DMPexcel2mat.m refactor

workflow/templates/easy/DMPexcel2mat.m

@@ -1,34 +1,100 @@
 %% CALLED BY EASYconsole.m %%
-w=pwd
+
-numOfMPs=0;
+global mpdmFile
-%GUI input for selecting a MasterPlate Excel file
+global masterPlateFile
-questdlg('\fontsize{20} Select Master Plate File','File Selection','OK', struct('Default','OK','Interpreter','tex'))
+global drugMediaFile
-[Scanfiles, pathname]=uigetfile('*.*','MultiSelect','off');
+global matDir
-if ispc
+
-  MPdir= fullfile(pathname,'\');
+% If we already have mpdmFile, don't recreate
-else
+if exist(mpdmFile, 'file') && ~isempty(mpdmFile)
-  MPdir=fullfile(pathname,'/');
+  disp(strcat('The Drug Media/MasterPlate Annotation File: ', mpdmFile, ' exists, skipping DMPexcel2mat.m'));
+  return
 end
 
-infile= Scanfiles(1,:);
+% Do our best to find and load a relevant MasterPlate file
+if ~exist(masterPlateFile, 'file') || isempty(masterPlateFile)
+  if exist(fullfile(matDir), 'dir')
+    % Try to find the masterPlateFile automatically (newest created first)
+    try
+      files=dir(matDir)
+      mpFiles={files(strncmp(files.name, 'MasterPlate_', 12)).name};
+      isempty(mpFiles) && throw(MException('MATLAB:dir', 'No MasterPlate_ files in the default MasterPlate directory'));
+      % this sorts by date (newest first)
+      [~, sortedIndices]=sort(datenum({files(strncmp(mpFiles.name, 'MasterPlate_', 12)).date}), 'descend');
+      sortedFiles=mpFiles(sortedIndices);
+      masterPlateFile=sortedFiles{1};
+      disp('Using newest MasterPlate file: ', masterPlateFile, ', skipping directory selection');
+    catch Me
+      % This can be silent, not really an error
+    end
 
-cd(MPdir)
+    for i-1:5 % give users 5 chances to get it right
-
+      try
-%fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
+        % For standalone mode
+        % GUI input for selecting a MasterPlate Excel file
+        questdlg('Select MasterPlate Directory (containing DrugMedia_ & MasterPlate_ files)','Directory Selection','OK',...
+        struct('Default','OK','Interpreter','tex'))
+        dirToScan=uigetdir();
+        files=dir(dirToScan);
+        mpFiles={files(strncmp(files.name, 'MasterPlate_', 12)).name};
+        isempty(mpFiles) && throw(MException('MATLAB:dir', 'No MasterPlate_ files in directory'))
+        % this sorts by date (newest first)
+        [~, sortedIndices]=sort(datenum({files(strncmp(mpFiles.name, 'MasterPlate_', 12)).date}), 'descend');
+        sortedFiles=mpFiles{sortedIndices};
+        masterPlateFile=sortedFiles{1};
+        disp('Using newest MasterPlate file: ', masterPlateFile, ', skipping directory selection');
+        break
+      catch ME
+        h = msgbox(ME.message, 'Error', 'error');
+        disp('Rerunning directory selection');
+        % I don't know what else we'll need to do here
+      end
+    end
+  else
+    for i-1:5 % give users 5 chances to get it right
+      try
+        % For standalone mode
+        % GUI input for selecting a MasterPlate Excel file
+        questdlg('Select MasterPlate Directory (containing DrugMedia_ & MasterPlate_ files)','Directory Selection','OK',...
+        struct('Default','OK','Interpreter','tex'))
+        dirToScan=uigetdir();
+        files=dir(dirToScan);
+        mpFiles={files(strncmp(files.name, 'MasterPlate_', 12)).name};
+        isempty(mpFiles) && throw (MException('MATLAB:dir', 'No MasterPlate_ files in directory'))
+        % this sorts by date (newest first)
+        [~, sortedIndices]=sort(datenum({files(strncmp(mpFiles.name, 'MasterPlate_', 12)).date}), 'descend');
+        sortedFiles=mpFiles{sortedIndices};
+        masterPlateFile=sortedFiles{1};
+        disp('Using newest MasterPlate file: ', masterPlateFile, ', skipping directory selection');
+        break
+      catch ME
+        h = msgbox(ME.message, 'Error', 'error');
+        uiwait(h);
+        disp('Rerunning directory selection');
+        % I don't know what else we'll need to do here
+      end
+    end
+  end
+else
+  disp(strcat('Using MasterPlate file: ', masterPlateFile, ', skipping directory selection');
+end
 
+% fid=fopen(masterPlateFile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
+% TODO needs explanation, it isn't clear what it is for
+% The input files should be csv, not xlsx
+% This whole file could be much better and more portable
 if ispc
-  [num, txt, raw] = xlsread(infile);  %,'Yor1HitsMPsetFinal');
+  [num, txt, raw] = xlsread(masterPlateFile);  %,'Yor1HitsMPsetFinal');
   fields= {txt(2,1:15)}; %or 1:17 for later but dont wish to exceed and cause error ? if used  
 else
   clear MPtbl
-  opts = detectImportOptions(infile);
+  opts=detectImportOptions(masterPlateFile);
-  MPtbl = readtable(infile,opts);
+  MPtbl=readtable(masterPlateFile,opts);
-  MPtbl= readtable(infile);
+  MPtbl=readtable(masterPlateFile);
-  fields= {opts.VariableNames};  %? if used anywhere although 'saved' to MPDMmat
+  fields={opts.VariableNames};  %? if used anywhere although 'saved' to MPDMmat
-  MPcell= readcell(infile);
+  MPcell=readcell(masterPlateFile);
 end
 
-cd(w)
 numb=0;
 clear MP;
 try
@@ -44,24 +110,20 @@ try
       MP(numb).drug= {raw((excLnNum+1):(excLnNum+384),8)};
       MP(numb).media= {raw((excLnNum+1):(excLnNum+384),7)};
       if size(raw,2)>15
-        MP(numb).orfRep= {raw((excLnNum+1):(excLnNum+384),16)};  %added 12_1005 to specify replicates Orfs in MP
+        MP(numb).orfRep= {raw((excLnNum+1):(excLnNum+384),16)}; % added 12_1005 to specify replicates Orfs in MP
-        MP(numb).specifics= {raw((excLnNum+1):(excLnNum+384),17)};  %added 12_1008 to specify replicates Specific details in MP
+        MP(numb).specifics= {raw((excLnNum+1):(excLnNum+384),17)}; % added 12_1008 to specify replicates Specific details in MP
       else
         MP(numb).orfRep= ' ';   
         MP(numb).specifics= ' ';
       end
-
       % Future MP field
       % if size(raw,2)>17 
-      %   MP(numb).specifics2= {raw((excLnNum+1):(excLnNum+384),18)};  %added 12_1008 to specify strain Bkground in MP
+      %   MP(numb).specifics2= {raw((excLnNum+1):(excLnNum+384),18)};  % added 12_1008 to specify strain Bkground in MP
       % else
       %   MP(numb).specifics2=' ';
       % end
-
       excLnNum=excLnNum+385;
-
       msg=strcat('NumberOfMP = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum));
-
     end
   else 
     excLnNum=1;
@@ -80,57 +142,104 @@ try
       MP(numb).media= {MPtbl((excLnNum+1):(excLnNum+384),7)};
       MP(numb).media{1}= table2cell(MP(numb).media{1});
       if size(MPtbl,2)>15
-        MP(numb).orfRep= {MPtbl((excLnNum+1):(excLnNum+384),16)};  %added 12_1005 to specify replicates Orfs in MP
+        MP(numb).orfRep= {MPtbl((excLnNum+1):(excLnNum+384),16)}; % added 12_1005 to specify replicates Orfs in MP
         MP(numb).orfRep{1}=table2cell(MP(numb).orfRep{1});
-        MP(numb).specifics={MPtbl((excLnNum+1):(excLnNum+384),17)};  %added 12_1008 to specify replicates Specific details in MP
+        MP(numb).specifics={MPtbl((excLnNum+1):(excLnNum+384),17)}; % added 12_1008 to specify replicates Specific details in MP
         MP(numb).specifics{1}=table2cell(MP(numb).specifics{1});
       else
         MP(numb).orfRep= ' ';   
         MP(numb).specifics= ' ';
       end
-
       excLnNum=excLnNum+385;
       msg=strcat('NumberOfMP = ',num2str(numb), 'lastLineNo. = ',num2str(excLnNum))
     end
   end
 catch ME
-  h = msgbox(msg,'Check Number of Master Plates and Excel Lines')
+  h = msgbox(ME.message, 'Error', 'error');
   uiwait(h);
-end %end for try MP excel sheet input
+end
 
 %DMupload
 %Drug and Media Plate setup  Upload from Excel
-cd(MPdir);
 excLnNum=1;
 numOfDrugs=0;
 numOfMedias=0;
 
-%GUI input for selecting a MasterPlate Excel file
+% Grabbing the bare filename from the MasterPlate file to see if we can automatically
-questdlg('\fontsize{20} Select DrugMedia File','File Selection','OK', struct('Default','OK','Interpreter','tex'));
+% find a matching DrugMedia file
-[Scanfiles, pathname]=uigetfile('*.*', 'MultiSelect','off');
+[mpFile, mpPath]=masterPlateFile
-DMdir=fullfile(pathname);
+mpFileParts=strsplit(mpFile, '_');
-clear infile;
+mpBareFileName=strjoin(parts(2:end-1), '_');
-infile= Scanfiles(1,:);
-cd(DMdir)
 
-if ispc
+if ~exist(drugMediaFile, 'file') || isempty(drugMediaFile)
-  [num, txt, raw] = xlsread(infile);  %,'Yor1HitsMPsetFinal');
+  if exist(fullfile(matDir), 'dir')
-  fields= {txt(2,1:5)};
+    try
-  Linked= num(1,1);
+      dmFileToTest=fullfile(mpPath, 'DrugMedia_', mpBareFileName, '.xlsx');
+      if exist(dmFileToTest, 'file') % Try to find a matching drug media file
+        drugMediaFile=dmFileToTest;
+        disp(strcat('Using matching DrugMedia file: ', drugMediaFile, ', skipping directory selection'));
+      else
+        % Try to find the DrugMedia file automatically (newest created first)
+        files=dir(matDir)
+        dmFiles={files(strncmp(files.name, 'DrugMedia_', 10)).name};
+        isempty(dmFiles) && throw (MException('MATLAB:dir', 'No DrugMedia_ files in directory'))
+        % this sorts by date (newest first)
+        [~, sortedIndices]=sort(datenum({files(strncmp(dmFiles.name, 'DrugMedia_', 10)).date}), 'descend');
+        sortedFiles=dmFiles{sortedIndices};
+        drugMediaFile=sortedFiles{1};
+        disp(strcat('Using newest DrugMedia file: ', drugMediaFile, ', skipping directory selection'));
+      end
+    catch Me
+      % This can be silent, not really an error
+    end
+  else
+    for i-1:5 % give users 5 chances to get it right
+      try
+        % GUI input for selecting a DrugMedia file
+        % sort by newest matching DrugMedia file and return that if we find one
+        % For standalone mode
+        % GUI input for selecting a MasterPlate Excel file
+        questdlg('Select DrugMedia directory','Directory Selection','OK',...
+        struct('Default','OK','Interpreter','tex'))
+        dirToScan=uigetdir();
+        files=dir(dirToScan)
+        dmFiles={files(strncmp(files.name, 'DrugMedia_', 10)).name};
+        isempty(dmFiles) && throw (MException('MATLAB:dir', 'No DrugMedia_ files in directory'))
+        % this sorts by date (newest first)
+        [~, sortedIndices]=sort(datenum({files(strncmp(dmFiles.name, 'DrugMedia_', 10)).date}), 'descend');
+        sortedFiles=dmFiles{sortedIndices};
+        drugMediaFile=sortedFiles{1};
+      catch ME
+        h = msgbox(ME.message, 'Error', 'error');
+        uiwait(h);
+        disp('Rerunning directory selection')
+        % I don't know what else we'll need to do here
+        end
+      end
+    end
+  end
 else
-  opts = detectImportOptions(infile); 
+  disp(strcat('Using drugMediaFile: ', drugMediaFile, ', skipping directory selection'));
-  DMtbl= readtable(infile,opts);
-  fields= opts.VariableOptions;   
-  Linked= DMtbl{1,1};
-  DMcell= readcell(infile);
 end
 
-cd(w)
+% Drug and Media Plate setup
-numb=0;
+% TODO needs better explanation
+if ispc
+  [num, txt, raw]=xlsread(drugMediaFile);  %'Yor1HitsMPsetFinal');
+  fields={txt(2,1:5)};
+  Linked=num(1,1);
+else
+  opts=detectImportOptions(drugMediaFile); 
+  DMtbl=readtable(drugMediaFile,opts);
+  fields=opts.VariableOptions;   
+  Linked=DMtbl{1,1};
+  DMcell=readcell(drugMediaFile);
+end
 
-if isequal(Linked,1)   %Drugs and Media are linked 1 to 1; else they are combinatorial
+% TODO needs better explanation
+numb=0;
+if isequal(Linked,1) % Drugs and Media are linked 1 to 1; else they are combinatorial
   clear DM;
-%try
   excLnNum=2;
   if ispc
     while (~isequal(txt{excLnNum,2},'###'))
@@ -169,8 +278,8 @@ if isequal(Linked,1)   %Drugs and Media are linked 1 to 1; else they are combina
     end
   end
 end
-%Legacy contengency  -Not ever used!!
+% Legacy contengency: not ever used
-if isequal(Linked,0)   %0 indicates Drugs and Media are combinatorial
+if isequal(Linked,0) % 0 indicates Drugs and Media are combinatorial
   clear DM;
   excLnNum=2;
   drgCnt=0;
@@ -188,7 +297,7 @@ if isequal(Linked,0)   %0 indicates Drugs and Media are combinatorial
       DM.media(medCnt) = {raw(excLnNum,4)};
       excLnNum=excLnNum+1;
     end
-  else %else if not PC (Then linux or other)
+  else
     excLnNum=1;
     while (~isequal(DMcell{excLnNum+1,2},'###'))
       drgCnt=drgCnt+1;    
@@ -206,7 +315,5 @@ if isequal(Linked,0)   %0 indicates Drugs and Media are combinatorial
   msg=strcat('NumberOfDrugs = ',num2str(drgCnt), '     NumberOfMedias = ',num2str(medCnt)  )
 end
 
-save (fullfile(MPdir,'MPDMmat'), 'fields','MP','DM','Linked');
+save(mpdmFile, 'fields','MP','DM','Linked');
-
+msgbox([strcat('Drug-Media-MasterPlate Annotation File', mpdmFile,'Generation Complete')])
-cd(w)
-msgbox(['Drug-Media-MasterPlate Annotation File   Generation Complete'])