From e765fe21b3103ba5df88f2e632960ea003f92c35 Mon Sep 17 00:00:00 2001
From: Nalin Gupta <nalin.gupta3142@gmail.com>
Date: Wed, 6 Dec 2023 22:22:50 +0000
Subject: [PATCH 01/11] Adding sniffer for magres datatype

---
 .../config/sample/datatypes_conf.xml.sample   |   2 +
 lib/galaxy/datatypes/molecules.py             |  24 +
 lib/galaxy/datatypes/sniff.py                 |   3 +
 lib/galaxy/datatypes/test/ethanol.magres      | 520 ++++++++++++++++++
 4 files changed, 549 insertions(+)
 create mode 100644 lib/galaxy/datatypes/test/ethanol.magres

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 10876393db4f..4289d9b69d7b 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -972,6 +972,7 @@
     <datatype extension="gds" type="galaxy.datatypes.tabular:CSV" subclass="true" description="CSV representing GDS parameters."/>
     <datatype extension="feff" type="galaxy.datatypes.tabular:CSV" subclass="true" description="CSV representing summary of FEFF paths."/>
     <datatype extension="feffit" type="galaxy.datatypes.data:Text" subclass="true" description="Report of Artemis FEFFIT."/>
+    <datatype extension="magres" type="galaxy.datatypes.text:Magres" display_in_upload="true"/>
     <!-- ECOLOGY types -->
     <datatype extension="bil" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" display_in_upload="true" subclass="true" description="ENVI file with band interleave by line (BIL) format"/>
     <datatype extension="hdr" type="galaxy.datatypes.data:Text" mimetype="text/plain" display_in_upload="true" subclass="true" description="ENVI metadata header file"/>
@@ -1240,6 +1241,7 @@
     <sniffer type="galaxy.datatypes.text:CTLresult"/>
     <sniffer type="galaxy.datatypes.text:FormattedDensity" />
     <sniffer type="galaxy.datatypes.text:Param" />
+    <sniffer type="galaxy.datatypes.text:Magres" />
     <sniffer type="galaxy.datatypes.text:Yaml" />
     <!--
     Keep this commented until the sniff method in the assembly.py
diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index 643c7a4a0614..e0cd61abe112 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -1767,3 +1767,27 @@ def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
         else:
             dataset.peek = "file does not exist"
             dataset.blurb = "file purged from disk"
+
+@build_sniff_from_prefix
+class Magres(GenericMolFile):
+    """Report on a MAGRES calculation"""
+
+    file_ext = "magres"
+
+    def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
+        """Determines whether the file is a MAGRES log
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('ethanol.magres')
+        >>> Magres().sniff(fname)
+        True
+        >>> fname = get_test_fname('<file>.param')
+        >>> Magres().sniff(fname)
+        False
+        """
+        fh = file_prefix.string_io()
+
+        for lines in fh:
+            if not re.search(r'\#\$magres-abinitio-v([0-9]+).([0-9]+)', lines[0]):
+                return False        
+        return True
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index 6d65f4c36919..bac624937e96 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -420,6 +420,9 @@ def guess_ext(fname_or_file_prefix: Union[str, "FilePrefix"], sniff_order, is_bi
     >>> fname = get_test_fname('Si.den_fmt')
     >>> guess_ext(fname, sniff_order)
     'den_fmt'
+    >>> fname = get_test_fname('ethanol.magres')
+    >>> guess_ext(fname, sniff_order)
+    'magres'
     >>> fname = get_test_fname('mothur_datatypetest_true.mothur.otu')
     >>> guess_ext(fname, sniff_order)
     'mothur.otu'
diff --git a/lib/galaxy/datatypes/test/ethanol.magres b/lib/galaxy/datatypes/test/ethanol.magres
new file mode 100644
index 000000000000..3ea98a9a73c1
--- /dev/null
+++ b/lib/galaxy/datatypes/test/ethanol.magres
@@ -0,0 +1,520 @@
+#$magres-abinitio-v1.0
+# Generated by format.py. For format definition and code samples see http://www.ccpnc.ac.uk/pmwiki.php/CCPNC/Fileformat
+[calculation]
+calc_code CASTEP
+calc_code_version 7.0
+calc_comment 
+calc_kpoint_mp_grid 1 1 1
+calc_code_hgversion 0d37235409d7+ magres-efg 2013-02-07
+calc_cutoffenergy 4.0000000000000000E+01
+calc_xcfunctional PBE
+calc_kpoint_mp_offset 0.25000000 0.25000000 0.25000000
+calc_code_platform linux_x86_64_ifort12
+units calc_cutoffenergy Hartree
+calc_name ethanol
+[/calculation]
+[atoms]
+  units lattice Angstrom
+  units atom Angstrom
+  lattice 6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0
+  symmetry P1
+  atom H H 1 -0.870341 -0.176289 -0.650057
+  atom H H 2 0.182454 -0.924201 0.559623
+  atom H H 3 0.86813 0.197626 -0.629783
+  atom H H 4 -1.130705 0.974874 1.564773
+  atom H H 5 -0.438769 2.078941 0.371865
+  atom H H 6 1.060671 0.677653 2.297066
+  atom C C 1 -0.004 -0.004 -0.004
+  atom C C 2 -0.247915 1.164107 0.937396
+  atom O O 1 0.895314 1.458074 1.741964
+[/atoms]
+[magres]
+  units ms ppm
+  units efg au
+  units isc_fc 10^19.T^2.J^-1
+  units isc_orbital_p 10^19.T^2.J^-1
+  units isc_orbital_d 10^19.T^2.J^-1
+  units isc_spin 10^19.T^2.J^-1
+  units isc 10^19.T^2.J^-1
+  units isc_fc 10^19.T^2.J^-1
+  units isc_orbital_p 10^19.T^2.J^-1
+  units isc_orbital_d 10^19.T^2.J^-1
+  units isc_spin 10^19.T^2.J^-1
+  units isc 10^19.T^2.J^-1
+  units isc_fc 10^19.T^2.J^-1
+  units isc_orbital_p 10^19.T^2.J^-1
+  units isc_orbital_d 10^19.T^2.J^-1
+  units isc_spin 10^19.T^2.J^-1
+  units isc 10^19.T^2.J^-1
+  units isc_fc 10^19.T^2.J^-1
+  units isc_orbital_p 10^19.T^2.J^-1
+  units isc_orbital_d 10^19.T^2.J^-1
+  units isc_spin 10^19.T^2.J^-1
+  units isc 10^19.T^2.J^-1
+  units isc_fc 10^19.T^2.J^-1
+  units isc_orbital_p 10^19.T^2.J^-1
+  units isc_orbital_d 10^19.T^2.J^-1
+  units isc_spin 10^19.T^2.J^-1
+  units isc 10^19.T^2.J^-1
+  units isc_fc 10^19.T^2.J^-1
+  units isc_orbital_p 10^19.T^2.J^-1
+  units isc_orbital_d 10^19.T^2.J^-1
+  units isc_spin 10^19.T^2.J^-1
+  units isc 10^19.T^2.J^-1
+  units isc_fc 10^19.T^2.J^-1
+  units isc_orbital_p 10^19.T^2.J^-1
+  units isc_orbital_d 10^19.T^2.J^-1
+  units isc_spin 10^19.T^2.J^-1
+  units isc 10^19.T^2.J^-1
+  units isc_fc 10^19.T^2.J^-1
+  units isc_orbital_p 10^19.T^2.J^-1
+  units isc_orbital_d 10^19.T^2.J^-1
+  units isc_spin 10^19.T^2.J^-1
+  units isc 10^19.T^2.J^-1
+  units isc_fc 10^19.T^2.J^-1
+  units isc_orbital_p 10^19.T^2.J^-1
+  units isc_orbital_d 10^19.T^2.J^-1
+  units isc_spin 10^19.T^2.J^-1
+  units isc 10^19.T^2.J^-1
+  ms H 1 30.2981796159 1.2051069281 3.67274492938 1.96313294552 27.5765250451 2.57545224195 4.21834131673 2.16271307552 30.9031525163
+  ms H 2 26.9742092612 -0.420221330647 0.603628166501 -0.387611330052 35.3313827464 -1.80447967738 -0.578564493964 -1.44841641969 28.4625610177
+  ms H 3 29.9943370458 0.804017870839 -3.41596793698 -0.538358436872 27.8109854077 -0.130246475692 -3.56604211569 -0.0418632950686 32.5029379989
+  ms H 4 32.2898154856 0.584330480731 -1.63639006642 0.778952021344 22.6711049351 1.80797334282 -0.0810936558433 2.01393309009 25.9791612443
+  ms H 5 25.946849893 -2.77588906551 3.75442739434 -1.77463107727 29.7225814726 -0.398037457666 3.04599241075 -1.46601607492 26.5018075671
+  ms H 6 28.6085193533 -2.06023026024 4.73450589133 -0.308253194156 32.9520121318 -6.48661920164 4.68678352951 -5.89383717672 34.3943957639
+  ms C 1 150.363398078 -10.1551572591 -0.228392095331 0.262621541636 160.896219614 23.0932964082 7.6058979745 15.6796898709 158.142036855
+  ms C 2 133.676840084 0.262423773157 30.3803502689 3.67357096609 87.087341646 13.766471363 33.4352726046 12.5980254544 108.80723859
+  ms O 1 246.617726076 4.67835886314 23.439961146 -25.5598430959 289.39716395 -21.152670085 18.297484257 -4.25541343242 268.070670505
+  efg_local H 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+  efg_local H 2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+  efg_local H 3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+  efg_local H 4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+  efg_local H 5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+  efg_local H 6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+  efg_local C 1 -0.0250863245422 -0.0201770085446 -0.00412773044863 -0.0201770085446 0.019590013125 0.034603122236 -0.00412773044863 0.034603122236 0.00549631141718
+  efg_local C 2 0.18069118986 0.0616787382743 0.26613664065 0.0616787382743 -0.179575675203 0.11466220516 0.26613664065 0.11466220516 -0.00111551465673
+  efg_local O 1 0.118861288007 0.135560088603 1.49199510969 0.135560088603 0.0010287580134 -0.861525967236 1.49199510969 -0.861525967236 -0.11989004602
+  efg_nonlocal H 1 -0.248884029127 -0.15886792949 -0.510061683836 -0.15886792949 0.31790645627 -0.164617997629 -0.510061683836 -0.164617997629 -0.0690224271437
+  efg_nonlocal H 2 0.413666682454 0.14659469133 -0.101224264464 0.14659469133 -0.557394043688 0.377626548075 -0.101224264464 0.377626548075 0.143727361235
+  efg_nonlocal H 3 -0.240472505532 -0.1201678195 0.512637552144 -0.1201678195 0.352737517928 0.0258286832003 0.512637552144 0.0258286832003 -0.112265012396
+  efg_nonlocal H 4 -0.47263265592 -0.148232439756 0.491190116538 -0.148232439756 0.40383299567 0.0474885223735 0.491190116538 0.0474885223735 0.06879966025
+  efg_nonlocal H 5 0.345536759085 0.227490107486 -0.192663085782 0.227490107486 -0.428940178047 0.468128657615 -0.192663085782 0.468128657615 0.083403418962
+  efg_nonlocal H 6 0.682455309103 0.347422629338 -0.345110329811 0.347422629338 -0.57839260253 1.04274527009 -0.345110329811 1.04274527009 -0.104062706573
+  efg_nonlocal C 1 0.130515539747 -0.00113106162527 -0.0103315568603 -0.00113106162527 -0.0778325541782 -0.186058494954 -0.0103315568603 -0.186058494954 -0.0526829855687
+  efg_nonlocal C 2 -0.10120809182 -0.0606319177341 -0.25184927724 -0.0606319177341 0.10366108656 -0.201110715697 -0.25184927724 -0.201110715697 -0.00245299473989
+  efg_nonlocal O 1 -0.0499340762424 -0.0597999337628 -0.341995493801 -0.0597999337628 0.070460923598 0.0611629807928 -0.341995493801 0.0611629807928 -0.0205268473556
+  efg H 1 0.12793404309 0.0514298737569 0.20226839328 0.0514298737569 -0.133531745662 0.0414560149276 0.20226839328 0.0414560149276 0.00559770257191
+  efg H 2 -0.133979130361 -0.0609040781878 0.0374120243967 -0.0609040781878 0.157638296763 -0.184442244602 0.0374120243967 -0.184442244602 -0.0236591664019
+  efg H 3 0.12986839977 0.0652645621537 -0.201061065166 0.0652645621537 -0.128376570683 -0.0454082281587 -0.201061065166 -0.0454082281587 -0.00149182908676
+  efg H 4 0.125522205339 0.060319384091 -0.183473060621 0.060319384091 -0.129847323513 -0.040585650492 -0.183473060621 -0.040585650492 0.00432511817317
+  efg H 5 -0.126596501712 -0.0582754965986 0.0467662219879 -0.0582754965986 0.15405837804 -0.184288654121 0.0467662219879 -0.184288654121 -0.0274618763279
+  efg H 6 -0.190199778929 -0.0789692888392 0.0920151083512 -0.0789692888392 0.199082123801 -0.306948344129 0.0920151083512 -0.306948344129 -0.00888234487242
+  efg C 1 -0.0173552373 -0.0176045247437 -0.000136955319678 -0.0176045247437 0.0135099098682 0.0274798976768 -0.000136955319678 0.0274798976768 0.00384532743183
+  efg C 2 0.184546017444 0.0651728710368 0.269047132476 0.0651728710368 -0.18101177765 0.104663940666 0.269047132476 0.104663940666 -0.0035342397939
+  efg O 1 0.103201288239 0.138401445413 1.52917490275 0.138401445413 0.023733007643 -0.902715992177 1.52917490275 -0.902715992177 -0.126934295882
+  isc_fc C 1 H 1 35.9946358421 1.08660078313 4.35110864214 1.08660078175 30.2365892665 0.812257453852 4.35110864168 0.812257453841 33.2357617836
+  isc_fc C 1 H 2 31.1380312992 -1.21890555465 0.824294625004 -1.21890555432 37.2471446158 -4.19417641023 0.82429462563 -4.19417640926 33.6716733223
+  isc_fc C 1 H 3 37.3134614796 1.5695753567 -4.23203198436 1.56957535695 31.7651945551 -1.13050653797 -4.23203198415 -1.13050653608 34.3953843096
+  isc_fc C 1 H 4 1.171394881 -0.00245959281176 0.0888907042389 -0.00245959297273 1.4655854168 0.1064401538 0.0888907048839 0.106440153617 1.2444823826
+  isc_fc C 1 H 5 0.480278947603 0.00779303492979 -0.0370551454302 0.00779303431011 0.372884818496 0.142437254584 -0.0370551459683 0.142437254725 0.589135204716
+  isc_fc C 1 H 6 0.263119906174 0.00342470624062 -0.0207661093985 0.00342470637378 0.33742556529 0.0544173442504 -0.0207661083489 0.0544173453321 0.256170911424
+  isc_fc C 1 C 1 -2802.07279605 -0.191050131725 -0.152689735333 -0.191050131709 -2801.10464395 0.728294531712 -0.152689742695 0.728294528496 -2801.44000714
+  isc_fc C 1 C 2 31.8521200277 -1.73214565844 -1.45770280596 -1.73214565845 42.6480074009 9.04909872335 -1.45770280301 9.04909872098 39.1202320354
+  isc_fc C 1 O 1 2.81101504079 -0.0406937892024 0.356042705931 -0.0406938003965 2.09289123888 -0.0442360147 0.356042706141 -0.0442360168606 1.6706317224
+  isc_fc C 2 H 1 1.14414565227 -0.173500290471 -0.166894404479 -0.17350029037 1.20586181655 -0.0469014051319 -0.166894404049 -0.046901405484 0.99485526508
+  isc_fc C 2 H 2 -0.488019233922 0.12451758949 -0.0119954139149 0.124517589368 -0.483092341025 0.170094957926 -0.0119954137686 0.170094958286 -0.39073770577
+  isc_fc C 2 H 3 -0.765860440993 0.048712148947 0.12378979193 0.0487121484793 -0.509352319826 0.0759724695125 0.123789792317 0.0759724700755 -0.518874555715
+  isc_fc C 2 H 4 40.0379264054 1.553077095 -4.84993950481 1.55307709563 34.8065771989 -1.3555725686 -4.84993950378 -1.35557256943 38.4908234851
+  isc_fc C 2 H 5 34.9351080721 -1.05253139779 0.61218469604 -1.05253139791 42.2757584933 -4.60210322886 0.612184696098 -4.60210322888 37.660158525
+  isc_fc C 2 H 6 0.216361013817 0.0878406280712 0.224067616248 0.087840628522 -0.180013124411 0.13394126665 0.224067616503 0.13394126723 0.0283503474047
+  isc_fc C 2 C 1 33.0988763926 -4.00479724423 -2.88426386109 -4.0047972431 42.8683144345 8.13181995887 -2.88426386415 8.13181996122 37.6928670983
+  isc_fc C 2 C 2 -2836.37598024 0.421303044923 1.97222480333 0.421303041951 -2838.74178312 1.08252819987 1.97222480915 1.08252819921 -2837.65686816
+  isc_fc C 2 O 1 -43.4631275515 -2.04626259138 3.64667833856 -2.04626259518 -48.2972063886 -1.11218080624 3.6466783468 -1.11218080326 -44.1432517463
+  isc_fc H 1 H 1 -80.4096038787 0.149883072227 0.611882525888 0.149883072227 -81.2026660922 0.118043734733 0.611882525762 0.118043734733 -80.8027508182
+  isc_fc H 1 H 2 -0.418303238482 0.137900147953 0.183196353353 0.137900147953 -0.581477432275 0.0435438482087 0.183196353356 0.0435438482087 -0.578994457654
+  isc_fc H 1 H 3 -0.397504641289 0.0455001721399 0.180618168528 0.0455001721399 -0.647001117992 0.0199822757169 0.180618168543 0.0199822757169 -0.302003339512
+  isc_fc H 1 H 4 0.084047515237 0.0312449952927 0.0426071191305 0.0312449952927 0.100455890346 0.0165292920602 0.0426071191739 0.0165292920602 0.0532479494699
+  isc_fc H 1 H 5 0.127091022129 0.00487819149814 0.0229593387828 0.00487819149814 0.0820570806384 0.0180925271879 0.0229593385842 0.0180925271879 0.184008397438
+  isc_fc H 1 H 6 -0.0310705116171 0.00753702820518 0.0249028119296 0.00753702820518 -0.010987989109 0.0209945403493 0.0249028117287 0.0209945403493 -0.0328719933904
+  isc_fc H 1 C 1 29.1554766966 -1.65738145349 -6.30546124516 -1.65738145349 37.3052973069 -1.25168052919 -6.30546124495 -1.25168052919 32.859953062
+  isc_fc H 1 C 2 1.734529092 -0.263244735784 0.220776022455 -0.263244735784 0.827600940808 -0.183475111672 0.220776021931 -0.183475111672 0.80909698424
+  isc_fc H 1 O 1 3.07272640793 -0.0223030691327 -0.0749119025458 -0.0223030691327 3.09892619176 -0.0734018542939 -0.0749119005415 -0.0734018542939 2.95859229252
+  isc_fc H 2 H 1 -0.66231601841 0.0369393704404 0.0262127745375 0.0369393704404 -0.282206881192 -0.154133183044 0.0262127745375 -0.154133183044 -0.633477997403
+  isc_fc H 2 H 2 -81.2821474664 -0.181179389648 0.0772948566004 -0.181179389648 -80.3446467464 -0.575462031071 0.0772948566004 -0.575462031071 -81.0551624919
+  isc_fc H 2 H 3 -0.414025108949 -0.140866775063 0.024200882331 -0.140866775063 -0.221785073806 -0.16496052298 0.024200882331 -0.16496052298 -0.478012773656
+  isc_fc H 2 H 4 0.302163789208 0.0186101115393 0.0150453044275 0.0186101115393 0.404493397488 -0.0131929554751 0.0150453044275 -0.0131929554751 0.317364050861
+  isc_fc H 2 H 5 0.930066163717 -0.0413616645029 -0.00685575482673 -0.0413616645029 0.99067204749 0.0292961488218 -0.00685575482673 0.0292961488218 0.941925708619
+  isc_fc H 2 H 6 0.016970527038 -0.0129209518533 -0.0183760302242 -0.0129209518533 0.059747319775 -0.0270217896573 -0.0183760302242 -0.0270217896573 -0.0268260441406
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+  isc C 1 H 3 31.5792071064 -1.45775468352 5.45503557239 -1.51896704435 38.9040980182 1.09338844913 5.41420686054 1.09742561781 35.1845328299
+  isc C 1 H 4 1.49045503749 0.640802986263 0.0564090745134 0.558318551113 1.62034708178 -0.327857401277 0.0597938688448 -0.357106525719 0.737157643099
+  isc C 1 H 5 0.351443385545 -0.00552353321262 0.0383607452002 0.0320753460182 -0.144325901487 -0.449501112964 -0.0151350052527 -0.384315238715 1.23290172147
+  isc C 1 H 6 0.214783366703 -0.0918896762745 -0.105158018894 -0.0406903764847 0.596319610649 -0.376254013685 -0.196456305509 -0.541913474443 0.227998628905
+  isc C 1 C 1 -2967.15897373 -0.0567797533567 -0.253895528567 -0.0427306188074 -2965.7944856 0.986726899261 -0.252603057537 0.983872712214 -2966.22024839
+  isc C 1 C 2 27.7189556609 -6.4449869178 -4.00615165115 -6.40221256585 48.1439909835 18.3175598986 -3.89028772154 18.3051868033 39.1397675446
+  isc C 1 O 1 -5.16909230347 -3.57645970541 -4.2479653284 -3.96726534402 4.19637912733 8.30275269583 -2.56474178964 8.41482324898 2.82924647793
+  isc C 2 H 1 2.05022964856 -0.639291161367 0.0149130109705 -0.670861344044 0.980676265707 -0.387128999111 -0.0065763797666 -0.383782114346 0.579389710985
+  isc C 2 H 2 -0.550515570171 0.0802627736288 0.14750286673 0.179102072927 -1.01393757159 -0.386069684761 0.0514614188944 -0.285598808935 0.315346623319
+  isc C 2 H 3 -0.382575390568 0.685576895304 0.123193184207 0.540902590659 -0.317871613199 -0.231216545328 0.15669723815 -0.337552386225 -0.969953828999
+  isc C 2 H 4 33.4723624677 -1.32821090621 4.86819073335 -1.32789670884 41.4605686848 0.658998183375 4.99706193394 0.698947247295 39.7469627326
+  isc C 2 H 5 41.872535955 2.5731289266 -1.28067669934 2.68117630449 34.9743795357 4.863876123 -1.3343721286 4.78756109976 39.2686060364
+  isc C 2 H 6 -0.277593622598 0.648066417286 -0.534666352821 1.05409011646 1.5298817447 -0.0365924505193 -0.747530893431 -0.28414228215 -0.523664701047
+  isc C 2 C 1 27.8124299673 -6.41599539941 -3.89643169542 -6.44208619509 48.1687111086 18.3096732363 -4.00427666381 18.2807417781 39.1469587798
+  isc C 2 C 2 -2997.42946986 0.0968084747702 -0.0624244779836 0.0995468206394 -2995.42057109 0.336167323973 -0.032748271037 0.33683813873 -2996.06812132
+  isc C 2 O 1 -21.5247906043 9.4620584897 24.1059733484 7.61232662301 -52.1418846015 5.54882338421 25.1860141402 6.8218292721 -40.0701132738
+  isc H 1 H 1 2.97410483503 -2.70165892166 1.50707455761 -2.7430539658 6.9658745472 0.810814767339 1.60306958778 0.890235069266 -8.5269946386
+  isc H 1 H 2 -0.498615363307 0.217200750472 0.403409922666 0.199353115064 -0.267223309797 -0.204995898897 0.404649610705 -0.184766422109 -0.675840704294
+  isc H 1 H 3 -0.169181559836 0.155921977877 0.0509658662849 0.163764458914 -0.983894731714 -0.0200731077399 0.00720217972707 -0.032035487293 -0.0182117600016
+  isc H 1 H 4 0.10333898357 0.00892814613052 0.00789750719001 -0.00991323894355 0.0689546520892 0.0692766888876 -0.0147839319182 0.060922336088 0.0372243677199
+  isc H 1 H 5 0.0865932063208 -0.0313316516112 0.036626367258 -0.0498089888109 0.143015314072 0.027756102664 0.0255542481556 0.042649692979 0.140067196824
+  isc H 1 H 6 -0.150214659126 0.00838272030295 0.0712741572671 0.0261624912664 -0.0807151575722 0.0274744545661 0.067009549412 -0.00493427877876 0.0400920483225
+  isc H 1 C 1 31.7476521007 -0.990381201009 -3.42485657825 -1.00259551278 36.0477688911 -0.7215773568 -3.49857740767 -0.737264050525 33.5988947272
+  isc H 1 C 2 1.80168809985 -0.518775744223 -0.0684002089343 -0.426694149442 0.937576616273 -0.328875866807 0.00531669849026 -0.386121582716 0.668119181714
+  isc H 1 O 1 1.97240909487 0.627202700452 0.511227750355 0.479858815939 3.07867201137 0.973264643821 0.518704043241 1.12188438016 3.03584902255
+  isc H 2 H 1 -0.542290769968 0.17331151944 0.372596437436 0.216742531282 -0.196547127496 -0.218453678223 0.355496896228 -0.257119411836 -0.677144060763
+  isc H 2 H 2 10.8778621973 -3.60475230244 -2.57372651163 -3.67610391942 7.56003441589 -4.55584847879 -2.53752171837 -4.45619007774 -13.9214687085
+  isc H 2 H 3 -0.155101364178 -0.208127093545 -0.259326990441 -0.239661618357 -0.27922702007 -0.353003279136 -0.248023505657 -0.38679128024 -0.566124815685
+  isc H 2 H 4 0.270326580539 0.00992288293244 -0.0440686803595 0.000251398962481 0.34815203204 0.0416997665363 -0.0383805023489 0.0241550036055 0.367632276639
+  isc H 2 H 5 0.825720480992 -0.0585341016811 -0.0065594122703 -0.073337230798 1.02743097586 0.0717573848063 -0.000517064783312 0.0739820215663 0.88451565739
+  isc H 2 H 6 -0.0540602673514 -0.0296157803272 -0.00726386117536 0.00999266268426 0.0240124414207 -0.0104958865771 -0.00519650500483 -0.0349399067687 -0.0267123386241
+  isc H 2 C 1 36.7569262776 1.08389286047 -0.626202499709 1.17268917271 31.5601561136 3.11475736614 -0.609091003826 2.97627169031 35.5352005124
+  isc H 2 C 2 -0.585680430616 0.198399605578 0.0128660309318 0.14550178373 -0.907858019491 -0.285523281542 0.0783800085424 -0.335664333495 0.0557699172386
+  isc H 2 O 1 0.925680308985 -0.0618160579251 0.215811770404 -0.111886715129 1.0671316834 -0.275740363057 0.107698330175 -0.233259766783 0.697811993456
+  isc H 3 H 1 -0.174486654215 0.174826215955 -0.0741710296022 0.16847313206 -0.973006462332 -0.0399365407525 -0.0205620248471 -0.0275370445833 -0.0251744585641
+  isc H 3 H 2 -0.112466301606 -0.232181800953 -0.274240622793 -0.215854567289 -0.33419133672 -0.355361886804 -0.278651307319 -0.332095480566 -0.537952533761
+  isc H 3 H 3 -11.6760610129 0.0389239648627 -4.63475457 0.0377952307334 8.60381419178 -0.464252825253 -4.82003469079 -0.473620432752 -7.90902347897
+  isc H 3 H 4 0.834823196204 -0.038484239403 -0.0440036561035 -0.0324776649979 0.908556084483 0.103255708706 -0.0475426979489 0.106119345486 0.915213244073
+  isc H 3 H 5 0.22641642479 0.00260962293405 -0.0265245430191 0.0181079061587 0.36760324601 0.0126931694775 -0.0284319079881 0.0313662159075 0.320300577274
+  isc H 3 H 6 -0.100563297934 0.00589815496076 0.00988691434754 0.0191840775719 -0.0982375428087 0.101628901438 0.0362217271075 0.0402592635805 -0.0280282008519
+  isc H 3 C 1 32.7186513826 -0.856204200421 3.38543177849 -0.767165636699 37.4690308196 0.591596523367 3.49068310529 0.622782767566 35.0946110477
+  isc H 3 C 2 -0.424821311062 0.427643320159 0.180430780063 0.512823777012 -0.485609666544 -0.313690672451 0.127950509663 -0.273952051531 -0.923863128775
+  isc H 3 O 1 -0.117691533359 0.066664328548 -0.0645599105307 -0.163390689379 0.274808540148 -0.280649206215 0.192094211638 -0.223456896036 0.240751671652
+  isc H 4 H 1 0.106264252477 -0.00329971119232 -0.0191249787247 0.00678549995373 0.0817799520549 0.0590244924063 -0.00682414753215 0.0533450062552 0.04528431874
+  isc H 4 H 2 0.279969715262 0.00234083525374 -0.0333489113071 0.00792536578491 0.376471477119 0.00429964297264 -0.0461896182454 0.0284737245065 0.350330478107
+  isc H 4 H 3 0.838739565601 -0.0298502859437 -0.0472512750264 -0.0481634676757 0.920076777302 0.105957422252 -0.0486923697372 0.0928445743941 0.925801258544
+  isc H 4 H 4 4.06040781209 -5.0256254251 -6.76437464831 -4.93420697404 7.604406207 -5.02812945735 -6.65605628281 -4.98646661419 -3.46743555013
+  isc H 4 H 5 -0.172749190825 -0.211146609184 -0.279058263758 -0.178247455502 -0.311780841075 -0.33105552977 -0.318323285828 -0.338262940313 -0.554088438447
+  isc H 4 H 6 0.180019337653 0.00754867698386 0.0611157715288 0.0642308243757 0.190250635206 -0.0383037405642 -0.000200151014689 -0.0837776487628 0.155975285186
+  isc H 4 C 1 1.46703059168 0.398593102101 0.125866170133 0.399878742422 1.47626790187 -0.200621149363 0.0624973943779 -0.228422178524 0.839943837455
+  isc H 4 C 2 34.8313806819 -0.615170286728 3.09624623454 -0.626424696804 39.9596538788 0.266388598222 2.90803201855 0.206584738846 39.2911684277
+  isc H 4 O 1 1.3756918616 0.0953832727605 -1.90202701243 -0.0590283324024 0.750814082369 -0.955568315841 -1.56491189909 -0.519120730893 1.60822403405
+  isc H 5 H 1 0.101750958421 -0.0457028114389 0.0167716714245 -0.0345635554182 0.134759310804 0.0371667504802 0.0237300616941 0.0265427112988 0.155033102305
+  isc H 5 H 2 0.774483503752 -0.0575480329385 -0.00683176219737 -0.0478506231201 1.02823780851 0.0723612860281 -0.0145408212831 0.0818549376702 0.826258285868
+  isc H 5 H 3 0.254179632739 0.0141617902454 -0.0196856331776 -0.00914104876672 0.341651366046 0.0259304982645 -0.0257433601749 0.00788129933172 0.33601231799
+  isc H 5 H 4 -0.212438267573 -0.196279247917 -0.286421161011 -0.234449145778 -0.273830677095 -0.362686393762 -0.241180503396 -0.357953310222 -0.528120584505
+  isc H 5 H 5 -7.97806815757 -4.49879685242 -5.2169180624 -4.3617836933 11.7533032524 -5.08193925503 -5.20045957363 -5.22444129025 5.36156356127
+  isc H 5 H 6 1.17984880096 -0.0261536661101 0.175061993876 0.0212188554153 1.00554925543 -0.0111366663549 0.143064084541 -0.0369574417967 1.12107905699
+  isc H 5 C 1 0.334363590358 0.0564929377599 0.0322579251143 0.0110423944319 0.00821544911402 -0.341553740772 0.0489789801213 -0.335245007716 0.948930180383
+  isc H 5 C 2 40.40334991 1.7447934796 -0.737164952269 1.60622694843 36.2347013114 2.737968833 -0.670510516191 2.87622924725 38.9327436648
+  isc H 5 O 1 7.05032760413 0.507769403213 -0.828210169009 0.782834524585 9.13176686547 0.135373787916 -0.912700759626 -0.215466033663 7.059156412
+  isc H 6 H 1 -0.14312060858 0.00754088025044 0.047738514881 -8.28454026369e-05 -0.057168555792 0.00328657266518 0.052896359173 0.0171831924333 0.0234138715999
+  isc H 6 H 2 -0.0269614765625 -0.00282460743916 0.00120461777299 -0.0338661468316 0.0421468681056 -0.0389409975216 -0.00271362673178 -0.0278373672552 -0.00428767630498
+  isc H 6 H 3 -0.0853489481656 0.010497348151 0.0383212204882 0.000568036729305 -0.0583936875691 0.0404363232804 0.0132757205897 0.072250171327 -0.023601509733
+  isc H 6 H 4 0.201311356646 0.0731058633305 -0.000950849712595 0.0327161567842 0.176467136988 -0.0835176876921 0.052756283177 -0.041629032184 0.151977611665
+  isc H 6 H 5 1.16962978918 0.0260979473149 0.14615218636 -0.00527527324828 1.02298631666 -0.0320250689503 0.166208347926 -0.0108693233221 1.10582788762
+  isc H 6 H 6 -18.7687713446 -3.67555273866 0.14451118412 -3.83817618203 6.24054408214 -2.60913691332 0.147429719909 -2.54657374015 13.8761638472
+  isc H 6 C 1 0.153531855681 -0.0493901019368 -0.256331574004 -0.0725622458316 0.506949534512 -0.444292553303 -0.1368169793 -0.358030218284 0.143969816034
+  isc H 6 C 2 -0.321656925841 0.749219957524 -0.645250780279 0.478175161648 1.25923203052 -0.228185709608 -0.517719173418 -0.0817056029894 -0.435551184552
+  isc H 6 O 1 41.5298155885 3.87053767991 2.40197075905 4.67737612025 36.5746032841 3.74944514163 1.85634117553 3.13531309597 35.992778484
+  isc O 1 H 1 2.3814248719 0.595053861624 0.716430978947 0.701021677467 3.24756470426 1.22690670403 0.762156767053 1.14304989914 3.11625214566
+  isc O 1 H 2 1.11581247064 0.0256357687188 0.0348516607744 -0.0170075572746 1.09915524615 -0.189145710671 0.122751713086 -0.0785891076516 0.883989966241
+  isc O 1 H 3 0.468501790422 -0.00213745228057 0.205446957902 0.111112452847 0.550356552054 -0.122894936675 -0.0622048938207 -0.0774607238982 0.22598974211
+  isc O 1 H 4 1.1790644819 -0.118268986872 -1.79901520629 -0.0411371680149 1.00697559969 -0.665094827746 -1.85895459625 -0.931514215033 1.77889432978
+  isc O 1 H 5 6.83529084996 1.16859534664 -1.31953936171 0.962403076145 9.59009452892 -0.120641069566 -1.28598179774 0.16897809553 6.76480531876
+  isc O 1 H 6 43.2094556559 5.56276147619 1.51735336201 5.49897369013 36.4008010217 5.09293286667 1.68008117155 5.08264113455 36.1863087744
+  isc O 1 C 1 -5.03359646533 -3.74418912421 -2.43422419175 -3.58830421782 4.11915008984 8.2735601603 -4.28015854016 8.28129073691 2.76448022907
+  isc O 1 C 2 -21.6358972308 7.5812507502 25.2542332838 9.56566888858 -52.3552660487 6.88191840075 24.0727075218 5.53536215469 -40.2888897851
+  isc O 1 O 1 -12954.4649666 59.5242259199 -49.3184606393 59.5174759308 -12913.1706944 22.3404222136 -49.6095076843 22.2358144557 -13018.8655741
+[/magres]

From f3f9e6c2790816db7db91bfa875e8f482f57ac24 Mon Sep 17 00:00:00 2001
From: Patrick Austin <patrick.austin@stfc.ac.uk>
Date: Fri, 8 Dec 2023 12:08:57 +0000
Subject: [PATCH 02/11] Fix CI linting, tests for Magres datatype #26

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample |  3 ++-
 lib/galaxy/datatypes/molecules.py                  | 10 +++-------
 2 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 4289d9b69d7b..f7ac063c5740 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -782,6 +782,7 @@
     <datatype extension="cif" type="galaxy.datatypes.molecules:CIF" display_in_upload="true"/>
     <datatype extension="xyz" type="galaxy.datatypes.molecules:XYZ" display_in_upload="true"/>
     <datatype extension="extxyz" type="galaxy.datatypes.molecules:ExtendedXYZ" display_in_upload="true"/>
+    <datatype extension="magres" type="galaxy.datatypes.molecules:Magres" display_in_upload="true"/>
     <datatype extension="trr" type="galaxy.datatypes.binary:Trr" display_in_upload="true">
       <converter file="mdconvert.xml" target_datatype="xtc"/>
       <converter file="mdconvert.xml" target_datatype="dcd"/>
@@ -1141,6 +1142,7 @@
     <sniffer type="galaxy.datatypes.molecules:CIF"/>
     <sniffer type="galaxy.datatypes.molecules:ExtendedXYZ"/>
     <sniffer type="galaxy.datatypes.molecules:XYZ"/>
+    <sniffer type="galaxy.datatypes.molecules:Magres" />
     <sniffer type="galaxy.datatypes.molecules:MOL2"/>
     <sniffer type="galaxy.datatypes.molecules:InChI"/>
     <sniffer type="galaxy.datatypes.molecules:FPS"/>
@@ -1241,7 +1243,6 @@
     <sniffer type="galaxy.datatypes.text:CTLresult"/>
     <sniffer type="galaxy.datatypes.text:FormattedDensity" />
     <sniffer type="galaxy.datatypes.text:Param" />
-    <sniffer type="galaxy.datatypes.text:Magres" />
     <sniffer type="galaxy.datatypes.text:Yaml" />
     <!--
     Keep this commented until the sniff method in the assembly.py
diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index e0cd61abe112..fccd305a8569 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -1768,6 +1768,7 @@ def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
             dataset.peek = "file does not exist"
             dataset.blurb = "file purged from disk"
 
+
 @build_sniff_from_prefix
 class Magres(GenericMolFile):
     """Report on a MAGRES calculation"""
@@ -1781,13 +1782,8 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         >>> fname = get_test_fname('ethanol.magres')
         >>> Magres().sniff(fname)
         True
-        >>> fname = get_test_fname('<file>.param')
+        >>> fname = get_test_fname('Si.cif')
         >>> Magres().sniff(fname)
         False
         """
-        fh = file_prefix.string_io()
-
-        for lines in fh:
-            if not re.search(r'\#\$magres-abinitio-v([0-9]+).([0-9]+)', lines[0]):
-                return False        
-        return True
\ No newline at end of file
+        return file_prefix.startswith("#$magres-abinitio-v")

From b27bd519c6400b52ea86bcd0487b19da5c65bd4c Mon Sep 17 00:00:00 2001
From: Nalin Gupta <nalin.gupta3142@gmail.com>
Date: Wed, 20 Dec 2023 17:01:56 +0000
Subject: [PATCH 03/11] Added capability to show metadata for magres file

---
 CONTRIBUTORS.md                   |   1 +
 lib/galaxy/datatypes/molecules.py | 119 ++++++++++++++++++++++++++++++
 2 files changed, 120 insertions(+)

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
index 87e587cac534..bf3dad91480b 100644
--- a/CONTRIBUTORS.md
+++ b/CONTRIBUTORS.md
@@ -74,6 +74,7 @@ The following individuals have contributed code to Galaxy:
 * Björn Grüning <bjoern.gruening@gmail.com> <bjoern@gruenings.eu>
 * Aysam Guerler <aysam.guerler@gmail.com>
 * Simon Guest <simon.guest@agresearch.co.nz>
+* Nalin Gupta <nalin.gupta@stfc.ac.uk>
 * Jianbin He <jbhe@bx.psu.edu>
 * Peter van Heusden <pvh@sanbi.ac.za>
 * Morita Hideyuki <h-morita@esm.co.jp>
diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index fccd305a8569..3b5003025658 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -1774,6 +1774,45 @@ class Magres(GenericMolFile):
     """Report on a MAGRES calculation"""
 
     file_ext = "magres"
+    meta_error = False
+    MetadataElement(
+        name="data_block_names",
+        default=[],
+        desc="Names of the data blocks",
+        readonly=True,
+        visible=True,
+    )
+    MetadataElement(
+        name="atom_data",
+        default=[],
+        desc="Atom symbols and positions",
+        readonly=True,
+        visible=False,
+    )
+    MetadataElement(
+        name="number_of_atoms",
+        desc="Number of atoms",
+        readonly=True,
+        visible=True,
+    )
+    MetadataElement(
+        name="chemical_formula",
+        desc="Chemical formula",
+        readonly=True,
+        visible=True,
+    )
+    MetadataElement(
+        name="is_periodic",
+        desc="Periodic boundary conditions",
+        readonly=True,
+        visible=True,
+    )
+    MetadataElement(
+        name="lattice_parameters",
+        desc="Lattice parameters",
+        readonly=True,
+        visible=True,
+    )
 
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         """Determines whether the file is a MAGRES log
@@ -1787,3 +1826,83 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         False
         """
         return file_prefix.startswith("#$magres-abinitio-v")
+
+    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
+        """
+        Find Atom IDs for metadata.
+        """
+        self.meta_error = False
+        if ase_io is None:
+            # Don't have optional dependency, can't set advanced values
+            return
+        else:
+            # enhanced metadata
+            try:
+                ase_data = ase_io.read(dataset.get_file_name(), index=":", format="magres")
+            except Exception as e:
+                log.warning("%s, set_meta Exception during ASE read: %s", self, unicodify(e))
+                self.meta_error = True
+                return
+
+            atom_data = []
+            chemical_formula = []
+            is_periodic = []
+            lattice_parameters = []
+            try:
+                for block in ase_data:
+                    atom_data.append(
+                        [str(sym) + str(pos) for sym, pos in zip(block.get_chemical_symbols(), block.get_positions())]
+                    )
+                    chemical_formula.append(block.get_chemical_formula())
+                    pbc = block.get_pbc()
+                    try:
+                        p = bool(pbc)
+                    except ValueError:  # pbc is an array
+                        p = bool(pbc.any())
+                    is_periodic.append(p)
+                    lattice_parameters.append(list(block.get_cell().cellpar()))
+            except Exception as e:
+                log.warning("%s, set_meta Exception during ASE metadata collection: %s", self, unicodify(e))
+                self.meta_error = True
+                return
+
+            dataset.metadata.number_of_molecules = len(ase_data)
+            dataset.metadata.atom_data = atom_data
+            dataset.metadata.number_of_atoms = [len(atoms) for atoms in dataset.metadata.atom_data]
+            dataset.metadata.chemical_formula = chemical_formula
+            dataset.metadata.is_periodic = is_periodic
+            dataset.metadata.lattice_parameters = list(lattice_parameters)
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek(dataset.get_file_name())
+            dataset.info = self.get_dataset_info(dataset.metadata)
+            structure_string = "structure" if dataset.metadata.number_of_molecules == 1 else "structures"
+            dataset.blurb = f"MAGRES file containing {dataset.metadata.number_of_molecules} {structure_string}"
+
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+    def get_dataset_info(self, metadata):
+        if self.meta_error:
+            info = "Error finding metadata. The file may be formatted incorrectly."
+        elif ase_io:
+            # enhanced info
+            info_list = []
+            info_list.append(f"Chemical formula:\n{metadata.chemical_formula[0]}")
+            if metadata.is_periodic[0]:
+                info_list.append("Periodic:\nYes")
+                info_list.append(
+                    f"Lattice parameters in axis-angle format:\n{', '.join([str(round(x, 2)) for x in metadata.lattice_parameters[0]])}"
+                )
+            else:
+                info_list.append("Periodic:\nNo")
+            info_list.append(f"Atoms in file:\n{metadata.number_of_atoms[0]}")
+        else:
+            info = """
+Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.
+You can still use this dataset in tools and workflows.
+For full metadata, ask your admin to install the 'ase' Python package."""
+
+        return info

From ded1e993360bf0dc458c4caa6184bd4d779bea40 Mon Sep 17 00:00:00 2001
From: Nalin Gupta <nalin.gupta3142@gmail.com>
Date: Tue, 2 Jan 2024 08:50:55 +0000
Subject: [PATCH 04/11] Small fix made to magres metadata output

---
 lib/galaxy/datatypes/molecules.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index 3b5003025658..3e1750ee11a2 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -1866,7 +1866,8 @@ def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> N
                 self.meta_error = True
                 return
 
-            dataset.metadata.number_of_molecules = len(ase_data)
+            # MAGRES file can only have one molecule
+            dataset.metadata.number_of_molecules = 1
             dataset.metadata.atom_data = atom_data
             dataset.metadata.number_of_atoms = [len(atoms) for atoms in dataset.metadata.atom_data]
             dataset.metadata.chemical_formula = chemical_formula
@@ -1899,6 +1900,7 @@ def get_dataset_info(self, metadata):
             else:
                 info_list.append("Periodic:\nNo")
             info_list.append(f"Atoms in file:\n{metadata.number_of_atoms[0]}")
+            info = "\n--\n".join(info_list)
         else:
             info = """
 Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.

From bf89543b3b5f4d5410f2f3e45b727b2094c3c152 Mon Sep 17 00:00:00 2001
From: Nalin Gupta <nalin.gupta3142@gmail.com>
Date: Mon, 8 Jan 2024 06:21:52 +0000
Subject: [PATCH 05/11] Moved ASE metadata parsing to abstract class Transfered
 the metadata parsing using the ASE IO library to an abstract class
 "AtomicStructFile"

---
 lib/galaxy/datatypes/molecules.py | 612 +++++++-----------------------
 1 file changed, 137 insertions(+), 475 deletions(-)

diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index 3e1750ee11a2..ec498781dd37 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -198,6 +198,135 @@ def get_mime(self) -> str:
     ]
 
 
+class AtomicStructFile(Text):
+    """
+    Abstract class for structure files which use the ASE IO library for metadata.
+    """
+
+    meta_error = False
+    file_ext = ""
+    ase_format = ""
+
+    MetadataElement(
+        name="atom_data",
+        default=[],
+        desc="Atom symbols and positions",
+        readonly=True,
+        visible=False,
+    )
+    MetadataElement(
+        name="number_of_atoms",
+        desc="Number of atoms",
+        readonly=True,
+        visible=True,
+    )
+    MetadataElement(
+        name="chemical_formula",
+        desc="Chemical formula",
+        readonly=True,
+        visible=True,
+    )
+    MetadataElement(
+        name="is_periodic",
+        desc="Periodic boundary conditions",
+        readonly=True,
+        visible=True,
+    )
+    MetadataElement(
+        name="lattice_parameters",
+        desc="Lattice parameters",
+        readonly=True,
+        visible=True,
+    )
+
+    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
+        """
+        Find Atom IDs for metadata.
+        """
+        self.meta_error = False
+        if ase_io is None:
+            # Don't have optional dependency, can't set advanced values
+            return
+        else:
+            # enhanced metadata
+            try:
+                # ASE recommend always parsing as extended xyz
+                ase_data = ase_io.read(dataset.get_file_name(), index=":", format=self.ase_format)
+            except Exception as e:
+                log.warning("%s, set_meta Exception during ASE read: %s", self, unicodify(e))
+                self.meta_error = True
+                return
+
+            atom_data = []
+            chemical_formula = []
+            is_periodic = []
+            lattice_parameters = []
+            try:
+                for block in ase_data:
+                    atom_data.append(
+                        [str(sym) + str(pos) for sym, pos in zip(block.get_chemical_symbols(), block.get_positions())]
+                    )
+                    chemical_formula.append(block.get_chemical_formula())
+                    pbc = block.get_pbc()
+                    try:
+                        p = bool(pbc)
+                    except ValueError:  # pbc is an array
+                        p = bool(pbc.any())
+                    is_periodic.append(p)
+                    lattice_parameters.append(list(block.get_cell().cellpar()))
+            except Exception as e:
+                log.warning("%s, set_meta Exception during ASE metadata collection: %s", self, unicodify(e))
+                self.meta_error = True
+                return
+
+            dataset.metadata.number_of_molecules = len(ase_data)
+            dataset.metadata.atom_data = atom_data
+            dataset.metadata.number_of_atoms = [len(atoms) for atoms in dataset.metadata.atom_data]
+            dataset.metadata.chemical_formula = chemical_formula
+            dataset.metadata.is_periodic = is_periodic
+            dataset.metadata.lattice_parameters = list(lattice_parameters)
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek(dataset.get_file_name())
+            dataset.info = self.get_dataset_info(dataset.metadata)
+            structure_string = "structure" if dataset.metadata.number_of_molecules == 1 else "structures"
+            dataset.blurb = f"{self.file_ext.upper()} file containing {dataset.metadata.number_of_molecules} {structure_string}"
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+    def get_dataset_info(self, metadata):
+        if self.meta_error:
+            info = "Error finding metadata. The file may be formatted incorrectly."
+        elif ase_io:
+            # enhanced info
+            info_list = []
+            if metadata.number_of_molecules == 1:
+                info_list.append(f"Chemical formula:\n{metadata.chemical_formula[0]}")
+                if metadata.is_periodic[0]:
+                    info_list.append("Periodic:\nYes")
+                    info_list.append(
+                        f"Lattice parameters in axis-angle format:\n{', '.join([str(round(x, 2)) for x in metadata.lattice_parameters[0]])}"
+                    )
+                else:
+                    info_list.append("Periodic:\nNo")
+                info_list.append(f"Atoms in file:\n{metadata.number_of_atoms[0]}")
+            elif metadata.number_of_molecules > 1:
+                info_list.append("File contains multiple structures; full metadata will not be displayed.")
+                formulae = "\n".join(metadata.chemical_formula)
+                info_list.append(f"Chemical formula for each structure in this file:\n{formulae}")
+            info = "\n--\n".join(info_list)
+        else:
+            info = """
+            Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.
+            You can still use this dataset in tools and workflows.
+            For full metadata, ask your admin to install the 'ase' Python package
+            """
+
+        return info
+
+
 class MOL(GenericMolFile):
     file_ext = "mol"
 
@@ -817,44 +946,13 @@ def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
 
 
 @build_sniff_from_prefix
-class Cell(GenericMolFile):
+class Cell(AtomicStructFile):
     """
     CASTEP CELL format.
     """
 
     file_ext = "cell"
-    meta_error = False
-    MetadataElement(
-        name="atom_data",
-        default=[],
-        desc="Atom symbols and positions",
-        readonly=True,
-        visible=False,
-    )
-    MetadataElement(
-        name="number_of_atoms",
-        desc="Number of atoms",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="chemical_formula",
-        desc="Chemical formula",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="is_periodic",
-        desc="Periodic boundary conditions",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="lattice_parameters",
-        desc="Lattice parameters",
-        readonly=True,
-        visible=True,
-    )
+    ase_format = "castep-cell"
 
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         """
@@ -882,128 +980,15 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
                 return True
         return False
 
-    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
-        """
-        Find Atom IDs for metadata.
-        """
-        self.meta_error = False
-        if ase_io is None:
-            # Don't have optional dependency, can't set advanced values
-            return
-        else:
-            # enhanced metadata
-            try:
-                ase_data = ase_io.read(dataset.get_file_name(), format="castep-cell")
-            except Exception as e:
-                log.warning("%s, set_meta Exception during ASE read: %s", self, unicodify(e))
-                self.meta_error = True
-                return
-
-            try:
-                atom_data = [
-                    str(sym) + str(pos) for sym, pos in zip(ase_data.get_chemical_symbols(), ase_data.get_positions())
-                ]
-                chemical_formula = ase_data.get_chemical_formula()
-                pbc = ase_data.get_pbc()
-                lattice_parameters = ase_data.get_cell().cellpar()
-            except Exception as e:
-                log.warning("%s, set_meta Exception during ASE metadata collection: %s", self, unicodify(e))
-                self.meta_error = True
-                return
-
-            # CELL file can only have one molecule
-            dataset.metadata.number_of_molecules = 1
-            dataset.metadata.atom_data = atom_data
-            dataset.metadata.number_of_atoms = len(dataset.metadata.atom_data)
-            dataset.metadata.chemical_formula = chemical_formula
-            try:
-                dataset.metadata.is_periodic = bool(pbc)
-            except ValueError:  # pbc is an array
-                dataset.metadata.is_periodic = bool(pbc.any())
-            dataset.metadata.lattice_parameters = list(lattice_parameters)
-
-    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
-        if not dataset.dataset.purged:
-            dataset.peek = get_file_peek(dataset.get_file_name())
-            dataset.info = self.get_dataset_info(dataset.metadata)
-            structure_string = "structure" if dataset.metadata.number_of_molecules == 1 else "structures"
-            dataset.blurb = f"CASTEP CELL file containing {dataset.metadata.number_of_molecules} {structure_string}"
-
-        else:
-            dataset.peek = "file does not exist"
-            dataset.blurb = "file purged from disk"
-
-    def get_dataset_info(self, metadata):
-        if self.meta_error:
-            info = "Error finding metadata. The file may be formatted incorrectly."
-        elif ase_io:
-            # enhanced info
-            info_list = []
-            info_list.append(f"Chemical formula:\n{metadata.chemical_formula}")
-            if metadata.is_periodic:
-                info_list.append("Periodic:\nYes")
-                info_list.append(
-                    f"Lattice parameters in axis-angle format:\n{', '.join([str(round(x, 2)) for x in metadata.lattice_parameters])}"
-                )
-            else:
-                info_list.append("Periodic:\nNo")
-            info_list.append(f"Atoms in file:\n{metadata.number_of_atoms}")
-            info = "\n--\n".join(info_list)
-        else:
-            info = """
-Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.
-You can still use this dataset in tools and workflows.
-For full metadata, ask your admin to install the 'ase' Python package."""
-
-        return info
-
 
 @build_sniff_from_prefix
-class CIF(GenericMolFile):
+class CIF(AtomicStructFile):
     """
     CIF format.
     """
 
     file_ext = "cif"
-    meta_error = False
-    MetadataElement(
-        name="data_block_names",
-        default=[],
-        desc="Names of the data blocks",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="atom_data",
-        default=[],
-        desc="Atom symbols and positions",
-        readonly=True,
-        visible=False,
-    )
-    MetadataElement(
-        name="number_of_atoms",
-        desc="Number of atoms",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="chemical_formula",
-        desc="Chemical formula",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="is_periodic",
-        desc="Periodic boundary conditions",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="lattice_parameters",
-        desc="Lattice parameters",
-        readonly=True,
-        visible=True,
-    )
+    ase_format = "cif"
 
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         """
@@ -1043,132 +1028,15 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
                 return False
         return False
 
-    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
-        """
-        Find Atom IDs for metadata.
-        """
-        self.meta_error = False
-        if ase_io is None:
-            # Don't have optional dependency, can't set advanced values
-            return
-        else:
-            # enhanced metadata
-            try:
-                ase_data = ase_io.read(dataset.get_file_name(), index=":", format="cif")
-            except Exception as e:
-                log.warning("%s, set_meta Exception during ASE read: %s", self, unicodify(e))
-                self.meta_error = True
-                return
-
-            atom_data = []
-            chemical_formula = []
-            is_periodic = []
-            lattice_parameters = []
-            try:
-                for block in ase_data:
-                    atom_data.append(
-                        [str(sym) + str(pos) for sym, pos in zip(block.get_chemical_symbols(), block.get_positions())]
-                    )
-                    chemical_formula.append(block.get_chemical_formula())
-                    pbc = block.get_pbc()
-                    try:
-                        p = bool(pbc)
-                    except ValueError:  # pbc is an array
-                        p = bool(pbc.any())
-                    is_periodic.append(p)
-                    lattice_parameters.append(list(block.get_cell().cellpar()))
-            except Exception as e:
-                log.warning("%s, set_meta Exception during ASE metadata collection: %s", self, unicodify(e))
-                self.meta_error = True
-                return
-
-            dataset.metadata.number_of_molecules = len(ase_data)
-            dataset.metadata.atom_data = atom_data
-            dataset.metadata.number_of_atoms = [len(atoms) for atoms in dataset.metadata.atom_data]
-            dataset.metadata.chemical_formula = chemical_formula
-            dataset.metadata.is_periodic = is_periodic
-            dataset.metadata.lattice_parameters = list(lattice_parameters)
-
-    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
-        if not dataset.dataset.purged:
-            dataset.peek = get_file_peek(dataset.get_file_name())
-            dataset.info = self.get_dataset_info(dataset.metadata)
-            structure_string = "structure" if dataset.metadata.number_of_molecules == 1 else "structures"
-            dataset.blurb = f"CIF file containing {dataset.metadata.number_of_molecules} {structure_string}"
-
-        else:
-            dataset.peek = "file does not exist"
-            dataset.blurb = "file purged from disk"
-
-    def get_dataset_info(self, metadata):
-        if self.meta_error:
-            info = "Error finding metadata. The file may be formatted incorrectly."
-        elif ase_io:
-            # enhanced info
-            info_list = []
-            if metadata.number_of_molecules == 1:
-                info_list.append(f"Chemical formula:\n{metadata.chemical_formula[0]}")
-                if metadata.is_periodic[0]:
-                    info_list.append("Periodic:\nYes")
-                    info_list.append(
-                        f"Lattice parameters in axis-angle format:\n{', '.join([str(round(x, 2)) for x in metadata.lattice_parameters[0]])}"
-                    )
-                else:
-                    info_list.append("Periodic:\nNo")
-                info_list.append(f"Atoms in file:\n{metadata.number_of_atoms[0]}")
-            elif metadata.number_of_molecules > 1:
-                info_list.append("File contains multiple structures; full metadata will not be displayed.")
-                formulae = "\n".join(metadata.chemical_formula)
-                info_list.append(f"Chemical formula for each structure in this file:\n{formulae}")
-            info = "\n--\n".join(info_list)
-        else:
-            info = """
-Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.
-You can still use this dataset in tools and workflows.
-For full metadata, ask your admin to install the 'ase' Python package."""
-
-        return info
-
 
 @build_sniff_from_prefix
-class XYZ(GenericMolFile):
+class XYZ(AtomicStructFile):
     """
     XYZ format.
     """
 
     file_ext = "xyz"
-    meta_error = False
-    MetadataElement(
-        name="atom_data",
-        default=[],
-        desc="Atom symbols and positions",
-        readonly=True,
-        visible=False,
-    )
-    MetadataElement(
-        name="number_of_atoms",
-        desc="Number of atoms",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="chemical_formula",
-        desc="Chemical formula",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="is_periodic",
-        desc="Periodic boundary conditions",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="lattice_parameters",
-        desc="Lattice parameters",
-        readonly=True,
-        visible=True,
-    )
+    ase_format = "xyz"
 
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         """
@@ -1240,92 +1108,6 @@ def read_blocks(self, lines: List) -> List:
                     raise
         return blocks
 
-    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
-        """
-        Find Atom IDs for metadata.
-        """
-        self.meta_error = False
-        if ase_io is None:
-            # Don't have optional dependency, can't set advanced values
-            return
-        else:
-            # enhanced metadata
-            try:
-                # ASE recommend always parsing as extended xyz
-                ase_data = ase_io.read(dataset.get_file_name(), index=":", format="extxyz")
-            except Exception as e:
-                log.warning("%s, set_meta Exception during ASE read: %s", self, unicodify(e))
-                self.meta_error = True
-                return
-
-            atom_data = []
-            chemical_formula = []
-            is_periodic = []
-            lattice_parameters = []
-            try:
-                for block in ase_data:
-                    atom_data.append(
-                        [str(sym) + str(pos) for sym, pos in zip(block.get_chemical_symbols(), block.get_positions())]
-                    )
-                    chemical_formula.append(block.get_chemical_formula())
-                    pbc = block.get_pbc()
-                    try:
-                        p = bool(pbc)
-                    except ValueError:  # pbc is an array
-                        p = bool(pbc.any())
-                    is_periodic.append(p)
-                    lattice_parameters.append(list(block.get_cell().cellpar()))
-            except Exception as e:
-                log.warning("%s, set_meta Exception during ASE metadata collection: %s", self, unicodify(e))
-                self.meta_error = True
-                return
-
-            dataset.metadata.number_of_molecules = len(ase_data)
-            dataset.metadata.atom_data = atom_data
-            dataset.metadata.number_of_atoms = [len(atoms) for atoms in dataset.metadata.atom_data]
-            dataset.metadata.chemical_formula = chemical_formula
-            dataset.metadata.is_periodic = is_periodic
-            dataset.metadata.lattice_parameters = list(lattice_parameters)
-
-    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
-        if not dataset.dataset.purged:
-            dataset.peek = get_file_peek(dataset.get_file_name())
-            dataset.info = self.get_dataset_info(dataset.metadata)
-            structure_string = "structure" if dataset.metadata.number_of_molecules == 1 else "structures"
-            dataset.blurb = f"XYZ file containing {dataset.metadata.number_of_molecules} {structure_string}"
-        else:
-            dataset.peek = "file does not exist"
-            dataset.blurb = "file purged from disk"
-
-    def get_dataset_info(self, metadata):
-        if self.meta_error:
-            info = "Error finding metadata. The file may be formatted incorrectly."
-        elif ase_io:
-            # enhanced info
-            info_list = []
-            if metadata.number_of_molecules == 1:
-                info_list.append(f"Chemical formula:\n{metadata.chemical_formula[0]}")
-                if metadata.is_periodic[0]:
-                    info_list.append("Periodic:\nYes")
-                    info_list.append(
-                        f"Lattice parameters in axis-angle format:\n{', '.join([str(round(x, 2)) for x in metadata.lattice_parameters[0]])}"
-                    )
-                else:
-                    info_list.append("Periodic:\nNo")
-                info_list.append(f"Atoms in file:\n{metadata.number_of_atoms[0]}")
-            elif metadata.number_of_molecules > 1:
-                info_list.append("File contains multiple structures; full metadata will not be displayed.")
-                formulae = "\n".join(metadata.chemical_formula)
-                info_list.append(f"Chemical formula for each structure in this file:\n{formulae}")
-            info = "\n--\n".join(info_list)
-        else:
-            info = """
-Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.
-You can still use this dataset in tools and workflows.
-For full metadata, ask your admin to install the 'ase' Python package."""
-
-        return info
-
 
 @build_sniff_from_prefix
 class ExtendedXYZ(XYZ):
@@ -1770,49 +1552,11 @@ def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
 
 
 @build_sniff_from_prefix
-class Magres(GenericMolFile):
+class Magres(AtomicStructFile):
     """Report on a MAGRES calculation"""
 
     file_ext = "magres"
-    meta_error = False
-    MetadataElement(
-        name="data_block_names",
-        default=[],
-        desc="Names of the data blocks",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="atom_data",
-        default=[],
-        desc="Atom symbols and positions",
-        readonly=True,
-        visible=False,
-    )
-    MetadataElement(
-        name="number_of_atoms",
-        desc="Number of atoms",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="chemical_formula",
-        desc="Chemical formula",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="is_periodic",
-        desc="Periodic boundary conditions",
-        readonly=True,
-        visible=True,
-    )
-    MetadataElement(
-        name="lattice_parameters",
-        desc="Lattice parameters",
-        readonly=True,
-        visible=True,
-    )
+    ase_format = "magres"
 
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         """Determines whether the file is a MAGRES log
@@ -1826,85 +1570,3 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         False
         """
         return file_prefix.startswith("#$magres-abinitio-v")
-
-    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
-        """
-        Find Atom IDs for metadata.
-        """
-        self.meta_error = False
-        if ase_io is None:
-            # Don't have optional dependency, can't set advanced values
-            return
-        else:
-            # enhanced metadata
-            try:
-                ase_data = ase_io.read(dataset.get_file_name(), index=":", format="magres")
-            except Exception as e:
-                log.warning("%s, set_meta Exception during ASE read: %s", self, unicodify(e))
-                self.meta_error = True
-                return
-
-            atom_data = []
-            chemical_formula = []
-            is_periodic = []
-            lattice_parameters = []
-            try:
-                for block in ase_data:
-                    atom_data.append(
-                        [str(sym) + str(pos) for sym, pos in zip(block.get_chemical_symbols(), block.get_positions())]
-                    )
-                    chemical_formula.append(block.get_chemical_formula())
-                    pbc = block.get_pbc()
-                    try:
-                        p = bool(pbc)
-                    except ValueError:  # pbc is an array
-                        p = bool(pbc.any())
-                    is_periodic.append(p)
-                    lattice_parameters.append(list(block.get_cell().cellpar()))
-            except Exception as e:
-                log.warning("%s, set_meta Exception during ASE metadata collection: %s", self, unicodify(e))
-                self.meta_error = True
-                return
-
-            # MAGRES file can only have one molecule
-            dataset.metadata.number_of_molecules = 1
-            dataset.metadata.atom_data = atom_data
-            dataset.metadata.number_of_atoms = [len(atoms) for atoms in dataset.metadata.atom_data]
-            dataset.metadata.chemical_formula = chemical_formula
-            dataset.metadata.is_periodic = is_periodic
-            dataset.metadata.lattice_parameters = list(lattice_parameters)
-
-    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
-        if not dataset.dataset.purged:
-            dataset.peek = get_file_peek(dataset.get_file_name())
-            dataset.info = self.get_dataset_info(dataset.metadata)
-            structure_string = "structure" if dataset.metadata.number_of_molecules == 1 else "structures"
-            dataset.blurb = f"MAGRES file containing {dataset.metadata.number_of_molecules} {structure_string}"
-
-        else:
-            dataset.peek = "file does not exist"
-            dataset.blurb = "file purged from disk"
-
-    def get_dataset_info(self, metadata):
-        if self.meta_error:
-            info = "Error finding metadata. The file may be formatted incorrectly."
-        elif ase_io:
-            # enhanced info
-            info_list = []
-            info_list.append(f"Chemical formula:\n{metadata.chemical_formula[0]}")
-            if metadata.is_periodic[0]:
-                info_list.append("Periodic:\nYes")
-                info_list.append(
-                    f"Lattice parameters in axis-angle format:\n{', '.join([str(round(x, 2)) for x in metadata.lattice_parameters[0]])}"
-                )
-            else:
-                info_list.append("Periodic:\nNo")
-            info_list.append(f"Atoms in file:\n{metadata.number_of_atoms[0]}")
-            info = "\n--\n".join(info_list)
-        else:
-            info = """
-Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.
-You can still use this dataset in tools and workflows.
-For full metadata, ask your admin to install the 'ase' Python package."""
-
-        return info

From 0e16e39e805226ad504515b4c9594bcc9e136cc0 Mon Sep 17 00:00:00 2001
From: Nalin Gupta <nalin.gupta3142@gmail.com>
Date: Mon, 8 Jan 2024 09:53:39 +0000
Subject: [PATCH 06/11] Changed parent of AtomicStructFile Earlier parent class
 was Text but was changed to GenericMol file for XYZ and Extended XYZ files

---
 lib/galaxy/datatypes/molecules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index ec498781dd37..d23b2f61bb7a 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -198,7 +198,7 @@ def get_mime(self) -> str:
     ]
 
 
-class AtomicStructFile(Text):
+class AtomicStructFile(GenericMolFile):
     """
     Abstract class for structure files which use the ASE IO library for metadata.
     """

From 75a66821b65c678d971bf35731b43b27c9a66fb7 Mon Sep 17 00:00:00 2001
From: Nalin Gupta <nalin.gupta3142@gmail.com>
Date: Tue, 9 Jan 2024 10:19:08 +0000
Subject: [PATCH 07/11] Improved linting, Fixed PBC not showing for EXTXYZ Also
 removed set_peek() method from extxyz due to functionality being present in
 AtomicStructFile abstract class.

---
 lib/galaxy/datatypes/molecules.py | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index d23b2f61bb7a..9bc768854037 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -250,7 +250,6 @@ def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> N
         else:
             # enhanced metadata
             try:
-                # ASE recommend always parsing as extended xyz
                 ase_data = ase_io.read(dataset.get_file_name(), index=":", format=self.ase_format)
             except Exception as e:
                 log.warning("%s, set_meta Exception during ASE read: %s", self, unicodify(e))
@@ -290,8 +289,10 @@ def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
         if not dataset.dataset.purged:
             dataset.peek = get_file_peek(dataset.get_file_name())
             dataset.info = self.get_dataset_info(dataset.metadata)
-            structure_string = "structure" if dataset.metadata.number_of_molecules == 1 else "structures"
-            dataset.blurb = f"{self.file_ext.upper()} file containing {dataset.metadata.number_of_molecules} {structure_string}"
+            number_of_molecules = dataset.metadata.number_of_molecules
+            file_ext_upper = self.file_ext.upper()
+            structure_string = "structure" if number_of_molecules == 1 else "structures"
+            dataset.blurb = f"{file_ext_upper} file containing {number_of_molecules} {structure_string}"
         else:
             dataset.peek = "file does not exist"
             dataset.blurb = "file purged from disk"
@@ -1036,7 +1037,8 @@ class XYZ(AtomicStructFile):
     """
 
     file_ext = "xyz"
-    ase_format = "xyz"
+    # ASE recommend always parsing as extended xyz
+    ase_format = "extxyz"
 
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         """
@@ -1224,10 +1226,6 @@ def read_blocks(self, lines: List) -> List:
             blocks.append({"number_of_atoms": n_atoms, "comment": comment, "atom_data": atoms})
         return blocks
 
-    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
-        super().set_peek(dataset)
-        dataset.blurb = "Extended " + dataset.blurb
-
 
 class grd(Text):
     file_ext = "grd"

From 50e6656f0bc73d07d4e2523d3f6d0e407fd600ee Mon Sep 17 00:00:00 2001
From: Nalin Gupta <nalin.gupta3142@gmail.com>
Date: Wed, 7 Feb 2024 15:50:39 +0000
Subject: [PATCH 08/11] Added description tags to datatypes Added description
 (and sometimes description_url) tags for param, castep, den_fmt, call, cif
 and magres datatypes

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index f7ac063c5740..2ab88aa5b3c0 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -778,11 +778,11 @@
     </datatype>
     <datatype extension="pdbqt" type="galaxy.datatypes.molecules:PDBQT" display_in_upload="true"/>
     <datatype extension="pqr" type="galaxy.datatypes.molecules:PQR" display_in_upload="true" />
-    <datatype extension="cell" type="galaxy.datatypes.molecules:Cell" display_in_upload="true"/>
-    <datatype extension="cif" type="galaxy.datatypes.molecules:CIF" display_in_upload="true"/>
+    <datatype extension="cell" type="galaxy.datatypes.molecules:Cell" display_in_upload="true" description="CASTEP input file contains geometry information, including cell parameters, atomic coordinates, and k-point coordinates and weights. The file consists of lines containing keywords and data blocks, and associated values"/>
+    <datatype extension="cif" type="galaxy.datatypes.molecules:CIF" display_in_upload="true" description="CIF or Crystallographic Information File is the standard format for storing crystallographic structural data" description_url="https://www.iucr.org/resources/cif"/>
     <datatype extension="xyz" type="galaxy.datatypes.molecules:XYZ" display_in_upload="true"/>
     <datatype extension="extxyz" type="galaxy.datatypes.molecules:ExtendedXYZ" display_in_upload="true"/>
-    <datatype extension="magres" type="galaxy.datatypes.molecules:Magres" display_in_upload="true"/>
+    <datatype extension="magres" type="galaxy.datatypes.molecules:Magres" display_in_upload="true" description="Ab initio Nuclear Magnetic Resonance file format providing a complete archival and data processing format for the results of first principles calculation of NMR parameters" description_url="https://www.ccpnc.ac.uk/docs/magres"/>
     <datatype extension="trr" type="galaxy.datatypes.binary:Trr" display_in_upload="true">
       <converter file="mdconvert.xml" target_datatype="xtc"/>
       <converter file="mdconvert.xml" target_datatype="dcd"/>

From 319f9ef768ba82ff87405298599b1f7dbc89a7c5 Mon Sep 17 00:00:00 2001
From: Nalin Gupta <nalin.gupta3142@gmail.com>
Date: Thu, 8 Feb 2024 16:59:56 +0000
Subject: [PATCH 09/11] Added urls for datatype descriptions

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 2ab88aa5b3c0..454f86e9796f 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -778,10 +778,10 @@
     </datatype>
     <datatype extension="pdbqt" type="galaxy.datatypes.molecules:PDBQT" display_in_upload="true"/>
     <datatype extension="pqr" type="galaxy.datatypes.molecules:PQR" display_in_upload="true" />
-    <datatype extension="cell" type="galaxy.datatypes.molecules:Cell" display_in_upload="true" description="CASTEP input file contains geometry information, including cell parameters, atomic coordinates, and k-point coordinates and weights. The file consists of lines containing keywords and data blocks, and associated values"/>
+    <datatype extension="cell" type="galaxy.datatypes.molecules:Cell" display_in_upload="true" description="The .cell file contains geometry information, including cell parameters, atomic coordinates, and k-point coordinates and weights. The file consists of lines containing keywords and data blocks, and associated values" description_url="https://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/content/modules/castep/expcastepfilecell.htm"/>
     <datatype extension="cif" type="galaxy.datatypes.molecules:CIF" display_in_upload="true" description="CIF or Crystallographic Information File is the standard format for storing crystallographic structural data" description_url="https://www.iucr.org/resources/cif"/>
-    <datatype extension="xyz" type="galaxy.datatypes.molecules:XYZ" display_in_upload="true"/>
-    <datatype extension="extxyz" type="galaxy.datatypes.molecules:ExtendedXYZ" display_in_upload="true"/>
+    <datatype extension="xyz" type="galaxy.datatypes.molecules:XYZ" display_in_upload="true" description="Basic format for atomic positions in a structure" description_url="https://open-babel.readthedocs.io/en/latest/FileFormats/XYZ_cartesian_coordinates_format.html"/>
+    <datatype extension="extxyz" type="galaxy.datatypes.molecules:ExtendedXYZ" display_in_upload="true" description="Extended XYZ format is an enhanced version of the basic XYZ format that allows extra columns to be present in the file for additonal per-atom properties as well as standardising the format of the comment line to include the cell lattice and other per-frame parameters" description_url="https://wiki.fysik.dtu.dk/ase/ase/io/formatoptions.html#extxyz"/>
     <datatype extension="magres" type="galaxy.datatypes.molecules:Magres" display_in_upload="true" description="Ab initio Nuclear Magnetic Resonance file format providing a complete archival and data processing format for the results of first principles calculation of NMR parameters" description_url="https://www.ccpnc.ac.uk/docs/magres"/>
     <datatype extension="trr" type="galaxy.datatypes.binary:Trr" display_in_upload="true">
       <converter file="mdconvert.xml" target_datatype="xtc"/>

From d5587ceef0e1d454bc7396ab29cfe60a87c228b1 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Mon, 19 Feb 2024 11:42:24 -0800
Subject: [PATCH 10/11] remove duplicated datatype entry

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 454f86e9796f..081ffc294391 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -973,7 +973,6 @@
     <datatype extension="gds" type="galaxy.datatypes.tabular:CSV" subclass="true" description="CSV representing GDS parameters."/>
     <datatype extension="feff" type="galaxy.datatypes.tabular:CSV" subclass="true" description="CSV representing summary of FEFF paths."/>
     <datatype extension="feffit" type="galaxy.datatypes.data:Text" subclass="true" description="Report of Artemis FEFFIT."/>
-    <datatype extension="magres" type="galaxy.datatypes.text:Magres" display_in_upload="true"/>
     <!-- ECOLOGY types -->
     <datatype extension="bil" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" display_in_upload="true" subclass="true" description="ENVI file with band interleave by line (BIL) format"/>
     <datatype extension="hdr" type="galaxy.datatypes.data:Text" mimetype="text/plain" display_in_upload="true" subclass="true" description="ENVI metadata header file"/>

From 65dcd585bbf072ce0d7924c69789ce70e795f1da Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Mon, 19 Feb 2024 11:47:31 -0800
Subject: [PATCH 11/11] re-add expanded related datatypes definitions

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 081ffc294391..8a5c7e69029a 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -963,9 +963,9 @@
     <datatype extension="storm.check" type="galaxy.datatypes.text:StormCheck" display_in_upload="true"/>
     <datatype extension="ctl.result" type="galaxy.datatypes.text:CTLresult" display_in_upload="true"/>
     <!-- CASTEP types -->
-    <datatype extension="castep" type="galaxy.datatypes.text:Castep" display_in_upload="true"/>
-    <datatype extension="param" type="galaxy.datatypes.text:Param" display_in_upload="true"/>
-    <datatype extension="den_fmt" type="galaxy.datatypes.text:FormattedDensity" display_in_upload="true"/>
+    <datatype extension="castep" type="galaxy.datatypes.text:Castep" display_in_upload="true" description="numerical output of a CASTEP job in ASCII format" description_url="https://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/content/modules/castep/expcastepfilecastep.htm"/>
+    <datatype extension="param" type="galaxy.datatypes.text:Param" display_in_upload="true" description="the param file contains all the input control parameters required to run a CASTEP job. Consists of lines containing keywords and associated values" description_url="https://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/content/modules/castep/expcastepfileparam.htm"/>
+    <datatype extension="den_fmt" type="galaxy.datatypes.text:FormattedDensity" display_in_upload="true" description="formatted electronic density file output by CASTEP containing value of electron density for a grid of points"/>
     <!-- Larch types -->
     <datatype extension="prj" type="galaxy.datatypes.larch:AthenaProject" display_in_upload="true" description="Athena project file."/>
     <datatype extension="inp" type="galaxy.datatypes.larch:FEFFInput" display_in_upload="true" description="FEFF input file."/>