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Content update & add Galaxy tool versions
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supernord committed Nov 6, 2023
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14 changes: 7 additions & 7 deletions docs/2_1_workflows.html
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12 changes: 6 additions & 6 deletions docs/2_tools.html
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4 changes: 2 additions & 2 deletions docs/5_attributions.html
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HD(a)&&!mj()&&(d._ono=1);d.gtm=cn();d._p=SD();c&&(d.em=c);a.metadata.create_google_join&&(d._gaz=1);pE(d,a);Q(51)&&(qm()&&(d.dma_cps=nm()),d.dma=pm());Q(85)&&Kl(Tl())&&(d.tcfd=rm());var g=a.h[N.g.ub];g&&(d.gdid=g);e.en=String(a.eventName);a.metadata.is_first_visit&&(e._fv=a.metadata.is_first_visit_conversion?2:1);a.metadata.is_new_to_site&&(e._nsi=1);a.metadata.is_session_start&&(e._ss=a.metadata.is_session_start_conversion?2:1);a.metadata.is_conversion&&
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15 changes: 15 additions & 0 deletions finders/common.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -159,6 +159,21 @@ def get_data(self):

return pd.DataFrame(data)


def get_data_only(self):
data = []
for i in self.db:
line = []
for dp in self.dataprovider:
line.append(dp.render(self.db[i]))
result = {}
for element in line:
result.update(element)
data.append(result)

return data


@abstractmethod
def get_formatted_table(self) -> pd.DataFrame:
pass
15 changes: 8 additions & 7 deletions finders/toolfinder.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,8 @@ def __init__(self, parent, look_up_file):

def _query_remote(self):
self.available_data = {}
req = requests.request("get", "https://usegalaxy.org.au/api/tools")
#req = requests.request("get", "https://usegalaxy.org.au/api/tools/?in_panel=False")
req = requests.request("get", "https://usegalaxy.org.au/api/tools/")
if req.status_code != 200:
raise FileNotFoundError(req.url)
tool_sections = json.loads(req.text)
Expand All @@ -120,6 +121,7 @@ def _query_remote(self):
other_galaxy_id_types = {}
for tool in tools:
galaxy_id = tool["id"]
version = tool["version"]
# https://stackoverflow.com/a/70672659
# https://stackoverflow.com/a/12595082
# https://stackoverflow.com/a/4843178
Expand All @@ -133,14 +135,12 @@ def _query_remote(self):
galaxy_id = galaxy_id
#print(other_galaxy_id_types[galaxy_id]["id"])
### example datasource_tool link "/tool_runner/data_source_redirect?tool_id=ucsc_table_direct1"
if isinstance(tool["model_class"], str) and tool["model_class"] != "ToolSectionLabel" and tool["model_class"] != "ToolSection":
if tool["model_class"] != "ToolSectionLabel" and tool["model_class"] != "ToolSection":
if tool["model_class"] == "DataSourceTool":
tool["link"] = tool["link"]
if tool["model_class"] == "Tool":
else:
# https://stackoverflow.com/a/4945558
tool["link"] = "root?" + tool["link"][13:]
#else:
# tool["link"] = "root?" + tool["link"][13:]
biotools_id = None
if "xrefs" in tool:
for item in tool["xrefs"]:
Expand All @@ -161,7 +161,7 @@ def _query_remote(self):

def _render(self, data):
retval = {}
retval[Dataprovider.FIELD_NAMES.GALAXY_AUSTRALIA_LAUNCH_LINK] = [(d["link"], d["name"]) for d in data if "link" in d and "name" in d]
retval[Dataprovider.FIELD_NAMES.GALAXY_AUSTRALIA_LAUNCH_LINK] = [(d["link"], d["name"], d["version"]) for d in data if "link" in d and "name" in d and "version" in d]
return retval

def get_alt_ids(self):
Expand Down Expand Up @@ -342,6 +342,7 @@ def __init__(self, tool_matrix_file):
def get_formatted_table(self):
import urllib
tool_table = self.get_data()
tool_data = self.get_data_only()
formatted_list = []
for index, row in tool_table.iterrows():
if not row[Dataprovider.FIELD_NAMES.INCLUSION]:
Expand Down Expand Up @@ -377,7 +378,7 @@ def get_formatted_table(self):
# see https://stackoverflow.com/a/2906586
# see https://stackoverflow.com/questions/5618878/how-to-convert-list-to-string
#tool_line.append("<br \>".join(["""<button class="galaxy-link" onclick="window.open('https://usegalaxy.org.au/%s','_blank').focus()">%s</button>""" %d for d in row[Dataprovider.FIELD_NAMES.GALAXY_AUSTRALIA_LAUNCH_LINK]]))
a = ["""<button class="galaxy-link" onclick="window.open('https://usegalaxy.org.au/%s','_blank').focus()" ga-product="galaxy" ga-id="%s">%s</button>"""% (x[0], row[Dataprovider.FIELD_NAMES.TOOL_IDENTIFIER], x[1]) for x in row[Dataprovider.FIELD_NAMES.GALAXY_AUSTRALIA_LAUNCH_LINK]]
a = ["""<button class="galaxy-link" onclick="window.open('https://usegalaxy.org.au/%s','_blank').focus()" ga-product="galaxy" ga-id="%s">%s</button>"""% (x[0], row[Dataprovider.FIELD_NAMES.TOOL_IDENTIFIER], x[1] + "-" + x[2]) for x in row[Dataprovider.FIELD_NAMES.GALAXY_AUSTRALIA_LAUNCH_LINK]]
#%d for d in row[Dataprovider.FIELD_NAMES.GALAXY_AUSTRALIA_LAUNCH_LINK]]
if len(a)>1:
tool_line.append("""<ul class="galaxy-links-holder"><li class="closed galaxy-collapsible" onclick="$(this).parent('.galaxy-links-holder').find('.galaxy-links').toggle({duration:200,start:function(){$(this).parent('.galaxy-links-holder').find('.galaxy-collapsible').toggleClass('closed open')}})" ><span class="galaxy-link-toggle">""" + str(len(a)) + " tool" + ("s" if len(a)>1 else "") + """</span><span class="button"/></li><ul class="galaxy-links" style="display: none;">""" + str("".join(a)) + "</li></ul></ul>")
Expand Down

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