to the +current directory. Additionally, the name given for the output file +assumes in every case that it did not exist before +.Nm +was invoked. +.Pp +Dump the TrueType font contained in +.Pa FreeSans.ttf +to +.Pa FreeSans.ttx : +.Pp +.Dl ttx FreeSans.ttf +.Pp +Compile +.Pa MyFont.ttx +into a TrueType or OpenType font file: +.Pp +.Dl ttx MyFont.ttx +.Pp +List the tables in +.Pa FreeSans.ttf +along with some information: +.Pp +.Dl ttx -l FreeSans.ttf +.Pp +Dump the +.Sq cmap +table from +.Pa FreeSans.ttf +to +.Pa FreeSans.ttx : +.Pp +.Dl ttx -t cmap FreeSans.ttf +.Sh NOTES +On MS\-Windows and MacOS, +.Nm +is available as a graphical application to which files can be dropped. +.Sh SEE ALSO +.Pa documentation.html +.Pp +.Xr fontforge 1 , +.Xr ftinfo 1 , +.Xr gfontview 1 , +.Xr xmbdfed 1 , +.Xr Font::TTF 3pm +.Sh AUTHORS +.Nm +was written by +.An -nosplit +.An "Just van Rossum" Aq just@letterror.com . +.Pp +This manual page was written by +.An "Florent Rougon" Aq f.rougon@free.fr +for the Debian GNU/Linux system based on the existing FontTools +documentation. It may be freely used, modified and distributed without +restrictions. +.\" For Emacs: +.\" Local Variables: +.\" fill-column: 72 +.\" sentence-end: "[.?!][]\"')}]*\\($\\| $\\| \\| \\)[ \n]*" +.\" sentence-end-double-space: t +.\" End: \ No newline at end of file diff --git a/src/Workflow.py b/src/Workflow.py index 4766c31..e49a6e8 100644 --- a/src/Workflow.py +++ b/src/Workflow.py @@ -19,12 +19,12 @@ def upload(self)-> None: t = st.tabs(["MS data", "Nucleotide sequences"]) with t[0]: # Use the upload method from StreamlitUI to handle mzML file uploads. - self.ui.upload_widget(key="mzML-files", name="MS data", file_type="mzML") + self.ui.upload_widget(key="mzML-files", name="MS data", file_types=["mzML"]) if st.button("Load Example Data", type="primary", help="Import the example mzML files", key="example_mzml"): fileupload.load_example_files("mzML",Path(self.workflow_dir,"input-files")) with t[1]: # Example with fallback data (not used in workflow) - self.ui.upload_widget(key="fasta-files", name="nucleotide sequence file", file_type="fasta") + self.ui.upload_widget(key="fasta-files", name="nucleotide sequence file", file_types=["fasta"]) if st.button("Load Example Data", type="primary", help="Import the example mzML files", key="example_fasta" ): fileupload.load_example_files("fasta",Path(self.workflow_dir,"input-files")) @@ -74,7 +74,7 @@ def execution(self) -> None: # Run FeatureFinderMetabo tool with input and output files. self.executor.run_topp( - "DecoyDatabase", input_output={"in": in_fasta, "out": out_fasta} + "base", input_output={"in": in_fasta, "out": out_fasta} ) self.params["NucleicAcidSearchEngine"]["fdr:cutoff"] = self.params["FDR_cutoff"] self.params["NucleicAcidSearchEngine"]["fdr:decoy_pattern"] = "DECOY_"